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1. Seasonal and algal diet-driven patterns of the digestive microbiota of the European abalone Haliotis tuberculata, a generalist marine herbivore

Author: Angélique Gobet, Laëtitia Mest, Morgan Perennou, Simon M Dittami, Claire Caralp, Céline Coulombet, Sylvain Huchette, Sabine Roussel, Gurvan Michel, and Catherine Leblanc
Subjects: Microbe-host interactions, Digestive microbiota, Abalone, Macroalgae, Holobiont, Microbial ecology, QR100-130
Abstract: Abstract Background Holobionts have a digestive microbiota with catabolic abilities allowing the degradation of complex dietary compounds for the host. In terrestrial herbivores, the digestive microbiota is known to degrade complex polysaccharides from land plants while in marine herbivores, the digestive microbiota is poorly characterized. Most of the latter are generalists and consume red, green, and brown macroalgae, three distinct lineages characterized by a specific composition in complex polysaccharides, which represent half of their biomass. Subsequently, each macroalga features a specific epiphytic microbiota, and the digestive microbiota of marine herbivores is expected to vary with a monospecific algal diet. We investigated the effect of four monospecific diets (Palmaria palmata, Ulva lactuca, Saccharina latissima, Laminaria digitata) on the composition and specificity of the digestive microbiota of a generalist marine herbivore, the abalone, farmed in a temperate coastal area over a year. The microbiota from the abalone digestive gland was sampled every 2 months and explored using metabarcoding. Results Diversity and multivariate analyses showed that patterns of the microbiota were significantly linked to seasonal variations of contextual parameters but not directly to a specific algal diet. Three core genera: Psychrilyobacter, Mycoplasma, and Vibrio constantly dominated the microbiota in the abalone digestive gland. Additionally, a less abundant and diet-specific core microbiota featured genera representing aerobic primary degraders of algal polysaccharides. Conclusions This study highlights the establishment of a persistent core microbiota in the digestive gland of the abalone since its juvenile state and the presence of a less abundant and diet-specific core community. While composed of different microbial taxa compared to terrestrial herbivores, the digestive gland constitutes a particular niche in the abalone holobiont, where bacteria (i) may cooperate to degrade algal polysaccharides to products assimilable by the host or (ii) may have acquired these functions through gene transfer from the aerobic algal microbiota.
Published: 2018
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2. Double blind microarray-based polysaccharide profiling enables parallel identification of uncharacterized polysaccharides and carbohydrate-binding proteins with unknown specificities

Author: Armando A. Salmeán, Alexia Guillouzo, Delphine Duffieux, Murielle Jam, Maria Matard-Mann, Robert Larocque, Henriette L. Pedersen, Gurvan Michel, Mirjam Czjzek, William G. T. Willats, and Cécile Hervé
Subjects: Medicine, Science
Abstract: Abstract Marine algae are one of the largest sources of carbon on the planet. The microbial degradation of algal polysaccharides to their constitutive sugars is a cornerstone in the global carbon cycle in oceans. Marine polysaccharides are highly complex and heterogeneous, and poorly understood. This is also true for marine microbial proteins that specifically degrade these substrates and when characterized, they are frequently ascribed to new protein families. Marine (meta)genomic datasets contain large numbers of genes with functions putatively assigned to carbohydrate processing, but for which empirical biochemical activity is lacking. There is a paucity of knowledge on both sides of this protein/carbohydrate relationship. Addressing this ‘double blind’ problem requires high throughput strategies that allow large scale screening of protein activities, and polysaccharide occurrence. Glycan microarrays, in particular the Comprehensive Microarray Polymer Profiling (CoMPP) method, are powerful in screening large collections of glycans and we described the integration of this technology to a medium throughput protein expression system focused on marine genes. This methodology (Double Blind CoMPP or DB-CoMPP) enables us to characterize novel polysaccharide-binding proteins and to relate their ligands to algal clades. This data further indicate the potential of the DB-CoMPP technique to accommodate samples of all biological sources.
Published: 2018
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3. Carrageenan catabolism is encoded by a complex regulon in marine heterotrophic bacteria

Author: Elizabeth Ficko-Blean, Aurélie Préchoux, François Thomas, Tatiana Rochat, Robert Larocque, Yongtao Zhu, Mark Stam, Sabine Génicot, Murielle Jam, Alexandra Calteau, Benjamin Viart, David Ropartz, David Pérez-Pascual, Gaëlle Correc, Maria Matard-Mann, Keith A. Stubbs, Hélène Rogniaux, Alexandra Jeudy, Tristan Barbeyron, Claudine Médigue, Mirjam Czjzek, David Vallenet, Mark J. McBride, Eric Duchaud, and Gurvan Michel
Subjects: Science
Abstract: Carrageenans, major cell wall polysaccharides of red macroalgae, are metabolised by marine heterotrophic bacteria through unclear mechanisms. Here, the authors identify an unusual polysaccharide-utilization locus encoding carrageenan catabolism in a marine bacterium, and characterise the complete pathway.
Published: 2017
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4. Insoluble (1 → 3), (1 → 4)-β-D-glucan is a component of cell walls in brown algae (Phaeophyceae) and is masked by alginates in tissues

Author: Armando A. Salmeán, Delphine Duffieux, Jesper Harholt, Fen Qin, Gurvan Michel, Mirjam Czjzek, William G. T. Willats, and Cécile Hervé
Subjects: Medicine, Science
Abstract: Abstract Brown algae are photosynthetic multicellular marine organisms. They belong to the phylum of Stramenopiles, which are not closely related to land plants and green algae. Brown algae share common evolutionary features with other photosynthetic and multicellular organisms, including a carbohydrate-rich cell-wall. Brown algal cell walls are composed predominantly of the polyanionic polysaccharides alginates and fucose-containing sulfated polysaccharides. These polymers are prevalent over neutral and crystalline components, which are believed to be mostly, if not exclusively, cellulose. In an attempt to better understand brown algal cell walls, we performed an extensive glycan array analysis of a wide range of brown algal species. Here we provide the first demonstration that mixed-linkage (1 → 3), (1 → 4)-β-d-glucan (MLG) is common in brown algal cell walls. Ultra-Performance Liquid Chromatography analyses indicate that MLG in brown algae solely consists of trisaccharide units of contiguous (1 → 4)-β-linked glucose residues joined by (1 → 3)-β-linkages. This regular conformation may allow long stretches of the molecule to align and to form well-structured microfibrils. At the tissue level, immunofluorescence studies indicate that MLG epitopes in brown algae are unmasked by a pre-treatment with alginate lyases to remove alginates. These findings are further discussed in terms of the origin and evolution of MLG in the Stramenopile lineage.
Published: 2017
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5. SulfAtlas, the sulfatase database: state of the art and new developments

Author: Mark Stam, Pernelle Lelièvre, Mark Hoebeke, Erwan Corre, Tristan Barbeyron, Gurvan Michel, Génomique métabolique (UMR 8030), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), 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)-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)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Analyse Bio-Informatique pour la Génomique et le Métabolisme (LABGeM), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS)-Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Laboratoire de Biologie Intégrative des Modèles Marins (LBI2M), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff (SBR), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), ABiMS - Informatique et bioinformatique = Analysis and Bioinformatics for Marine Science (ABIMS), Fédération de recherche de Roscoff (FR2424), Station biologique de Roscoff (SBR), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff (SBR), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), ANR-14-CE19-0020,BLUE ENZYMES,Découverte de nouvelles enzymes pour la valorisation de la biomasse algale(2014), ANR-10-BTBR-0004,IDEALG,Biotechnologies pour la valorisation des macroalgues(2010), and ANR-11-INBS-0013,IFB (ex Renabi-IFB),Institut français de bioinformatique(2011)
Subjects: [SDV]Life Sciences [q-bio], Genetics
Abstract: SulfAtlas (https://sulfatlas.sb-roscoff.fr/) is a knowledge-based resource dedicated to a sequence-based classification of sulfatases. Currently four sulfatase families exist (S1–S4) and the largest family (S1, formylglycine-dependent sulfatases) is divided into subfamilies by a phylogenetic approach, each subfamily corresponding to either a single characterized specificity (or few specificities in some cases) or to unknown substrates. Sequences are linked to their biochemical and structural information according to an expert scrutiny of the available literature. Database browsing was initially made possible both through a keyword search engine and a specific sequence similarity (BLAST) server. In this article, we will briefly summarize the experimental progresses in the sulfatase field in the last 6 years. To improve and speed up the (sub)family assignment of sulfatases in (meta)genomic data, we have developed a new, freely-accessible search engine using Hidden Markov model (HMM) for each (sub)family. This new tool (SulfAtlas HMM) is also a key part of the internal pipeline used to regularly update the database. SulfAtlas resource has indeed significantly grown since its creation in 2016, from 4550 sequences to 162 430 sequences in August 2022.
Published: 2023

6. Evolutionary Evidence of Algal Polysaccharide Degradation Acquisition by Pseudoalteromonas carrageenovora 9T to Adapt to Macroalgal Niches

Author: Angélique Gobet, Tristan Barbeyron, Maria Matard-Mann, Ghislaine Magdelenat, David Vallenet, Eric Duchaud, and Gurvan Michel
Subjects: carrageenan, CAZymes, alginate, Gammaproteobacteria, Pseudoalteromonas, marine bacteria, Microbiology, QR1-502
Abstract: About half of seaweed biomass is composed of polysaccharides. Most of these complex polymers have a marked polyanionic character. For instance, the red algal cell wall is mainly composed of sulfated galactans, agars and carrageenans, while brown algae contain alginate and fucose-containing sulfated polysaccharides (FCSP) as cell wall polysaccharides. Some marine heterotrophic bacteria have developed abilities to grow on such macroalgal polysaccharides. This is the case of Pseudoalteromonas carrageenovora 9T (ATCC 43555T), a marine gammaproteobacterium isolated in 1955 and which was an early model organism for studying carrageenan catabolism. We present here the genomic analysis of P. carrageenovora. Its genome is composed of two chromosomes and of a large plasmid encompassing 109 protein-coding genes. P. carrageenovora possesses a diverse repertoire of carbohydrate-active enzymes (CAZymes), notably specific for the degradation of macroalgal polysaccharides (laminarin, alginate, FCSP, carrageenans). We confirm these predicted capacities by screening the growth of P. carrageenovora with a large collection of carbohydrates. Most of these CAZyme genes constitute clusters located either in the large chromosome or in the small one. Unexpectedly, all the carrageenan catabolism-related genes are found in the plasmid, suggesting that P. carrageenovora acquired its hallmark capacity for carrageenan degradation by horizontal gene transfer (HGT). Whereas P. carrageenovora is able to use lambda-carrageenan as a sole carbon source, genomic and physiological analyses demonstrate that its catabolic pathway for kappa- and iota-carrageenan is incomplete. This is due to the absence of the recently discovered 3,6-anhydro-D-galactosidase genes (GH127 and GH129 families). A genomic comparison with 52 Pseudoalteromonas strains confirms that carrageenan catabolism has been recently acquired only in a few species. Even though the loci for cellulose biosynthesis and alginate utilization are located on the chromosomes, they were also horizontally acquired. However, these HGTs occurred earlier in the evolution of the Pseudoalteromonas genus, the cellulose- and alginate-related loci being essentially present in one large, late-diverging clade (LDC). Altogether, the capacities to degrade cell wall polysaccharides from macroalgae are not ancestral in the Pseudoalteromonas genus. Such catabolism in P. carrageenovora resulted from a succession of HGTs, likely allowing an adaptation to the life on the macroalgal surface.
Published: 2018
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7. Gene Expression Analysis of Zobellia galactanivorans during the Degradation of Algal Polysaccharides Reveals both Substrate-Specific and Shared Transcriptome-Wide Responses

Author: François Thomas, Philippe Bordron, Damien Eveillard, and Gurvan Michel
Subjects: polysaccharide utilization locus, flavobacteria-algae interactions, regulation of gene expression, operon, microarray, Microbiology, QR1-502
Abstract: Flavobacteriia are recognized as key players in the marine carbon cycle, due to their ability to efficiently degrade algal polysaccharides both in the open ocean and in coastal regions. The chemical complexity of algal polysaccharides, their differences between algal groups and variations through time and space, imply that marine flavobacteria have evolved dedicated degradation mechanisms and regulation of their metabolism during interactions with algae. In the present study, we report the first transcriptome-wide gene expression analysis for an alga-associated flavobacterium during polysaccharide degradation. Zobellia galactanivorans DsijT, originally isolated from a red alga, was grown in minimal medium with either glucose (used as a reference monosaccharide) or one selected algal polysaccharide from brown (alginate, laminarin) or red algae (agar, porphyran, ι- or κ-carrageenan) as sole carbon source. Expression profiles were determined using whole-genome microarrays. Integration of genomic knowledge with the automatic building of a co-expression network allowed the experimental validation of operon-like transcription units. Differential expression analysis revealed large transcriptomic shifts depending on the carbon source. Unexpectedly, transcriptomes shared common signatures when growing on chemically divergent polysaccharides from the same algal phylum. Together with the induction of numerous transcription factors, this hints at complex regulation events that fine-tune the cell behavior during interactions with algal biomass in the marine environment. The results further highlight genes and loci that may participate in polysaccharide utilization, notably encoding Carbohydrate Active enZymes (CAZymes) and glycan binding proteins together with a number of proteins of unknown function. This constitutes a set of candidate genes potentially representing new substrate specificities. By providing an unprecedented view of global transcriptomic responses during polysaccharide utilization in an alga-associated model flavobacterium, this study expands the current knowledge on the functional role of flavobacteria in the marine carbon cycle and on their interactions with algae.
Published: 2017
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8. The Complete Genome Sequence of the Fish Pathogen Tenacibaculum maritimum Provides Insights into Virulence Mechanisms

Author: David Pérez-Pascual, Aurelie Lunazzi, Ghislaine Magdelenat, Zoe Rouy, Alain Roulet, Celine Lopez-Roques, Robert Larocque, Tristan Barbeyron, Angélique Gobet, Gurvan Michel, Jean-François Bernardet, and Eric Duchaud
Subjects: Tenacibaculum maritimum, fish pathogen, virulence factors, genome, toxins, Microbiology, QR1-502
Abstract: Tenacibaculum maritimum is a devastating bacterial pathogen of wild and farmed marine fish with a broad host range and a worldwide distribution. We report here the complete genome sequence of the T. maritimum type strain NCIMB 2154T. The genome consists of a 3,435,971-base pair circular chromosome with 2,866 predicted protein-coding genes. Genes encoding the biosynthesis of exopolysaccharides, the type IX secretion system, iron uptake systems, adhesins, hemolysins, proteases, and glycoside hydrolases were identified. They are likely involved in the virulence process including immune escape, invasion, colonization, destruction of host tissues, and nutrient scavenging. Among the predicted virulence factors, type IX secretion-mediated and cell-surface exposed proteins were identified including an atypical sialidase, a sphingomyelinase and a chondroitin AC lyase which activities were demonstrated in vitro.
Published: 2017
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9. Matching the Diversity of Sulfated Biomolecules: Creation of a Classification Database for Sulfatases Reflecting Their Substrate Specificity.

Author: Tristan Barbeyron, Loraine Brillet-Guéguen, Wilfrid Carré, Cathelène Carrière, Christophe Caron, Mirjam Czjzek, Mark Hoebeke, and Gurvan Michel
Subjects: Medicine, Science
Abstract: Sulfatases cleave sulfate groups from various molecules and constitute a biologically and industrially important group of enzymes. However, the number of sulfatases whose substrate has been characterized is limited in comparison to the huge diversity of sulfated compounds, yielding functional annotations of sulfatases particularly prone to flaws and misinterpretations. In the context of the explosion of genomic data, a classification system allowing a better prediction of substrate specificity and for setting the limit of functional annotations is urgently needed for sulfatases. Here, after an overview on the diversity of sulfated compounds and on the known sulfatases, we propose a classification database, SulfAtlas (http://abims.sb-roscoff.fr/sulfatlas/), based on sequence homology and composed of four families of sulfatases. The formylglycine-dependent sulfatases, which constitute the largest family, are also divided by phylogenetic approach into 73 subfamilies, each subfamily corresponding to either a known specificity or to an uncharacterized substrate. SulfAtlas summarizes information about the different families of sulfatases. Within a family a web page displays the list of its subfamilies (when they exist) and the list of EC numbers. The family or subfamily page shows some descriptors and a table with all the UniProt accession numbers linked to the databases UniProt, ExplorEnz, and PDB.
Published: 2016
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10. A single sulfatase is required to access colonic mucin by a gut bacterium

Author: Robert W. P. Glowacki, Dominic P. Byrne, Mark Reihill, Edwin A. Yates, James A. London, Arnaud Baslé, Nicholas A. Pudlo, Eric C. Martens, Mirjam Czjzek, Ana S. Luis, Stefan Oscarson, Sadie R. Gugel, Patrick A. Eyers, Alan Cartmell, Tristan Barbeyron, Gunnar C. Hansson, Chunsheng Jin, Gabriel V. Pereira, Niclas G. Karlsson, Gurvan Michel, Shaleni Singh, Department of Microbiology and Immunology, University of Michigan, Department of Medical Biochemistry, Institute for Biomedicine, Sahlgrenska Academy, University of Gothenburg, Department of Microbiology and Immunology, University of Michigan Medical School, University of Michigan [Ann Arbor], University of Michigan System-University of Michigan System, Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Institute for Cell and Molecular Biosciences, Newcastle University, Centre for Synthesis and Chemical Biology, University College Dublin, Laboratoire de Biologie Intégrative des Modèles Marins (LBI2M), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff (SBR), and Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Male, Models, Molecular, Glycan, Acetylgalactosamine, Colon, [SDV]Life Sciences [q-bio], Crystallography, X-Ray, Article, Substrate Specificity, Mice, 03 medical and health sciences, Animals, Bacteroides, Humans, 030304 developmental biology, chemistry.chemical_classification, 0303 health sciences, Multidisciplinary, biology, Glycobiology, Sulfatase, 030302 biochemistry & molecular biology, Mucin, Mucins, Galactose, biology.organism_classification, Mucus, Gastrointestinal Microbiome, Biochemistry, chemistry, biology.protein, Female, Sulfatases, Glycoprotein, Bacteroides thetaiotaomicron, Bacteria
Abstract: International audience; Humans have co-evolved with a dense community of microbial symbionts that 34 inhabit the lower intestine. In the colon, secreted mucus creates a physical barrier that 35 separates these microbes from the intestinal epithelium. Some gut bacteria are able to 36 utilize mucin glycoproteins, the main mucus component, as a nutrient source. However, 37 it remains unclear which enzymes initiate the degradation of the highly complex O-38 glycans found in mucins. In the colon, these glycans are heavily sulfated, but sulfatases active on colonic mucins have not been identified. Here, we show that sulfatases are essential to the utilization of colonic mucin O-linked glycans by the human gut symbiont Bacteroides thetaiotaomicron. We characterized the activity of 12 different sulfatases encoded by this species, showing that these enzymes collectively are active on all of the known sulfate linkages in colonic O-glycans and even possess the ability to cleave additional linkages not yet known to occur in host glycans. Crystal structures of 3 enzymes provide mechanistic insight into the molecular basis of substrate-specificity. Unexpectedly, we found that a single sulfatase is essential for utilization of sulfated Oglycans in vitro and also plays a major role in vivo. Our results provide insight into the mechanisms of mucin degradation by gut bacteria, an important process for both normal microbial gut colonization and diseases like inflammatory bowel disease (IBD). Sulfatase activity is likely to be a keystone step in bacterial mucin degradation and inhibition of these enzymes may therefore represent a viable therapeutic path for treatment of IBD and other diseases.
Published: 2021

11. In silico and in vitro analysis of an Aspergillus niger chitin deacetylase to decipher its subsite sugar preferences

Author: Gurvan Michel, Stefan Cord-Landwehr, Lisanne Hameleers, Bruno M. Moerschbacher, Lea Hembach, Martin Bonin, Thomas Roret, University of Münster, Station biologique de Roscoff (SBR), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Biologie Intégrative des Modèles Marins (LBI2M), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff (SBR), and Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)
Subjects: GlcNAc/A, N-acetylglucosamine, [SDV]Life Sciences [q-bio], paCOS, partially acetylated COS, 02 engineering and technology, GlcN/D, glucosamine, Crystallography, X-Ray, PA, pattern of acetylation, Biochemistry, Substrate Specificity, chemistry.chemical_compound, Glucosamine, CnCDA4, Cryptococcus neoformans CDA, 0303 health sciences, biology, COS, chitooligosaccharide, 021001 nanoscience & nanotechnology, MD, molecular dynamics, HILIC, hydrophilic liquid interaction chromatography, CDA, chitin deacetylase, Aspergillus niger, 0210 nano-technology, Research Article, GPI, glycosylphosphatidylinositol, crystal structure, carbohydrate function, In silico, carbohydrate biosynthesis, DA, degree of acetylation, RMSF, root mean square fluctuation, Acetylglucosamine, Amidohydrolases, Fungal Proteins, 03 medical and health sciences, Protein Domains, Chitin, PDB, Protein Data Bank, N-Acetylglucosamine, Computer Simulation, enzyme mechanism, Binding site, ClCDA, Colletotrichum lindemuthianum CDA, Molecular Biology, 030304 developmental biology, VcCDA, Vibrio cholerae CDA, Cell Biology, molecular docking, DP, degree of polymerization, CE4, carbohydrate esterase 4, biology.organism_classification, molecular dynamics, Chitin deacetylase, carbohydrates (lipids), chemistry, Acetylation, chitosan
Abstract: International audience; Chitin deacetylases (CDAs) are found in many different organisms ranging from marine bacteria to fungi and insects. These enzymes catalyze the removal of acetyl groups from chitinous substrates generating various chitosans, linear co- polymers consisting of N-acetylglucosamine (GlcNAc) and glucosamine (GlcN). CDAs influence the degree of acetylation (DA) of chitosans as well as their pattern of acetylation (PA), a parameter which was recently shown to influence the physicochemical properties and biological activities of chitosans. The binding site of CDAs typically consists of around four subsites, each accommodating a single sugar unit of the substrate. It has been hypothesized that the subsite preferences for GlcNAc or GlcN units play a crucial role in the acetylation pattern they generate, but so far, this characteristic was largely ignored, and still lacks structural data on the involved residues. Here, we determined the crystal structure of an Aspergillus niger CDA (AngCDA). Then, we used molecular dynamics simulations, backed up with a variety of in vitro activity assays using different well- defined polymeric and oligomeric substrates, to study this CDA in detail. We found that AngCDA strongly prefers a GlcNAc sugar unit at its -1 subsite and shows a weak GlcNAc preference at the other non-catalytic subsites, which was apparent both when de- and N- acetylating oligomeric substrates. Overall, our results show that the combination of in vitro and in silico methods used here enables the detailed analysis of CDAs, including their subsite preferences, which could influence their substrate targets and the characteristics of chitosans produced by these species.
Published: 2021

12. A single bacterial sulfatase is required for metabolism of colonic mucin O -glycans and intestinal colonization by a symbiotic human gut bacterium

Author: Shaleni Singh, Tristan Barbeyron, Ana S. Luis, Alan Cartmell, Eric C. Martens, Patrick A. Eyers, Niclas G. Karlsson, Stefan Oscarson, Robert W. P. Glowacki, Chunsheng Jin, Dominic P. Byrne, Mark Reihill, Edwin A. Yates, James A. London, Arnaud Baslé, Nicholas A. Pudlo, Sadie R. Gugel, Gunnar C. Hansson, Gurvan Michel, Czjzek Mirjam, Gabriel V. Pereira, Department of Microbiology and Immunology, University of Michigan Medical School, University of Michigan [Ann Arbor], University of Michigan System-University of Michigan System, Laboratoire de Biologie Intégrative des Modèles Marins (LBI2M), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff (SBR), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Institute of Integrative Biology [Liverpool, UK], and University of Liverpool
Subjects: chemistry.chemical_classification, 0303 health sciences, Glycan, biology, Chemistry, Sulfatase, 030302 biochemistry & molecular biology, Mucin, biology.organism_classification, Mucus, Intestinal epithelium, 03 medical and health sciences, Biochemistry, biology.protein, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Glycoprotein, Bacteroides thetaiotaomicron, Bacteria, 030304 developmental biology
Abstract: SummaryHumans have co-evolved with a dense community of microbial symbionts that inhabit the lower intestine. In the colon, secreted mucus creates a physical barrier that separates these microbes from the intestinal epithelium. Some gut bacteria are able to utilize mucin glycoproteins, the main mucus component, as a nutrient source. However, it remains unclear which bacterial enzymes initiate the degradation of the highly complex O-glycans found in mucins. In the colon, these glycans are heavily sulfated, but the specific sulfatases that are active on colonic mucins have not been identified. Here, we show that sulfatases are essential to the utilization of colonic mucin O-glycans by the human gut symbiont Bacteroides thetaiotaomicron. We have characterized the activity of 12 different sulfatases encoded by this species, showing that these enzymes collectively are active on all of the known sulfate linkages in colonic O-glycans. Crystal structures of 3 enzymes provide mechanistic insight into the molecular basis of substrate-specificity. Unexpectedly, we found that a single sulfatase is essential for utilization of sulfated O-glycans in vitro and also plays a major role in vivo. Our results provide insight into the mechanisms of mucin degradation by gut bacteria, an important process for both normal microbial gut colonization and diseases such as inflammatory bowel disease (IBD). Sulfatase activity is likely to be a keystone step in bacterial mucin degradation and inhibition of these enzymes may therefore represent a viable therapeutic path for treatment of IBD and other diseases.
Published: 2020

13. Purification, cloning, characterization and essential amino acid residues analysis of a new ι-carrageenase from Cellulophaga sp. QY3.

Author: Su Ma, Gaofei Duan, Wengang Chai, Cunliang Geng, Yulong Tan, Lushan Wang, Frédéric Le Sourd, Gurvan Michel, Wengong Yu, and Feng Han
Subjects: Medicine, Science
Abstract: ι-Carrageenases belong to family 82 of glycoside hydrolases that degrade sulfated galactans in the red algae known as ι-carrageenans. The catalytic mechanism and some substrate-binding residues of family GH82 have been studied but the substrate recognition and binding mechanism of this family have not been fully elucidated. We report here the purification, cloning and characterization of a new ι-carrageenase CgiA_Ce from the marine bacterium Cellulophaga sp. QY3. CgiA_Ce was the most thermostable carrageenase described so far. It was most active at 50°C and pH 7.0 and retained more than 70% of the original activity after incubation at 50°C for 1 h at pH 7.0 or at pH 5.0-10.6 for 24 h. CgiA_Ce was an endo-type ι-carrageenase; it cleaved ι-carrageenan yielding neo-ι-carrabiose and neo-ι-carratetraose as the main end products, and neo-ι-carrahexaose was the minimum substrate. Sequence analysis and structure modeling showed that CgiA_Ce is indeed a new member of family GH82. Moreover, sequence analysis of ι-carrageenases revealed that the amino acid residues at subsites -1 and +1 were more conserved than those at other subsites. Site-directed mutagenesis followed by kinetic analysis identified three strictly conserved residues at subsites -1 and +1 of ι-carrageenases, G228, Y229 and R254 in CgiA_Ce, which played important roles for substrate binding. Furthermore, our results suggested that Y229 and R254 in CgiA_Ce interacted specifically with the sulfate groups of the sugar moieties located at subsites -1 and +1, shedding light on the mechanism of ι-carrageenan recognition in the family GH82.
Published: 2013
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14. Alterocin, an Antibiofilm Protein Secreted by Pseudoalteromonas sp. Strain 3J6

Author: Erwan Corre, David Vallenet, Emilie Portier, Marjolaine Simon, Alexis Bazire, Yannick Fleury, Fanny Gaillard, Angélique Gobet, Gurvan Michel, Morgan Perennou, Albane Jouault, Alain Dufour, Laboratoire de Biotechnologie et Chimie Marines (LBCM), Université de Bretagne Sud (UBS)-Université de Brest (UBO)-Institut Universitaire Européen de la Mer (IUEM), Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS), Station biologique de Roscoff (SBR), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), MARine Biodiversity Exploitation and Conservation (UMR MARBEC), Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Laboratoire des Sciences de l'Environnement Marin (LEMAR) (LEMAR), Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Brest (UBO)-Institut Universitaire Européen de la Mer (IUEM), Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Fédération de recherche de Roscoff (FR2424), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Analyse Bio-Informatique pour la Génomique et le Métabolisme (LABGeM), Génomique métabolique (UMR 8030), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), 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)-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)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS)-Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Institut de Recherche pour le Développement (IRD), Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), 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 d'Évry-Val-d'Essonne (UEVE)-Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), 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 d'Évry-Val-d'Essonne (UEVE), Institut Universitaire Européen de la Mer (IUEM), and Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Centre National de la Recherche Scientifique (CNRS)-Université de Brest (UBO)
Subjects: Signal peptide, Operon, [SDV]Life Sciences [q-bio], medicine.disease_cause, Applied Microbiology and Biotechnology, biofilm, Microbiology, 03 medical and health sciences, Pseudoalteromonas, Marine bacteriophage, medicine, 14. Life underwater, Gene, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, 0303 health sciences, Ecology, biology, 030306 microbiology, Pseudomonas aeruginosa, Biofilm, biology.organism_classification, 3. Good health, antibiofilm protein, Bacteria, Food Science, Biotechnology
Abstract: We sought to identify and study the antibiofilm protein secreted by the marine bacterium Pseudoalteromonas sp. strain 3J6. The latter is active against marine and terrestrial bacteria, including Pseudomonas aeruginosa clinical strains forming different biofilm types. Several amino acid sequences were obtained from the partially purified antibiofilm protein, named alterocin. The Pseudoalteromonas sp. 3J6 genome was sequenced, and a candidate alt gene was identified by comparing the genome-encoded proteins to the sequences from purified alterocin. Expressing the alt gene in another nonactive Pseudoalteromonas sp. strain, 3J3, demonstrated that it is responsible for the antibiofilm activity. Alterocin is a 139-residue protein that includes a predicted 20-residue signal sequence, which would be cleaved off upon export by the general secretion system. No sequence homology was found between alterocin and proteins of known functions. The alt gene is not part of an operon and adjacent genes do not seem related to alterocin production, immunity, or regulation, suggesting that these functions are not fulfilled by devoted proteins. During growth in liquid medium, the alt mRNA level peaked during the stationary phase. A single promoter was experimentally identified, and several inverted repeats could be binding sites for regulators. alt genes were found in about 30% of the Pseudoalteromonas genomes and in only a few instances of other marine bacteria of the Hahella and Paraglaciecola genera. Comparative genomics yielded the hypothesis that alt gene losses occurred within the Pseudoalteromonas genus. Overall, alterocin is a novel kind of antibiofilm protein of ecological and biotechnological interest. IMPORTANCE Biofilms are microbial communities that develop on solid surfaces or interfaces and are detrimental in a number of fields, including for example food industry, aquaculture, and medicine. In the latter, antibiotics are insufficient to clear biofilm infections, leading to chronic infections such as in the case of infection by Pseudomonas aeruginosa of the lungs of cystic fibrosis patients. Antibiofilm molecules are thus urgently needed to be used in conjunction with conventional antibiotics, as well as in other fields of application, especially if they are environmentally friendly molecules. Here, we describe alterocin, a novel antibiofilm protein secreted by a marine bacterium belonging to the Pseudoalteromonas genus, and its gene. Alterocin homologs were found in about 30% of Pseudoalteromonas strains, indicating that this new family of antibiofilm proteins likely plays an important albeit nonessential function in the biology of these bacteria. This study opens up the possibility of a variety of applications.
Published: 2020

15. A marine bacterial enzymatic cascade degrades the algal polysaccharide ulvan

Author: Robert Larocque, Jan-Hendrik Hehemann, Gurvan Michel, Marcus Bäumgen, Dörte Becher, Aurélie Préchoux, Mihovilovic, Thomas Schweder, Stephanie Markert, Thomas Roret, Uwe T. Bornscheuer, Christian Stanetty, Frank Unfried, Lukas Reisky, Tao Song, N. Gerlach, Marie-Katherin Zühlke, Craig S. Robb, Anke Trautwein-Schult, Laboratoire de Biologie Intégrative des Modèles Marins (LBI2M), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff (SBR), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Universität Greifswald - University of Greifswald, Leibniz Institute of Plant Genetics and Crop Plant Research [Gatersleben] (IPK-Gatersleben), Max Planck Institute for Marine Microbiology, and Max-Planck-Gesellschaft
Subjects: Models, Molecular, Protein Conformation, [SDV]Life Sciences [q-bio], Biomass, Polysaccharide, Algal bloom, Gene Expression Regulation, Enzymologic, 03 medical and health sciences, Bacterial Proteins, Algae, Polysaccharides, Botany, [CHIM.CRIS]Chemical Sciences/Cristallography, Glycoside hydrolase, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, 14. Life underwater, Molecular Biology, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, chemistry.chemical_classification, 0303 health sciences, biology, Chemistry, fungi, 030302 biochemistry & molecular biology, food and beverages, Gene Expression Regulation, Bacterial, Genomics, Cell Biology, biology.organism_classification, Metabolic pathway, Carbohydrate Metabolism, Fermentation, Sulfatases, Flavobacteriaceae, Genome, Bacterial, Flavobacterium
Abstract: Marine seaweeds increasingly grow into extensive algal blooms, which are detrimental to coastal ecosystems, tourism and aquaculture. However, algal biomass is also emerging as a sustainable raw material for the bioeconomy. The potential exploitation of algae is hindered by our limited knowledge of the microbial pathways-and hence the distinct biochemical functions of the enzymes involved-that convert algal polysaccharides into oligo- and monosaccharides. Understanding these processes would be essential, however, for applications such as the fermentation of algal biomass into bioethanol or other value-added compounds. Here, we describe the metabolic pathway that enables the marine flavobacterium Formosa agariphila to degrade ulvan, the main cell wall polysaccharide of bloom-forming Ulva species. The pathway involves 12 biochemically characterized carbohydrate-active enzymes, including two polysaccharide lyases, three sulfatases and seven glycoside hydrolases that sequentially break down ulvan into fermentable monosaccharides. This way, the enzymes turn a previously unexploited renewable into a valuable and ecologically sustainable bioresource.
Published: 2019

16. A subfamily roadmap of the evolutionarily diverse glycoside hydrolase family 16 (GH16)

Author: Harry Brumer, Vincent Lombard, Nicolas Terrapon, Mirjam Czjzek, Alexander Holm Viborg, Bernard Henrissat, and Gurvan Michel
Subjects: 0301 basic medicine, CAZy, Subfamily, Glycoside Hydrolases, beta-sandwich, Hidden Markov Model (HMM), Computational biology, Biology, Biochemistry, Evolution, Molecular, Fungal Proteins, carbohydrate-active enzymes (CAZymes), 03 medical and health sciences, Protein sequencing, Bacterial Proteins, Sequence Analysis, Protein, Phylogenetics, Catalytic Domain, structural biology, glycoside hydrolase, protein evolution, Glycomics, Molecular Biology, Phylogeny, Sequence (medicine), 030102 biochemistry & molecular biology, Phylogenetic tree, sequence similarity networks (SSN), Cell Biology, Enzyme structure, enzyme structure, phylogenetics, beta-jelly-roll fold, 030104 developmental biology, Structural biology, Enzymology, Algorithms, MULTIPLE SEQUENCE ALIGNMENT, CARBOHYDRATE-ACTIVE ENZYMES, XYLOGLUCAN ENDO-TRANSGLYCOSYLASES, CELL-WALL, KAPPA-CARRAGEENASE, PROTEIN, FEATURES, INSIGHT, TOOL, DEGRADATION
Abstract: Glycoside hydrolase family (GH) 16 comprises a large and taxonomically diverse family of glycosidases and transglycosidases that adopt a common β-jelly-roll fold and are active on a range of terrestrial and marine polysaccharides. Presently, broadly insightful sequence–function correlations in GH16 are hindered by a lack of a systematic subfamily structure. To fill this gap, we have used a highly scalable protein sequence similarity network analysis to delineate nearly 23,000 GH16 sequences into 23 robust subfamilies, which are strongly supported by hidden Markov model and maximum likelihood molecular phylogenetic analyses. Subsequent evaluation of over 40 experimental three-dimensional structures has highlighted key tertiary structural differences, predominantly manifested in active-site loops, that dictate substrate specificity across the GH16 evolutionary landscape. As for other large GH families (i.e. GH5, GH13, and GH43), this new subfamily classification provides a roadmap for functional glycogenomics that will guide future bioinformatics and experimental structure–function analyses. The GH16 subfamily classification is publicly available in the CAZy database. The sequence similarity network workflow used here, SSNpipe, is freely available from GitHub.
Published: 2019

17. The agar-specific hydrolase ZgAgaC from the marine bacterium Zobellia galactanivorans defines a new GH16 protein subfamily

Author: Charles Tellier, Hélène Rogniaux, Mirjam Czjzek, David Ropartz, Mathieu Fanuel, Robert Larocque, Gurvan Michel, Anaïs Naretto, Laboratoire de Biologie Intégrative des Modèles Marins (LBI2M), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff (SBR), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), INRA Plateforme BIBS, Unité de Recherche Biopolymères, Interactions, Assemblages, Unité de recherche sur les Biopolymères, Interactions Assemblages (BIA), Institut National de la Recherche Agronomique (INRA), Unité de Biotechnologie, Biocatalyse et Biorégulation (U3B), Université de Nantes (UN)-Centre National de la Recherche Scientifique (CNRS), Glyco-Ouest interregional network, ANR-08-BLAN-0065, and ANR-10-BTBR-04
Subjects: 0301 basic medicine, crystal structure, Subfamily, Red algae, Biochemistry, 03 medical and health sciences, chemistry.chemical_compound, Marine bacteriophage, Hydrolase, evolution, Glycoside hydrolase, glycoside hydrolase, [SDV.BBM.BC]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biochemistry [q-bio.BM], Molecular Biology, ComputingMilieux_MISCELLANEOUS, red algae, agar, mass spectrometry, chemistry.chemical_classification, sulfated polysaccharide, 030102 biochemistry & molecular biology, biology, pH microenvironment, [SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Structural Biology [q-bio.BM], Porphyran, Glycosidic bond, Cell Biology, biology.organism_classification, bacteria, polysaccharide, algae, GH16, marine bacteria, [SDV.BBM.BC]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biomolecules [q-bio.BM], [SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biomolecules [q-bio.BM], 030104 developmental biology, chemistry, Agarose, hydrolase, biologie marine
Abstract: International audience; Agars are sulfated galactans from red macroalgae and are composed of a D-galactose (G unit) and L-galactose (L unit) alternatively linked by α-1,3 and β-1,4 glycosidic bonds. These polysaccharides display high complexity, with numerous modifications of their backbone (e.g. presence of a 3,6-anhydro-bridge (LA unit) and sulfations and methylation). Currently, bacterial polysaccharidases that hydrolyze agars (β-agarases and β-porphyranases) have been characterized on simple agarose and more rarely on porphyran, a polymer containing both agarobiose (G-LA) and porphyranobiose (GL6S) motifs. How bacteria can degrade complex agars remains therefore an open question. Here, we studied an enzyme from the marine bacterium Zobellia galactanivorans (ZgAgaC) that is distantly related to the glycoside hydrolase 16 (GH16) family β-agarases and β-porphyranases. Using a large red algae collection, we demonstrate that ZgAgaC hydrolyzes not only agarose but also complex agars from Ceramiales species. Using tandem MS analysis, we elucidated the structure of a purified hexasaccharide product, L6S-G-LA2Me-G(2Pentose)-LA2S-G, released by the activity of ZgAgaC on agar extracted from Osmundea pinnatifida. By resolving the crystal structure of ZgAgaC at high resolution (1.3 Å) and comparison with the structures of ZgAgaB and ZgPorA in complex with their respective substrates, we determined that ZgAgaC recognizes agarose via a mechanism different from that of classical β-agarases. Moreover, we identified conserved residues involved in the binding of complex oligoagars and demonstrate a probable influence of the acidic polysaccharide's pH microenvironment on hydrolase activity. Finally, a phylogenetic analysis supported the notion that ZgAgaC homologs define a new GH16 subfamily distinct from β-porphyranases and classical β-agarases.
Published: 2019

18. Seasonal and algal diet-driven patterns of the digestive microbiota of the European abalone Haliotis tuberculata, a generalist marine herbivore

Author: Morgan Perennou, Laëtitia Mest, Sylvain Huchette, Céline Coulombet, Sabine Roussel, Claire Caralp, Gurvan Michel, Simon M. Dittami, Catherine Leblanc, Angélique Gobet, Laboratoire de Biologie Intégrative des Modèles Marins (LBI2M), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff (SBR), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Station biologique de Roscoff (SBR), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Laboratoire des Sciences de l'Environnement Marin (LEMAR) (LEMAR), Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Brest (UBO)-Institut Universitaire Européen de la Mer (IUEM), Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Scea France Haliotis, ANR-10-BTBR-0004,IDEALG,Biotechnologies pour la valorisation des macroalgues(2010), Fédération de recherche de Roscoff (FR2424), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Institut Universitaire Européen de la Mer (IUEM), and Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Centre National de la Recherche Scientifique (CNRS)-Université de Brest (UBO)
Subjects: 0301 basic medicine, Microbiology (medical), food.ingredient, Abalone, [SDV]Life Sciences [q-bio], Gastropoda, Zoology, Saccharina latissima, Generalist and specialist species, Microbiology, Holobiont, lcsh:Microbial ecology, 03 medical and health sciences, food, Microbial ecology, Macroalgae, Polysaccharides, Animals, 14. Life underwater, Haliotis, Herbivory, Herbivore, biology, Bacteria, Research, ACL, Microbe-host interactions, 15. Life on land, biology.organism_classification, Animal Feed, Gastrointestinal Microbiome, 030104 developmental biology, Palmaria palmata, lcsh:QR100-130, Digestive microbiota, Seasons, [SDE.BE]Environmental Sciences/Biodiversity and Ecology
Abstract: Background Holobionts have a digestive microbiota with catabolic abilities allowing the degradation of complex dietary compounds for the host. In terrestrial herbivores, the digestive microbiota is known to degrade complex polysaccharides from land plants while in marine herbivores, the digestive microbiota is poorly characterized. Most of the latter are generalists and consume red, green, and brown macroalgae, three distinct lineages characterized by a specific composition in complex polysaccharides, which represent half of their biomass. Subsequently, each macroalga features a specific epiphytic microbiota, and the digestive microbiota of marine herbivores is expected to vary with a monospecific algal diet. We investigated the effect of four monospecific diets (Palmaria palmata, Ulva lactuca, Saccharina latissima, Laminaria digitata) on the composition and specificity of the digestive microbiota of a generalist marine herbivore, the abalone, farmed in a temperate coastal area over a year. The microbiota from the abalone digestive gland was sampled every 2 months and explored using metabarcoding. Results Diversity and multivariate analyses showed that patterns of the microbiota were significantly linked to seasonal variations of contextual parameters but not directly to a specific algal diet. Three core genera: Psychrilyobacter, Mycoplasma, and Vibrio constantly dominated the microbiota in the abalone digestive gland. Additionally, a less abundant and diet-specific core microbiota featured genera representing aerobic primary degraders of algal polysaccharides. Conclusions This study highlights the establishment of a persistent core microbiota in the digestive gland of the abalone since its juvenile state and the presence of a less abundant and diet-specific core community. While composed of different microbial taxa compared to terrestrial herbivores, the digestive gland constitutes a particular niche in the abalone holobiont, where bacteria (i) may cooperate to degrade algal polysaccharides to products assimilable by the host or (ii) may have acquired these functions through gene transfer from the aerobic algal microbiota. Electronic supplementary material The online version of this article (10.1186/s40168-018-0430-7) contains supplementary material, which is available to authorized users.
Published: 2018

19. Ten years of CAZypedia: a living encyclopedia of carbohydrate-active enzymes

Author: Štefan Janeček, Rohan J. Williams, Geoff Pincher, Darrell Cockburn, Gurvan Michel, Wataru Saburi, David R. Rose, Brian P. Rempel, Glyn R. Hemsworth, Wim Van den Ende, Jerry Ståhlberg, Leila LoLeggio, Tom Wennekes, Kiyohiko Igarashi, Cedric Montanier, Etienne Rebuffet, Naotake Konno, Harry J. Gilbert, Markus Linder, Ed Bayer, Tirso Pons, Jan-Hendrik Hehemann, Tomomi Sumida, Thierry Fontaine, Takane Katayama, Elizabeth Ficko-Blean, Florence Vincent, Zui Fujimoto, Masafumi Hidaka, Kyle Robinson, Ana R. Luís, Yuichi Sakamoto, Bernard Henrissat, Gustav Vaaje-Kolstad, Jens M. Eklöf, Ian R. Greig, Harry Brumer, Ryuichiro Suzuki, Mats Sandgren, Takashi Tonozuka, Ryszard Brzezinski, Brian L. Mark, Bareket Dassa, Haruhide Mori, Junho Lee, Vivian L. Y. Yip, Birte Svensson, Wade Abbott, Alfons K. G. Felice, Juha Rouvinen, Takayuki Ohnuma, Satoshi Kaneko, Franz J. St John, Ramon Hurtado-Guerrero, Pedro M. Coutinho, Sine Larsen, Gideon J. Davies, Yuval Shoham, Kiyotaka Fujita, Warren W. Wakarchuk, Fathima Aidha Shaikh, Alisdair B. Boraston, Breeanna R. Urbanowicz, Vincent G. H. Eijsink, Daniel Kracher, Beatrice Cobucci-Ponzano, Ethan D. Goddard-Borger, Anthony J. Clarke, David J. Vocadlo, Katsuro Yaoi, Seino A. K. Jongkees, Anna A. Kulminskaya, Roland Ludwig, Mirko M. Maksimainen, Magali Remaud-Simeon, Edward J. Taylor, Motomitsu Kitaoka, Spencer J. Williams, Shinya Fushinobu, Marco Moracci, David Wilson, Richard McLean, Toki Taira, Jean-Guy Berrin, Ran Zhang, Hiroyuki Nakai, Tracey M. Gloster, Peter J. Reilly, Wim Nerinckx, Takuya Ishida, Alicia Lammerts van Bueren, Orly Alber, Mirjam Czjzek, Kathleen Piens, Annabelle Varrot, Stephen G. Withers, Nathalie Juge, Maxime Versluys, Gerlind Sulzenbacher, Richard W. Pickersgill, Michael D. L. Suits, Agriculture and Agri-Food [Ottawa] (AAFC), Weizmann Institute of Science [Rehovot, Israël], Laboratoire d'Ingénierie des Systèmes Biologiques et des Procédés (LISBP), Institut National de la Recherche Agronomique (INRA)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS), University of Victoria [Canada] (UVIC), University of British Columbia, Université de Sherbrooke (UdeS), University of Guelph, National Research Council (CNR), Pennsylvania State University (Penn State), Penn State System, Aix Marseille Université (AMU), Laboratoire de Biologie Intégrative des Modèles Marins (LBI2M), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff (SBR), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Sorbonne Université (SU), University of York, Norwegian University of Life Sciences (NMBU), University of Vienna [Vienna], University of Adelaide, Institut Pasteur [Paris], National Agriculture and Food Research Organization (NARO), Kagoshima University, University of Tokyo, Newcastle University, University of St Andrews [Scotland], The Walter and Eliza Hall Institute of Medical Research (WEHI), Simon Fraser University (SFU.ca), Max Planck Institute for Marine Microbiology, Max-Planck-Gesellschaft, University of Leeds, University of Zaragoza - Universidad de Zaragoza [Zaragoza], Slovak Academy of Sciences (SAS), Quadram Institute, University of the Ryukyus [Okinawa], Ishikawa Prefectural University, Utsunomiya University [Utsunomiya], St Petersburg Nuclear Physics Institute, University of Groningen, Aalto University, University of Copenhagen = Københavns Universitet (KU), University of Lisbon, University of Oulu, University of Manitoba [Winnipeg], University of Lethbridge, Hokkaido University [Sapporo, Japan], Niigata University, Ghent University, Kinki University, Queen Mary University of London (QMUL), Sveriges lantbruksuniversitet, National Center for Biotechnology, Centre de Recherche en Cancérologie de Marseille (CRCM), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut Paoli-Calmettes, Fédération nationale des Centres de lutte contre le Cancer (FNCLCC)-Fédération nationale des Centres de lutte contre le Cancer (FNCLCC)-Aix Marseille Université (AMU), Iowa State University (ISU), Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA), University of Waterloo [Waterloo], University of Eastern Finland, Iwate Biotechnology Research Center (IBRC), Technion - Israel Institute of Technology [Haifa], United States Department of Agriculture, Wilfrid Laurier University (WLU), Architecture et fonction des macromolécules biologiques (AFMB), Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU)-Institut National de la Recherche Agronomique (INRA), Institut National de la Recherche Agronomique (INRA), RIKEN - Institute of Physical and Chemical Research [Japon] (RIKEN), Akita University, Danmarks Tekniske Universitet (DTU), University of Lincoln, Tokyo University of Agriculture and Technology (TUAT), Univ Georgia, University of Georgia [USA], Université Catholique de Louvain = Catholic University of Louvain (UCL), Centre de Recherches sur les Macromolécules Végétales (CERMAV ), Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019]), Université Grenoble Alpes [2016-2019] (UGA [2016-2019]), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Ryerson University, Utrecht University [Utrecht], University of Melbourne, Cornell University [New York], National Institute of Advanced Industrial Science and Technology (AIST), Natural Sciences and Engineering Research Council of Canada (NSERC), Agriculture and Agri-Food (AAFC), Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Institut Pasteur [Paris] (IP), Biotechnology and Biological Sciences Research Council (BBSRC), University of Copenhagen = Københavns Universitet (UCPH), Universidade de Lisboa = University of Lisbon (ULISBOA), Universiteit Gent = Ghent University (UGENT), Aix Marseille Université (AMU)-Institut Paoli-Calmettes, Fédération nationale des Centres de lutte contre le Cancer (FNCLCC)-Fédération nationale des Centres de lutte contre le Cancer (FNCLCC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT), Institut National de la Recherche Agronomique (INRA)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Danmarks Tekniske Universitet = Technical University of Denmark (DTU), Weizmann Institute of Science, Centre National de la Recherche Scientifique (CNRS)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Institut National de la Recherche Agronomique (INRA), University of Victoria, Sherbrooke University, Sorbonne Universités, University of Vienna, National Agriculture and Food Research Organization, University of St Andrews, Walter and Eliza Hall Institute of Medical Research (WEHI), Slovak Academy of Sciences, Utsunomiya University, Hokkaido University, Iwate Biotechnol Res Ctr, Technion – Israel Institute of Technology, Akita Prefectural University, Université Catholique de Louvain (UCL), Centre de Recherches sur les Macromolécules Végétales (CERMAV), Université Joseph Fourier - Grenoble 1 (UJF)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA), Université Grenoble Alpes (UGA), Cornell University, Laboratoire Départemental Vétérinaire et d'Hygiène Alimentaire des Hautes Alpes, and Moracci, M
Subjects: 0301 basic medicine, History, Carbohydrate, CAZy, Bioinformatics, [SDV]Life Sciences [q-bio], 030106 microbiology, Polysaccharide-Lyases, Glycobiology, Carbohydrates, Glycosyltransferases/chemistry, Computational biology, Biology, Esterase, Biochemistry, History, 21st Century, Databases, 03 medical and health sciences, glycobiology, Esterases/chemistry, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Carbohydrates/chemistry, Glycoscience, Databases, Protein, ComputingMilieux_MISCELLANEOUS, bioinformatic, [SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Structural Biology [q-bio.BM], Protein, Polysaccharide-Lyases/chemistry, biocuration, Esterases, glycoscience, Glycosyltransferases, [SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, bioinformatics, 21st Century, Biocuration, [SDV.BBM.BP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biophysics, 030104 developmental biology, carbohydrate-active enzymes, Encyclopedia, Carbohydrate-active enzymes, carbohydrate-active enzyme, Carbohydrate active enzymes, Glycosyltransferase
Abstract: CAZypedia was initiated in 2007 to create a comprehensive, living encyclopedia of the carbohydrate-active enzymes (CAZymes) and associated carbohydrate-binding modules involved in the synthesis, modification, and degradation of complex carbohydrates. CAZypedia is closely connected with the actively-curated CAZy database, which provides a sequence-based foundation for the biochemical, mechanistic, and structural characterization of these diverse proteins. Now celebrating its 10th anniversary online, CAZypedia is a successful example of dynamic, community-driven, and expert-based biocuration. CAZypedia is an open-access resource available at URL http://www.cazypedia.org.
Published: 2018

20. Structural insights into marine carbohydrate degradation by family GH16 κ-carrageenases

Author: Murielle Jam, Thomas Bernard, Mirjam Czjzek, Aurélie Préchoux, Tristan Barbeyron, Robert Larocque, Gurvan Michel, Alexandra Jeudy, Cédric Leroux, Maria Matard-Mann, Pi Nyvall Collén, Laboratoire de Biologie Intégrative des Modèles Marins (LBI2M), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff (SBR), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Architecture et fonction des macromolécules biologiques (AFMB), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Station biologique de Roscoff (SBR), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Fédération de recherche de Roscoff (FR2424), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), 'Pôle Biotechnologique' du Haut Bois, Amadéite SAS, Fraunhofer Institute of Optronics, System Technologies and Image Exploitation (Fraunhofer IOSB), Fraunhofer (Fraunhofer-Gesellschaft), Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Station biologique de Roscoff [Roscoff] (SBR), and Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0301 basic medicine, Subfamily, Glycoside Hydrolases, Protein Conformation, [SDV]Life Sciences [q-bio], Mutagenesis (molecular biology technique), Marine Biology, Biology, Crystallography, X-Ray, Biochemistry, Catalysis, Substrate Specificity, Cell wall, 03 medical and health sciences, Marine bacteriophage, Hydrolase, [CHIM.CRIS]Chemical Sciences/Cristallography, Glycoside hydrolase, Molecular Biology, Pseudoalteromonas carrageenovora, Phylogeny, ComputingMilieux_MISCELLANEOUS, Enzyme substrate complex, 030102 biochemistry & molecular biology, [SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Structural Biology [q-bio.BM], Cell Biology, biology.organism_classification, Kinetics, Pseudoalteromonas, 030104 developmental biology, Enzymology, Carbohydrate Metabolism, Flavobacteriaceae
Abstract: Carrageenans are sulfated α-1,3-β-1,4-galactans found in the cell wall of some red algae that are practically valuable for their gelation and biomimetic properties but also serve as a potential carbon source for marine bacteria. Carbohydrate degradation has been studied extensively for terrestrial plant/bacterial systems, but sulfation is not present in these cases, meaning the marine enzymes used to degrade carrageenans must possess unique features to recognize these modifications. To gain insights into these features, we have focused on κ-carrageenases from two distant bacterial phyla, which belong to glycoside hydrolase family 16 and cleave the β-1,4 linkage of κ-carrageenan. We have solved the crystal structure of the catalytic module of ZgCgkA from Zobellia galactanivorans at 1.66 A resolution and compared it with the only other structure available, that of PcCgkA from Pseudoalteromonas carrageenovora 9T (ATCC 43555T). We also describe the first substrate complex in the inactivated mutant form of PcCgkA at 1.7 A resolution. The structural and biochemical comparison of these enzymes suggests key determinants that underlie the functional properties of this subfamily. In particular, we identified several arginine residues that interact with the polyanionic substrate, and confirmed the functional relevance of these amino acids using a targeted mutagenesis strategy. These results give new insight into the diversity of the κ-carrageenase subfamily. The phylogenetic analyses show the presence of several distinct clades of enzymes that relate to differences in modes of action or subtle differences within the same substrate specificity, matching the hybrid character of the κ-carrageenan polymer.
Published: 2017

21. Development of novel monoclonal antibodies against starch and ulvan - Implications for antibody production against polysaccharides with limited immunogenicity

Author: Casper Wilkens, David S. Domozych, Birte Svensson, Bodil Jørgensen, Marie-Christine Ralet, Gurvan Michel, Alexia Guillouzo, Jozef Mravec, Sabine Genicot, Jonatan U. Fangel, William G.T. Willats, Stjepan K. Kračun, Mohammed Saddik Motawia, Maja Gro Rydahl, Olivier Tranquet, Jesper Harholt, University of Copenhagen = Københavns Universitet (KU), Laboratoire de Biologie Intégrative des Modèles Marins (LBI2M), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff (SBR), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Technical University of Denmark [Lyngby] (DTU), Unité de recherche sur les Biopolymères, Interactions Assemblages (BIA), Institut National de la Recherche Agronomique (INRA), Skidmore College [Saratoga Springs], Newcastle University [Newcastle], Danish Strategic Research Council, Danish Council for Independent Research, Technology and Production Sciences under project GlycAct [10-093465], Danish National Advanced Technology Foundation project B21st, Danish Innovation Foundation, Villum foundation project Planet project [00009283], US National Science Foundation (NSF) Molecular and Cellular Bioscience [0919925, 1517345], NSF Division of Biological Infrastructure [0922805], Carlsberg Foundation, French National Research Agency program IDEALG [ANR-10-BTBR-04], European Project: 329830,EC:FP7:PEOPLE,FP7-PEOPLE-2012-IEF,CEWALDYN(2013), Rydahl, Maja G., University of Copenhagen = Københavns Universitet (UCPH), and Danmarks Tekniske Universitet = Technical University of Denmark (DTU)
Subjects: 0301 basic medicine, Glycan, [SDV.BIO]Life Sciences [q-bio]/Biotechnology, Plant molecular biology, medicine.drug_class, Glycobiology, lcsh:Medicine, Monoclonal antibody, Polysaccharide, Epitope, Article, Microbiology, 03 medical and health sciences, Epitopes, Plant evolution, Antigen, Polysaccharides, medicine, Journal Article, Animals, Viridiplantae, lcsh:Science, chemistry.chemical_classification, Mammals, Multidisciplinary, biology, Assay systems, Immunogenicity, lcsh:R, Antibodies, Monoclonal, Starch, Plants, biology.organism_classification, 030104 developmental biology, Biochemistry, chemistry, biology.protein, [SDV.IMM]Life Sciences [q-bio]/Immunology, lcsh:Q, Antibody, Glycogen
Abstract: Monoclonal antibodies (mAbs) are widely used and powerful research tools, but the generation of mAbs against glycan epitopes is generally more problematic than against proteins. This is especially significant for research on polysaccharide-rich land plants and algae (Viridiplantae). Most antibody production is based on using single antigens, however, there are significant gaps in the current repertoire of mAbs against some glycan targets with low immunogenicity. We approached mAb production in a different way and immunised with a complex mixture of polysaccharides. The multiplexed screening capability of carbohydrate microarrays was then exploited to deconvolute the specificities of individual mAbs. Using this strategy, we generated a set of novel mAbs, including one against starch (INCh1) and one against ulvan (INCh2). These polysaccharides are important storage and structural polymers respectively, but both are generally considered as having limited immunogenicity. INCh1 and INCh2 therefore represent important new molecular probes for Viridiplantae research. Moreover, since the α-(1-4)-glucan epitope recognised by INCh1 is also a component of glycogen, this mAb can also be used in mammalian systems. We describe the detailed characterisation of INCh1 and INCh2, and discuss the potential of a non-directed mass-screening approach for mAb production against some glycan targets.
Published: 2017

22. Innovating glycoside hydrolase activity on a same structural scaffold

Author: Mirjam Czjzek, Gurvan Michel, Laboratoire de Biologie Intégrative des Modèles Marins (LBI2M), Station biologique de Roscoff [Roscoff] (SBR), and Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0301 basic medicine, chemistry.chemical_classification, Multidisciplinary, Anomer, [SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Structural Biology [q-bio.BM], Stereochemistry, Glycoside, Glycosidic bond, Carbohydrate, 03 medical and health sciences, Hydrolysis, 030104 developmental biology, Enzyme, Glycolipid, chemistry, Biochemistry, Glycoside hydrolase
Abstract: Carbohydrates play many fundamental roles in the cell physiology and development of plants, animals, and microbes. They can take the form of glycoproteins, glycolipids, and polysaccharides and represent the largest reservoir of carbon resources that are fueling microbial communities as well as free-living microorganisms. The structural diversity of naturally occurring carbohydrate compounds is matched by an equally diverse class of enzymes tailored specifically to break down each and every glycosidic bond. The enzymes responsible for the hydrolysis of these glycosides are termed glycoside hydrolases (GHs), or glycosidases, and are grouped and classified in sequence-based families within the “Carbohydrate-Active enZYmes” Database (1). In general, they are very efficient catalysts that can enhance the reaction rate by an order of 1017-fold over the noncatalytic reaction rate (2). The mechanism by which they achieve this feat has thus been the subject of extensive work (reviewed in refs. 3, 4). The outcome of the hydrolytic reaction, in most cases involving a couple of carboxylic acid residues positioned to activate a water molecule that is added to the glycosidic bond, occurs either with net retention or inversion of the stereochemistry at the anomeric center, and the canonical mechanisms explaining these actions were described as early as 1953 in a seminal paper by Koshland (5). However, in recent years, the flow of new (bacterial) sequences and families has provided several new and unusual mechanisms (6), highlighting the variability of these catabolic processes but also the knowledge gap that still exists in the field of glycobiochemistry. In particular, the … [↵][1]1To whom correspondence should be addressed. Email: mirjam.czjzek{at}sb-roscoff.fr. [1]: #xref-corresp-1-1
Published: 2017

23. Halorhabdus tiamatea: proteogenomics and glycosidase activity measurements identify the first cultivated euryarchaeon from a deep-sea anoxic brine lake as potential polysaccharide degrader

Author: Manuel Ferrer, Alexander J. Mann, Hanno Teeling, Tran Hai, Peter N. Golyshin, Marco Taborda, Johannes Werner, Frank Oliver Glöckner, Silvia Juárez, Olga V. Golyshina, Violetta La Cono, Milton S. da Costa, Gurvan Michel, Sergio Ciordia, André Antunes, Sixing Huang, María Alcaide, Michail M. Yakimov, Juan Pablo Albar, Max Planck Institute for Marine Microbiology, Max-Planck-Gesellschaft, Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), Association pour la Formation Professionnelle des Adultes (AFPA), Association pour la Formation Professionnelle des Adultes, Princeton University, Biogéochimie et écologie des milieux continentaux (Bioemco), Centre National de la Recherche Scientifique (CNRS)-AgroParisTech-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Recherche Agronomique (INRA)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL), Proteomics facility, Centro Nacional de Biotecnología, Insitute for Coastal Marine Environment, Consiglio Nazionale delle Ricerche (CNR), Centro Interdisciplinar de Investigação Marinha e Ambiental (CIMAR/CIIMAR), Universidade do Porto, Departamento de Biologia, Institute for Biotechnology and Bioengineering (IBB), Technical University of Lisbon, Universidade de Coimbra [Coimbra], State Key Laboratory of Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences [Beijing], Sino-French Laboratory LABIOCEM, Jacobs University [Bremen], Microbial genomics and bioinformatics research group, Max-Planck-Gesellschaft-Max-Planck-Gesellschaft, School of Biological Sciences [Bangor], Bangor University, European Commission, Ministerio de Economía y Competitividad (España), Max Planck Society, École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut de Recherche pour le Développement (IRD)-Institut National de la Recherche Agronomique (INRA)-Université Pierre et Marie Curie - Paris 6 (UPMC)-AgroParisTech-Centre National de la Recherche Scientifique (CNRS), Centro Nacional de Biotecnología [Madrid] (CNB-CSIC), Consejo Superior de Investigaciones Científicas [Madrid] (CSIC)-Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), National Research Council of Italy | Consiglio Nazionale delle Ricerche (CNR), Universidade do Porto = University of Porto, Universidade do Minho, Consejo Superior de Investigaciones Científicas [Spain] (CSIC), and Universidade do Porto [Porto]
Subjects: MESH: Genome, Archaeal, [SDV]Life Sciences [q-bio], MESH: Indian Ocean, Sodium Chloride, Genome, Archaeal, Utah, Glycoside hydrolase, MESH: Ecosystem, Anaerobiosis, MESH: Phylogeny, Indian Ocean, extremophiles, Research Articles, Phylogeny, 0303 health sciences, Halobacteriaceae, biology, Ecology, Salt Tolerance, Anoxic waters, Adaptation, Physiological, Biological Evolution, Halorhabdus, Proteome, MESH: Lakes, MESH: Metagenomics, Water Microbiology, MESH: Oxygen, MESH: Sodium Chloride, Glycoside Hydrolases, MESH: Biological Evolution, Microbiology, 03 medical and health sciences, MESH: Halobacteriaceae, Phylogenetics, MESH: Enzyme Assays, Polysaccharides, Botany, MESH: Anaerobiosis, MESH: Glycoside Hydrolases, 14. Life underwater, Ecology, Evolution, Behavior and Systematics, Ecosystem, 030304 developmental biology, Enzyme Assays, Science & Technology, MESH: Salt-Tolerance, 030306 microbiology, Thermophile, MESH: Utah, deep sea brine, biology.organism_classification, MESH: Adaptation, Physiological, MESH: Water Microbiology, Oxygen, Lakes, MESH: Polysaccharides, euryarchaeon, 13. Climate action, Metagenomics, Archaea
Abstract: Summary: Euryarchaea from the genus Halorhabdus have been found in hypersaline habitats worldwide, yet are represented by only two isolates: Halorhabdus utahensisAX-2T from the shallow Great Salt Lake of Utah, and Halorhabdus tiamateaSARL4BT from the Shaban deep-sea hypersaline anoxic lake (DHAL) in the Red Sea. We sequenced the H.tiamatea genome to elucidate its niche adaptations. Among sequenced archaea, H.tiamatea features the highest number of glycoside hydrolases, the majority of which were expressed in proteome experiments. Annotations and glycosidase activity measurements suggested an adaptation towards recalcitrant algal and plant-derived hemicelluloses. Glycosidase activities were higher at 2% than at 0% or 5% oxygen, supporting a preference for low-oxygen conditions. Likewise, proteomics indicated quinone-mediated electron transport at 2% oxygen, but a notable stress response at 5% oxygen. Halorhabdus tiamatea furthermore encodes proteins characteristic for thermophiles and light-dependent enzymes (e.g. bacteriorhodopsin), suggesting that H.tiamatea evolution was mostly not governed by a cold, dark, anoxic deep-sea habitat. Using enrichment and metagenomics, we could demonstrate presence of similar glycoside hydrolase-rich Halorhabdus members in the Mediterranean DHAL Medee, which supports that Halorhabdus species can occupy a distinct niche as polysaccharide degraders in hypersaline environments., This study was supported by the EU FP7 project MAMBA (‘Marine Metagenomics for New Biotechnological Applications’, FP7‐KBBE‐2008–226977, the Spanish Ministry of Economy and Competitiveness (grant BIO2011–25012) and the Max Planck Society. H.T., O.V.G. and P.N.G. acknowledge the support of EU FP7 for the project MicroB3 (OCEAN‐2011‐287589).
Published: 2014

24. Matching the Diversity of Sulfated Biomolecules: Creation of a Classification Database for Sulfatases Reflecting Their Substrate Specificity

Author: Cathelène Carrière, Wilfrid Carré, Gurvan Michel, Mirjam Czjzek, Christophe Caron, Loraine Brillet-Guéguen, Mark Hoebeke, Tristan Barbeyron, Laboratoire de Biologie Intégrative des Modèles Marins (LBI2M), Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Station biologique de Roscoff [Roscoff] (SBR), and Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0301 basic medicine, Subfamily, [SDV]Life Sciences [q-bio], Protein Data Bank (RCSB PDB), lcsh:Medicine, Protein Sequencing, Pathology and Laboratory Medicine, computer.software_genre, Substrate Specificity, User-Computer Interface, Database and Informatics Methods, Protein sequencing, Catalytic Domain, Medicine and Health Sciences, lcsh:Science, Databases, Protein, Phylogeny, Multidisciplinary, Database, Phylogenetic tree, Sulfates, Pseudomonas Aeruginosa, Phylogenetic Analysis, Bacterial Pathogens, Chemistry, Medical Microbiology, Physical Sciences, Sulfatases, Pathogens, UniProt, Sequence Analysis, Research Article, Multiple Alignment Calculation, Sequence Databases, Sequence alignment, Context (language use), Biology, Research and Analysis Methods, Microbiology, 03 medical and health sciences, Sequence Motif Analysis, Phylogenetics, Pseudomonas, Computational Techniques, Animals, Humans, Molecular Biology Techniques, Sequencing Techniques, Molecular Biology, Microbial Pathogens, Internet, Molecular Biology Assays and Analysis Techniques, Bacteria, 030102 biochemistry & molecular biology, lcsh:R, Chemical Compounds, Organisms, Biology and Life Sciences, Split-Decomposition Method, Biological Databases, 030104 developmental biology, Biocatalysis, lcsh:Q, Salts, Sequence Alignment, computer
Abstract: International audience; Sulfatases cleave sulfate groups from various molecules and constitute a biologically and industrially important group of enzymes. However, the number of sulfatases whose substrate has been characterized is limited in comparison to the huge diversity of sulfated compounds, yielding functional annotations of sulfatases particularly prone to flaws and misinterpretations. In the context of the explosion of genomic data, a classification system allowing a better prediction of substrate specificity and for setting the limit of functional annotations is urgently needed for sulfatases. Here, after an overview on the diversity of sulfated compounds and on the known sulfatases, we propose a classification database, SulfAtlas (http://abims.sb-roscoff.fr/sulfatlas/), based on sequence homology and composed of four families of sulfatases. The formylglycine-dependent sulfatases, which constitute the largest family, are also divided by phylogenetic approach into 73 subfamilies, each subfamily corresponding to either a known specificity or to an uncharacterized substrate. SulfAtlas summarizes information about the different families of sulfatases. Within a family a web page displays the list of its subfamilies (when they exist) and the list of EC numbers. The family or subfamily page shows some descriptors and a table with all the UniProt accession numbers linked to the databases UniProt, ExplorEnz, and PDB.
Published: 2016

25. The genome of the seagrass Zostera marina reveals angiosperm adaptation to the sea

Author: Thierry Tonon, Jeremy Schmutz, Yao-Cheng Lin, Mats Töpel, Rolf Lohaus, Emanuela Dattolo, Christoffer Boström, Hope Tice, Anna R. Kersting, Jerry Jenkins, Erich Bornberg-Bauer, Pamela J. Green, Jane Grimwood, Florian Maumus, Gabriele Procaccini, Bram Verhelst, Simon M. Dittami, Emanuele De Paoli, Janina Brakel, Mojgan Amirebrahimi, Amy Mraz, Gurvan Michel, Jonas Collén, Mansi Chovatia, Kevin Vanneste, Chiara Lauritano, Alexander Jueterbock, Till Bayer, Pierre Rouzé, Thorsten B. H. Reusch, Gareth A. Pearson, Jeanine L. Olsen, Wytze T. Stam, Yves Van de Peer, Carlos M. Duarte, GELIFES, Ghent University [Belgium] (UGENT), GEOMAR - Helmholtz Centre for Ocean Research [Kiel] (GEOMAR), Laboratoire de Biologie Intégrative des Modèles Marins (LBI2M), Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Stazione Zoologica Napoli, Dipartimento di Scienze Agrarie ed Ambientali - Universita Udine (DISA), Università degli Studi di Udine - University of Udine [Italie], Unité de Recherche Génomique Info (URGI), Institut National de la Recherche Agronomique (INRA), Westfälische Wilhelms-Universität Münster (WWU), Heinrich-Heine-Universität Düsseldorf [Düsseldorf], University of Gothenburg (GU), US Department of Energy Joint Genome Institute, University of California, Åbo Akademi University [Turku], HudsonAlpha Institute for Biotechnology, Nord University [Bodø], Amplicon Express Inc., University of Delaware [Newark], University of Algarve [Portugal], King Abdullah University of Science and Technology (KAUST), Christian-Albrechts-Universität zu Kiel (CAU), University of Pretoria [South Africa], Universiteit Gent = Ghent University (UGENT), Helmholtz Centre for Ocean Research [Kiel] (GEOMAR), Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Stazione Zoologica Anton Dohrn (SZN), Westfälische Wilhelms-Universität Münster = University of Münster (WWU), Heinrich Heine Universität Düsseldorf = Heinrich Heine University [Düsseldorf], University of California (UC), HudsonAlpha Institute for Biotechnology [Huntsville, AL], and Universiteit Gent = Ghent University [Belgium] (UGENT)
Subjects: 0301 basic medicine, Salinity, Acclimatization, PROTEIN, Molecular engineering in plants, Evolutionary ecology, Plant evolution, Osmoregulation, Adaptation, Physiological, Cell Wall, Ethylenes, Gene Duplication, Genes, Plant, Genome, Plant, Metabolic Networks and Pathways, Molecular Sequence Data, Oceans and Seas, Phylogeny, Plant Leaves, Plant Stomata, Pollen, Salt-Tolerance, Seaweed, Terpenes, Zosteraceae, Evolution, Molecular, Seawater, Medicine (all), Multidisciplinary, ECOSYSTEMS, RNA-SEQ, MAXIMUM-LIKELIHOOD, NEW-JERSEY, [SDU.OCEAN]Sciences of the Universe [physics]/Ocean, Atmosphere, Genome, Ecology, FLOWERING PLANTS, food and beverages, Salt Tolerance, Seagrass, Mathematics and natural science: 400::Zoology and botany: 480::Marine biology: 497 [VDP], Zostera marina, CHROMOSOME-NUMBERS, Evolution, General Science & Technology, Physiological, Biology, 03 medical and health sciences, GENE LISTS, Botany, Genetics, Ecosystem, Marine ecosystem, 14. Life underwater, Genetic variation, Adaptation, Life Below Water, SEQUENCES, Human Genome, fungi, Biology and Life Sciences, Molecular, Plant, biology.organism_classification, Zostera marina Linnaeus, 1758, 030104 developmental biology, Genes
Abstract: Seagrasses colonized the sea on at least three independent occasions to form the basis of one of the most productive and widespread coastal ecosystems on the planet. Here we report the genome of Zostera marina (L.), the first, to our knowledge, marine angiosperm to be fully sequenced. This reveals unique insights into the genomic losses and gains involved in achieving the structural and physiological adaptations required for its marine lifestyle, arguably the most severe habitat shift ever accomplished by flowering plants. Key angiosperm innovations that were lost include the entire repertoire of stomatal genes, genes involved in the synthesis of terpenoids and ethylene signalling, and genes for ultraviolet protection and phytochromes for far-red sensing. Seagrasses have also regained functions enabling them to adjust to full salinity. Their cell walls contain all of the polysaccharides typical of land plants, but also contain polyanionic, low-methylated pectins and sulfated galactans, a feature shared with the cell walls of all macroalgae and that is important for ion homoeostasis, nutrient uptake and O2/CO2 exchange through leaf epidermal cells. The Z. marina genome resource will markedly advance a wide range of functional ecological studies from adaptation of marine ecosystems under climate warming, to unravelling the mechanisms of osmoregulation under high salinities that may further inform our understanding of the evolution of salt tolerance in crop plants.
Published: 2016

26. DISCOVERING NOVEL ENZYMES BY FUNCTIONAL SCREENING OF PLURIGENOMIC LIBRARIES FROM ALGA-ASSOCIATED FLAVOBACTERIIA AND GAMMAPROTEOBACTERIA

Author: Tristan Barbeyron, Marjolaine Martin, Gurvan Michel, Renée Martin, Marie Vandermies, Coline Joyeux, Micheline Vandenbol, Gembloux Agro-Bio Tech [Gembloux], Université de Liège, Laboratoire de Biologie Intégrative des Modèles Marins (LBI2M), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff (SBR), and Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0301 basic medicine, 030106 microbiology, Context (language use), Bacterial genome size, Phaeophyta, Esterase, Microbiology, Beta-glucosidase, 03 medical and health sciences, Phylogenetics, Gammaproteobacteria, Genomic library, Genetic Testing, 14. Life underwater, Kappa-carrageenase, Gene Library, Genetics, biology, Bacteroidetes, Xylanase, Marine bacteria, AgaraseIota-carrageenase, Sequence Analysis, DNA, biology.organism_classification, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Enzymes, Restriction enzyme, 030104 developmental biology, Marine enzymes, Flavobacteriia, Alga-associated microflora
Abstract: International audience; Alga-associated microorganisms, in the context of their numerous interactions with the host and the complexity of the marine environment, are known to produce diverse hydrolytic enzymes with original biochemistry. We recently isolated several macroalgal-polysaccharide-degrading bacteria from the surface of the brown alga Ascophyllum nodosum. These active isolates belong to two classes: the Flavobacteriia and the Gammaproteobacteria. In the present study, we constructed two "plurigenomic" (with multiple bacterial genomes) libraries with the 5 most interesting isolates (regarding their phylogeny and their enzymatic activities) of each class (Fv and Gm libraries). Both libraries were screened for diverse hydrolytic activities. Five activities, out of the 42 identified in the natural polysaccharolytic isolates, were recovered by functional screening: a xylanase (GmXyl7), a beta-glucosidase (GmBg1), an esterase (GmEst7) and two iota-carrageenases (Fvi2.5 and Gmi1.3). We discuss here the potential role of the used host-cell, the average DNA insert-sizes and the used restriction enzymes on the divergent screening yields obtained for both libraries and get deeper inside the “great screen anomaly”. Interestingly, the discovered esterase probably stands for a novel family of homoserine o-acetyltransferase-like-esterases, while the two iota-carrageenases represent new members of the poorly known GH82 family (containing only 19 proteins since its description in 2000). These original results demonstrate the efficiency of our uncommon “plurigenomic” library approach and the underexplored potential of alga-associated cultivable microbiota for the identification of novel and algal-specific enzymes.
Published: 2016

27. Unraveling the multivalent binding of a marine family 6 carbohydrate-binding module with its native laminarin ligand

Author: Elizabeth Ficko-Blean, Mirjam Czjzek, Aurore Labourel, Robert Larocque, Gurvan Michel, Murielle Jam, Laboratoire de Biologie Intégrative des Modèles Marins (LBI2M), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff (SBR), and Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0301 basic medicine, CBM6, Protein Conformation, Protein Data Bank (RCSB PDB), Marine Biology, Calorimetry, Biology, Crystallography, X-Ray, Ligands, Biochemistry, laminarinase, 03 medical and health sciences, Laminarin, chemistry.chemical_compound, Protein structure, Polysaccharides, Hydrolase, Protein–carbohydrate interactions, 14. Life underwater, Binding site, [SDV.BBM.BC]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biochemistry [q-bio.BM], Glucans, Molecular Biology, Phylogeny, carbohydrate-binding module, algae, [SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Structural Biology [q-bio.BM], Isothermal titration calorimetry, Cell Biology, 030104 developmental biology, Carbohydrate Sequence, chemistry, marine bacteria, protein-carbohydrate interactions, Mutagenesis, Site-Directed, Thermodynamics, Carbohydrate-binding module, Flavobacteriaceae, laminarin, Protein Binding
Abstract: UNLABELLED Laminarin is an abundant brown algal storage polysaccharide. Marine microorganisms, such as Zobellia galactanivorans, produce laminarinases for its degradation, which are important for the processing of this organic matter in the ocean carbon cycle. These laminarinases are often modular, as is the case with ZgLamC which has an N-terminal GH16 module, a central family 6 carbohydrate-binding module (CBM) and a C-terminal PorSS module. To date, no studies have characterized a true marine laminarin-binding CBM6 with its natural carbohydrate ligand. The crystal structure of ZgLamCCBM6 indicates that this CBM has two clefts for binding sugar (variable loop site, VLS; and concave face site, CFS). The ZgLamCCBM6 VLS binds in an exo-manner and the CFS interacts in an endo-manner with laminarin. Isothermal titration calorimetry (ITC) experiments on native and mutant ZgLamCCBM6 confirm that these binding sites have different modes of recognition for laminarin, in agreement with the 'regional model' postulated for CBM6-binding modules. Based on ITC data and structural data, we propose a model of ZgLamCCBM6 interacting with different chains of laminarin in a multivalent manner, forming a complex cross-linked protein-polysaccharide network. DATABASE PDB code 5FUI.
Published: 2016

28. The cultivable surface microbiota of the brown alga Ascophyllum nodosum is enriched in macroalgal-polysaccharide-degrading bacteria

Author: Tristan Barbeyron, Marjolaine Martin, Daniel Portetelle, Gurvan Michel, Micheline Vandenbol, Renée Martin, Microbiology and Genomics Unit, Laboratoire de Biologie Intégrative des Modèles Marins (LBI2M), Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Station biologique de Roscoff [Roscoff] (SBR), and Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Microbiology (medical), Cyanobacteria, macroalgae, algal polysaccharidase, lcsh:QR1-502, Microbiology, Flavobacteriia, lcsh:Microbiology, Cultivable bacteria, Botany, Gammaproteobacteria, carrageenase, 14. Life underwater, Original Research, biology, Ascophyllum nodosum, Agarase, Planctomycetes, Bacteroidetes, alginate lyase, biology.organism_classification, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Brown algae, Ascophyllum, Bacteria
Abstract: Bacteria degrading algal polysaccharides are key players in the global carbon cycle and in algal biomass recycling. Yet the water column, which has been studied largely by metagenomic approaches, is poor in such bacteria and their algal-polysaccharide-degrading enzymes. Even more surprisingly, the few published studies on seaweed-associated microbiomes have revealed low abundances of such bacteria and their specific enzymes. However, as macroalgal cell-wall polysaccharides do not accumulate in nature, these bacteria and their unique polysaccharidases must not be that uncommon. We, therefore, looked at the polysaccharide-degrading activity of the cultivable bacterial subpopulation associated with Ascophyllum nodosum. From A. nodosum triplicates, 324 bacteria were isolated and taxonomically identified. Out of these isolates, 78 (~25%) were found to act on at least one tested algal polysaccharide (agar, ?- or ?-carrageenan, or alginate). The isolates “active” on algal-polysaccharides belong to 11 genera: Cellulophaga, Maribacter, Algibacter, and Zobellia in the class Flavobacteriia (41) and Pseudoalteromonas, Vibrio, Cobetia, Shewanella, Colwellia, Marinomonas, and Paraglaceciola in the class Gammaproteobacteria (37). A major part represents likely novel species. Different proportions of bacterial phyla and classes were observed between the isolated cultivable subpopulation and the total microbial community previously identified on other brown algae. Here, Bacteroidetes and Gammaproteobacteria were found to be the most abundant and some phyla (as Planctomycetes and Cyanobacteria) frequently encountered on brown algae weren't identified. At a lower taxonomic level, twelve genera, well-known to be associated with algae (with the exception for Colwellia), were consistently found on all three A. nosodum samples. Even more interesting, 9 of the 11 above mentioned genera containing polysaccharolytic isolates were predominant in this common core. The cultivable fraction of the bacterial community associated with A. nodosum is, thus, significantly enriched in macroalgal-polysaccharide-degrading bacteria and these bacteria seem important for the seaweed holobiont even though they are under-represented in alga-associated microbiome studies.
Published: 2015

29. Vanadium haloperoxidases: from the discovery 30 years ago to X-Ray crystallographic and V K-edge absorption spectroscopic studies

Author: Gurvan Michel, Mirjam Czjzek, Philippe Potin, Catherine Leblanc, Martin C. Feiters, Jean-Baptiste Fournier, P.L. Solari, Ludovic Delage, Hans Vilter, Etienne Rebuffet, Laboratoire de Biologie Intégrative des Modèles Marins (LBI2M), Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Zurmaiener Strasse, Centre de Recherche en Cancérologie de Marseille (CRCM), Aix Marseille Université (AMU)-Institut Paoli-Calmettes, Fédération nationale des Centres de lutte contre le Cancer (FNCLCC)-Fédération nationale des Centres de lutte contre le Cancer (FNCLCC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Synchrotron SOLEIL (SSOLEIL), Centre National de la Recherche Scientifique (CNRS), Department Organic Chemistry, Radboud University [Nijmegen], Administateur, HAL Sorbonne Université, Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), and Radboud university [Nijmegen]
Subjects: X-ray absorption spectroscopy, biology, Chemistry, Vanadium coordination, Crystallographic structure, Oligomeric state, Active site, Halide, Vanadium, chemistry.chemical_element, Synthetic Organic Chemistry, X-ray absorption spectroscopy on biological vanadium, Catalysis, Inorganic Chemistry, Crystallography, Catalytic cycle, [CHIM] Chemical Sciences, Materials Chemistry, biology.protein, Structural evolution, [CHIM]Chemical Sciences, Vanadate, Physical and Theoretical Chemistry, Vanadium bromoperoxidase, Vanadium-dependent haloperoxidase
Abstract: International audience; In the environment, vanadium-dependent haloperoxidases (VHPO) are likely to play a key role in the production of biogenic organo-halogens. These enzymes contain vanadate as a prosthetic group, and catalyze, in the presence of hydrogen peroxide, the oxidation of halide ions (Cl−, Br− or I−). They are classified according to the most electronegative halide that they can oxidize. Since the first discovery of a vanadium bromoperoxidase in the brown alga Ascophyllum nodosum thirty years ago, structural and mechanistic studies have been mainly conducted on two types of VHPO, chloro- and bromoperoxidases, and more recently on a vanadium-dependent iodoperoxidase. In this review, we highlight the main progress obtained on the structure-function relation of these proteins, based on biochemistry, crystallography and X-ray absorption spectroscopy (XAS). The comparison of 3D protein structures of the different VHPO helped identify the residues that govern the molecular mechanisms of catalysis and specificity of VHPO. Vanadium K-edge XAS gave further important insight to understand the fine changes around the vanadium cofactor during the catalytic cycle. The combination of different structural approaches, at different scales of resolution, shed new light on biological vanadium coordination in the active site, and its importance for the catalytic cycle and halide specificity of vanadium haloperoxidases.
Published: 2015

30. Sweet and sour sugars from the sea: the biosynthesis and remodeling of sulfated cell wall polysaccharides from marine macroalgae

Author: Gurvan Michel, Cécile Hervé, Elizabeth Ficko-Blean, Laboratoire de Biologie Intégrative des Modèles Marins (LBI2M), Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Végétaux marins et biomolécules, Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-GOEMAR-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Station biologique de Roscoff [Roscoff] (SBR), and Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 02 engineering and technology, Biology, Polysaccharide, sulfated polysaccharides, glycosyltransferase, Microbiology, Cell wall, 03 medical and health sciences, chemistry.chemical_compound, Sulfation, ulvan, Biosynthesis, fucoidan, Glycosyltransferase, genomics, [CHIM]Chemical Sciences, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Glycoside hydrolase, glycoside hydrolase, 14. Life underwater, 030304 developmental biology, agar, chemistry.chemical_classification, 0303 health sciences, Fucoidan, 021001 nanoscience & nanotechnology, Carrageenan, seaweeds, chemistry, Biochemistry, biology.protein, carrageenan, biosynthesis, 0210 nano-technology
Abstract: International audience; The cell walls of green, red and brown seaweeds are dominated by the presence of sulfated polysaccharides. The recent genomic analyses of Chondrus crispus (Rhodophyta) and Ectocarpus siliculosus (Phaeophyceae) have revealed carbohydrate-active enzymes likely implicated in the biosynthesis of these polymers. The closest homologues of many of these algal enzymes are found in animals and are involved in the biosynthesis of sulfated glycosaminoglycans, indicating a shared ancestral pathway between animals, red and brown algae. Here, we review the structures of these algal sulfated polysaccharides and the current state of knowledge on the enzymes involved in their biosynthesis and remodeling. Based on the experimental and genomic data available, biosynthetic pathways for these essential cell wall polysaccharides are presented.
Published: 2015

31. Biochemical and structural investigation of two paralogous glycoside hydrolases from Zobellia galactanivorans: novel insights into the evolution, dimerization plasticity and catalytic mechanism of the GH117 family

Author: Robert Larocque, Gurvan Michel, Agnès Groisillier, Elizabeth Ficko-Blean, Delphine Duffieux, Etienne Rebuffet, Mirjam Czjzek, Laboratoire de Biologie Intégrative des Modèles Marins (LBI2M), Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Station biologique de Roscoff [Roscoff] (SBR), and Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Models, Molecular, Glycoside Hydrolases, Stereochemistry, Protein Conformation, Molecular Sequence Data, Crystallography, X-Ray, Cell wall, Evolution, Molecular, Residue (chemistry), Hydrolysis, Structural Biology, Hydrolase, Glycoside hydrolase, Amino Acid Sequence, Phylogeny, chemistry.chemical_classification, Binding Sites, [SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Structural Biology [q-bio.BM], biology, Galactose, General Medicine, biology.organism_classification, Phylogenetic diversity, [SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biomolecules [q-bio.BM], Enzyme, Biochemistry, chemistry, Metals, Protein Multimerization, Flavobacteriaceae, Sequence Alignment, Bacteria
Abstract: The family 117 glycoside hydrolase (GH117) enzymes have exo-α-1,3-(3,6-anhydro)-L-galactosidase activity, removing terminal nonreducing α-1,3-linked 3,6-anhydro-L-galactose residues from their red algal neoagarose substrate. These enzymes have previously been phylogenetically divided into clades, and only the clade A enzymes have been experimentally studied to date. The investigation of two GH117 enzymes, Zg3615 and Zg3597, produced by the marine bacteriumZobellia galactanivoransreveals structural, biochemical and further phylogenetic diversity between clades. A product complex with the unusual β-3,6-anhydro-L-galactose residue sheds light on the inverting catalytic mechanism of the GH117 enzymes as well as the structure of this unique sugar produced by hydrolysis of the agarophyte red algal cell wall.
Published: 2015

32. Structural and biochemical characterization of the laminarinase ZgLamCGH16 from Zobellia galactanivorans suggests preferred recognition of branched laminarin

Author: Laurent Legentil, Gurvan Michel, Mirjam Czjzek, Aurore Labourel, Vincent Ferrières, Jan-Hendrik Hehemann, Murielle Jam, Balla Sylla, Laboratoire de Biologie Intégrative des Modèles Marins (LBI2M), Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Institut des Sciences Chimiques de Rennes (ISCR), Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Ecole Nationale Supérieure de Chimie de Rennes (ENSCR)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Université européenne de Bretagne - European University of Brittany (UEB), Agence française de financement de la recherche sur projets, l’ANRCancéropole Grand Ouest, Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Ecole Nationale Supérieure de Chimie de Rennes (ENSCR)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Ecole Nationale Supérieure de Chimie de Rennes (ENSCR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), and Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)
Subjects: Models, Molecular, beta-Glucans, Protein Conformation, Molecular Sequence Data, Biology, Crystallography, X-Ray, Polysaccharide, medicine.disease_cause, laminarinase, Substrate Specificity, Laminarin, chemistry.chemical_compound, Marine bacteriophage, Structural Biology, Catalytic Domain, Hydrolase, medicine, Cellulases, oligosaccharide, [CHIM]Chemical Sciences, Glycoside hydrolase, Glycosyl, carbohydrate metabolism, glycoside hydrolase, Amino Acid Sequence, β-1, Glucans, Escherichia coli, Glucan, chemistry.chemical_classification, algae, [CHIM.ORGA]Chemical Sciences/Organic chemistry, General Medicine, 3-glucan, chemistry, Biochemistry, marine bacteria, Proteoglycans, GH16, Flavobacteriaceae, Sequence Alignment
Abstract: Laminarin is a β-1,3-D-glucan displaying occasional β-1,6 branches. This storage polysaccharide of brown algae constitutes an abundant source of carbon for marine bacteria such asZobellia galactanivorans. This marine member of the Bacteroidetes possesses five putative β-1,3-glucanases [four belonging to glycosyl hydrolase family 16 (GH16) and one to GH64] with various modular architectures. Here, the characterization of the β-glucanaseZgLamC is reported. The catalytic GH16 module (ZgLamCGH16) was produced inEscherichia coliand purified. This recombinant enzyme has a preferential specificity for laminarin but also a significant activity on mixed-linked glucan (MLG). The structure of an inactive mutant ofZgLamCGH16in complex with a thio-β-1,3-hexaglucan substrate unravelled a straight active-site cleft with three additional pockets flanking subsites −1, −2 and −3. These lateral pockets are occupied by a glycerol, an acetate ion and a chloride ion, respectively. The presence of these molecules in the vicinity of the O6 hydroxyl group of each glucose moiety suggests thatZgLamCGH16accommodates branched laminarins as substrates. Altogether,ZgLamC is a secreted laminarinase that is likely to be involved in the initial step of degradation of branched laminarin, while the previously characterizedZgLamA efficiently degrades unbranched laminarin and oligo-laminarins.
Published: 2015

33. The Mannitol Utilization System of the Marine Bacterium Zobellia galactanivorans

Author: Gurvan Michel, Agnès Groisillier, Thierry Tonon, Aurore Labourel, Laboratoire de Biologie Intégrative des Modèles Marins (LBI2M), Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Émergence-UPMC-2011 ANR-10-BTBR-02, Station biologique de Roscoff [Roscoff] (SBR), and Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Operon, [SDV]Life Sciences [q-bio], Mannose, Enzyme Activators, ATP-binding cassette transporter, Genetics and Molecular Biology, Biology, Applied Microbiology and Biotechnology, Fructokinase, Substrate Specificity, Fructokinases, chemistry.chemical_compound, Mannitol Dehydrogenases, Gene Order, medicine, Mannitol, Gene, Ions, Ecology, Gene Expression Profiling, biology.organism_classification, Carbon, Recombinant Proteins, chemistry, Biochemistry, Metals, Flavobacteriaceae, Flavobacteriia, Metabolic Networks and Pathways, Food Science, Biotechnology, medicine.drug
Abstract: Mannitol is a polyol that occurs in a wide range of living organisms, where it fulfills different physiological roles. In particular, mannitol can account for as much as 20 to 30% of the dry weight of brown algae and is likely to be an important source of carbon for marine heterotrophic bacteria. Zobellia galactanivorans ( Flavobacteriia ) is a model for the study of pathways involved in the degradation of seaweed carbohydrates. Annotation of its genome revealed the presence of genes potentially involved in mannitol catabolism, and we describe here the biochemical characterization of a recombinant mannitol-2-dehydrogenase (M2DH) and a fructokinase (FK). Among the observations, the M2DH of Z. galactanivorans was active as a monomer, did not require metal ions for catalysis, and featured a narrow substrate specificity. The FK characterized was active on fructose and mannose in the presence of a monocation, preferentially K + . Furthermore, the genes coding for these two proteins were adjacent in the genome and were located directly downstream of three loci likely to encode an ATP binding cassette (ABC) transporter complex, suggesting organization into an operon. Gene expression analysis supported this hypothesis and showed the induction of these five genes after culture of Z. galactanivorans in the presence of mannitol as the sole source of carbon. This operon for mannitol catabolism was identified in only 6 genomes of Flavobacteriaceae among the 76 publicly available at the time of the analysis. It is not conserved in all Bacteroidetes ; some species contain a predicted mannitol permease instead of a putative ABC transporter complex upstream of M2DH and FK ortholog genes.
Published: 2015

34. Microorganisms living on macroalgae: diversity, interactions, and biotechnological applications

Author: Marjolaine Martin, Micheline Vandenbol, Gurvan Michel, Daniel Portetelle, Gembloux Agro Bio Tech, Université de Liège - Gembloux, Végétaux marins et biomolécules, Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-GOEMAR-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Biologie Intégrative des Modèles Marins (LBI2M), Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), and Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)
Subjects: media_common.quotation_subject, Microorganism, [SDV]Life Sciences [q-bio], Microbial metabolism, Biodiversity, Biology, Applied Microbiology and Biotechnology, 03 medical and health sciences, Algae, 14. Life underwater, Symbiosis, 030304 developmental biology, media_common, Microbial Biofilms, 0303 health sciences, Biological Products, Bacteria, 030306 microbiology, Ecology, Aquatic ecosystem, General Medicine, biology.organism_classification, Seaweed, 13. Climate action, Ecological process, Diversity (politics), Biotechnology
Abstract: International audience; Marine microorganisms play key roles in every marine ecological process, hence the growing interest in studying their populations and functions. Microbial communities on algae remain underexplored, however, despite their huge biodiversity and the fact that they differ markedly from those living freely in seawater. The study of this microbiota and of its relationships with algal hosts should provide crucial information for ecological investigations on algae and aquatic ecosystems. Furthermore, because these microorganisms interact with algae in multiple, complex ways, they constitute an interesting source of novel bioactive compounds with biotechnological potential, such as dehalogenases, antimicrobials, and alga-specific polysaccharidases (e.g., agarases, carrageenases, and alginate lyases). Here, to demonstrate the huge potential of alga-associated organisms and their metabolites in developing future biotechnological applications, we first describe the immense diversity and density of these microbial biofilms. We further describe their complex interactions with algae, leading to the production of specific bioactive compounds and hydrolytic enzymes of biotechnological interest. We end with a glance at their potential use in medical and industrial applications.
Published: 2014

35. Mannitol metabolism in brown algae involves a new phosphatase family

Author: Catherine Boyen, Bernd Nidetzky, Sophie Goulitquer, Stefan Krahulec, Zhanru Shao, Gurvan Michel, Delin Duan, Agnès Groisillier, Patricia Bonin, Thierry Tonon, Végétaux marins et biomolécules, Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-GOEMAR-Centre National de la Recherche Scientifique (CNRS), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Institut méditerranéen d'océanologie (MIO), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS), Graz University of Technology [Graz] (TU Graz), and Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Toulon (UTLN)
Subjects: Models, Molecular, Light, Physiology, Sequence analysis, [SDV]Life Sciences [q-bio], Molecular Sequence Data, Phosphatase, Plant Science, Biology, Phaeophyta, medicine.disease_cause, Homology (biology), Gene Expression Regulation, Plant, Gene expression, medicine, Mannitol, Amino Acid Sequence, 14. Life underwater, Escherichia coli, Gene, Genetics, Ectocarpus siliculosus, Algal Proteins, biology.organism_classification, Carbon, Phosphoric Monoester Hydrolases, Recombinant Proteins, Molecular Weight, Brown algae, Biochemistry, Multigene Family, Sequence Alignment
Abstract: International audience; Brown algae belong to a phylogenetic lineage distantly related to green plants and animals, and are found predominantly in the intertidal zone, a harsh and frequently changing environment. Because of their unique evolutionary history and of their habitat, brown algae feature several peculiarities in their metabolism. One of these is the mannitol cycle, which plays a central role in their physiology, as mannitol acts as carbon storage, osmoprotectant, and antioxidant. This polyol is derived directly from the photoassimilate fructose-6-phosphate via the action of a mannitol-1-phosphate dehydrogenase and a mannitol-1-phosphatase (M1Pase). Genome analysis of the brown algal model Ectocarpus siliculosus allowed identification of genes potentially involved in the mannitol cycle. Among these, two genes coding for haloacid dehalogenase (HAD)-like enzymes were suggested to correspond to M1Pase activity, and thus were named EsM1Pase1 and EsM1Pase2, respectively. To test this hypothesis, both genes were expressed in Escherichia coli. Recombinant EsM1Pase2 was shown to hydrolyse the phosphate group from mannitol-1-phosphate to produce mannitol but was not active on the hexose monophosphates tested. Gene expression analysis showed that transcription of both E. siliculosus genes was under the influence of the diurnal cycle. Sequence analysis and three-dimensional homology modelling indicated that EsM1Pases, and their orthologues in Prasinophytes, should be seen as founding members of a new family of phosphatase with original substrate specificity within the HAD superfamily of proteins. This is the first report describing the characterization of a gene encoding M1Pase activity in photosynthetic organisms.
Published: 2014

36. Genome and metabolic network of 'Candidatus Phaeomarinobacter ectocarpi' Ec32, a new candidate genus of Alphaproteobacteria frequently associated with brown algae

Author: Simon M. Dittami, Catherine Leblanc, AgnÃ¨s Groisillier, AngÃ©lique Gobet, Catherine Boyen, Thierry Tonon, Jeanne Cambefort, Gurvan Michel, Anne Siegel, Ludovic Delage, Delphine Scornet, Guillaume Collet, Tristan Barbeyron, Javier E. Tapia, Laboratoire de Biologie Intégrative des Modèles Marins (LBI2M), Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Dynamics, Logics and Inference for biological Systems and Sequences (Dyliss), Inria Rennes – Bretagne Atlantique, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-GESTION DES DONNÉES ET DE LA CONNAISSANCE (IRISA-D7), Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), CentraleSupélec-Télécom Bretagne-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National de Recherche en Informatique et en Automatique (Inria)-École normale supérieure - Rennes (ENS Rennes)-Université de Bretagne Sud (UBS)-Centre National de la Recherche Scientifique (CNRS)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-CentraleSupélec-Télécom Bretagne-Université de Rennes 1 (UR1), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-École normale supérieure - Rennes (ENS Rennes)-Université de Bretagne Sud (UBS)-Centre National de la Recherche Scientifique (CNRS)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA), Departamento de Ecología, Facultad de Ciencias Biologicas, Pontificia Universidad Catolica de Chile, Santiago, Chile, Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-Institut National de Recherche en Informatique et en Automatique (Inria)-Télécom Bretagne-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-Institut National de Recherche en Informatique et en Automatique (Inria)-Télécom Bretagne-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-Télécom Bretagne-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS), and Pontificia Universidad Católica de Chile (UC)
Subjects: lcsh:QH426-470, Physiology, Metabolic network, transporters, Genome sequencing, Genome, metabolic network, Botany, Genetics, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Original Research Article, Symbiosis, Genetics (clinical), ComputingMilieux_MISCELLANEOUS, holobiont, biology, fungi, Alphaproteobacteria, food and beverages, Ectocarpus, Vitamins, biology.organism_classification, Rhizobiales, Brown algae, phytohormones, lcsh:Genetics, algal-bacterial interactions, Candidatus, Molecular Medicine, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], Symbiotic bacteria
Abstract: Rhizobiales and related orders of Alphaproteobacteria comprise several genera of nodule-inducing symbiotic bacteria associated with plant roots. Here we describe the genome and the metabolic network of "Candidatus Phaeomarinobacter ectocarpi" Ec32, a member of a new candidate genus closely related to Rhizobiales and found in association with cultures of the filamentous brown algal model Ectocarpus. The "Ca. P. ectocarpi" genome encodes numerous metabolic pathways that may be relevant for this bacterium to interact with algae. Notably, it possesses a large set of glycoside hydrolases and transporters, which may serve to process and assimilate algal metabolites. It also harbors several proteins likely to be involved in the synthesis of algal hormones such as auxins and cytokinins, as well as the vitamins pyridoxine, biotin, and thiamine. As of today, "Ca. P. ectocarpi" has not been successfully cultured, and identical 16S rDNA sequences have been found exclusively associated with Ectocarpus. However, related sequences (>= 97% identity) have also been detected free-living and in a Fucus vesiculosus microbiome barcoding project, indicating that the candidate genus "Phaeomarinobacter" may comprise several species, which may colonize different niches.
Published: 2014

37. Identification and Characterization of a Halotolerant, Cold-Active Marine Endo-β-1,4-Glucanase by Using Functional Metagenomics of Seaweed-Associated Microbiota

Author: Sébastien Steels, Tristan Barbeyron, Sophie Biver, Marjolaine Martin, Gurvan Michel, Daniel Portetelle, Micheline Vandenbol, Murielle Jam, Gembloux Agro-Bio Tech [Gembloux], Université de Liège, Laboratoire de Biologie Intégrative des Modèles Marins (LBI2M), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff (SBR), and Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Glycoside Hydrolases, Molecular Sequence Data, Sodium Chloride, Biology, Phaeophyta, Applied Microbiology and Biotechnology, Esterase, Microbiology, Bacterial Proteins, Enzyme Stability, Gene cluster, Glycoside hydrolase, Enzymology and Protein Engineering, [SDV.BBM.BC]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biochemistry [q-bio.BM], Phylogeny, Bacteria, Ecology, Microbiota, Glucanase, Seaweed, biology.organism_classification, Cold Temperature, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Biochemistry, Metagenomics, Halotolerance, Sample collection, Ascophyllum, Food Science, Biotechnology
Abstract: A metagenomic library was constructed from microorganisms associated with the brown alga Ascophyllum nodosum . Functional screening of this library revealed 13 novel putative esterase loci and two glycoside hydrolase loci. Sequence and gene cluster analysis showed the wide diversity of the identified enzymes and gave an idea of the microbial populations present during the sample collection period. Lastly, an endo-β-1,4-glucanase having less than 50% identity to sequences of known cellulases was purified and partially characterized, showing activity at low temperature and after prolonged incubation in concentrated salt solutions.
Published: 2014

38. The β-Glucanase ZgLamA from Zobellia galactanivorans Evolved a Bent Active Site Adapted for Efficient Degradation of Algal Laminarin*

Author: Mirjam Czjzek, Murielle Jam, Alexandra Jeudy, Jan-Hendrik Hehemann, Aurore Labourel, Gurvan Michel, Végétaux marins et biomolécules, Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-GOEMAR-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Biologie Intégrative des Modèles Marins (LBI2M), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Station biologique de Roscoff [Roscoff] (SBR), and Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)
Subjects: [SDV]Life Sciences [q-bio], MESH: Catalytic Domain, MESH: Protein Structure, Secondary, MESH: Flavobacteriaceae, Crystallography, X-Ray, Biochemistry, Protein Structure, Secondary, Substrate Specificity, Evolution, Molecular, Laminarin, chemistry.chemical_compound, Structure-Activity Relationship, MESH: Structure-Activity Relationship, Bacterial Proteins, Polysaccharides, Catalytic Domain, Hydrolase, Glycoside hydrolase, Molecular Biology, MESH: Bacterial Proteins, Glucans, MESH: Evolution, Molecular, biology, fungi, Active site, Substrate (chemistry), Cell Biology, Glucan 1,3-beta-Glucosidase, Glucanase, biology.organism_classification, MESH: Crystallography, X-Ray, MESH: Polysaccharides, chemistry, MESH: Glucan 1,3-beta-Glucosidase, Protein Structure and Folding, biology.protein, MESH: Substrate Specificity, Heterologous expression, Flavobacteriaceae, Bacteria
Abstract: International audience; Laminarinase is commonly used to describe β-1,3-glucanases widespread throughout Archaea, bacteria, and several eukaryotic lineages. Some β-1,3-glucanases have already been structurally and biochemically characterized, but very few from organisms that are in contact with genuine laminarin, the storage polysaccharide of brown algae. Here we report the heterologous expression and subsequent biochemical and structural characterization of ZgLamAGH16 from Zobellia galactanivorans, the first GH16 laminarinase from a marine bacterium associated with seaweeds. ZgLamAGH16 contains a unique additional loop, compared with other GH16 laminarinases, which is composed of 17 amino acids and gives a bent shape to the active site cleft of the enzyme. This particular topology is perfectly adapted to the U-shaped conformation of laminarin chains in solution and thus explains the predominant specificity of ZgLamAGH16 for this substrate. The three-dimensional structure of the enzyme and two enzyme-substrate complexes, one with laminaritetraose and the other with a trisaccharide of 1,3-1,4-β-d-glucan, have been determined at 1.5, 1.35, and 1.13 Å resolution, respectively. The structural comparison of substrate recognition pattern between these complexes allows the proposition that ZgLamAGH16 likely diverged from an ancestral broad specificity GH16 β-glucanase and evolved toward a bent active site topology adapted to efficient degradation of algal laminarin.
Published: 2013

39. Genome structure and metabolic features in the red seaweed Chondrus crispus shed light on evolution of the Archaeplastida

Author: Tristan Barbeyron, Wilfrid Carré, Michael Katinka, Loraine Brillet, Klaus Valentin, Karine Labadie, Betina M. Porcel, Zofia Nehr, Francisco Cabello-Hurtado, Mirjam Czjzek, Benjamin Noel, Philippe Deschamps, Susana M. Coelho, John H. F. Bothwell, Pascal J. Lopez, Marek Eliáš, François Artiguenave, François-Yves Bouget, Thierry Tonon, Jean Weissenbach, Christophe Colleoni, Deirdre H. McLachlan, Ahmed A. Moustafa, Cécile Hervé, Olivier Panaud, Catherine Boyen, Jonas Collén, Antonios Zambounis, Frédéric Partensky, Cristian Chaparro, Ludovic Delage, Jose Fernandes Barbosa-Neto, Salvador Capella-Gutierrez, Bernard Kloareg, Nathalie Kowalczyk, Gaelle Samson, Gurvan Michel, Simon M. Dittami, Jean-Marc Aury, J. Mark Cock, Patrick Wincker, Agnès Groisillier, Pi Nyvall Collén, Bénédicte Charrier, Corinne Da Silva, Catherine Leblanc, Lionel Cladière, Alok Arun, Laurence Meslet-Cladiere, Claire M. M. Gachon, Sylvie Rousvoal, Kamel Jabbari, Stefan A. Rensing, Toni Gabaldón, Steven G. Ball, Aikaterini Symeonidi, Julie Poulain, Végétaux marins et biomolécules, Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-GOEMAR-Centre National de la Recherche Scientifique (CNRS), Procaryotes Phototrophes Marins = MArine Phototrophic Prokaryotes (MAPP), Adaptation et diversité en milieu marin (AD2M), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Commissariat à l'Energie Atomique, Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Génomique métabolique (UMR 8030), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), 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)-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)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Unité de Glycobiologie Structurale et Fonctionnelle UMR 8576 (UGSF), Université de Lille-Centre National de la Recherche Scientifique (CNRS), Laboratoire Génome et développement des plantes (LGDP), Université de Perpignan Via Domitia (UPVD)-Centre National de la Recherche Scientifique (CNRS), Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung (AWI), Department of Plant Physiology, Faculty of Sciences, Charles University [Prague] (CU), Belfast e-Science Centre [Belfast] (BESC), Queen's University [Belfast] (QUB), Laboratoire d'Océanographie Microbienne (LOMIC), Observatoire océanologique de Banyuls (OOB), Ecosystèmes, biodiversité, évolution [Rennes] (ECOBIO), Université de Rennes (UR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR), Université de Rennes (UR)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Centre National de la Recherche Scientifique (CNRS), Universitat Pompeu Fabra [Barcelona] (UPF), Center for Genomic Regulation (CRG-UPF), CIBER de Epidemiología y Salud Pública (CIBERESP), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Laboratoire de Biologie Intégrative des Modèles Marins (LBI2M), Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), Scottish Association for Marine Science (SAMS), Institut de biologie de l'ENS Paris (IBENS), Département de Biologie - ENS Paris, 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)-Centre National de la Recherche Scientifique (CNRS)-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)-Centre National de la Recherche Scientifique (CNRS)-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 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), Laboratoire des Sciences de l'Environnement Marin (LEMAR) (LEMAR), Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Brest (UBO)-Institut Universitaire Européen de la Mer (IUEM), Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Department of Biology and Biotechnology Graduate Program, American University in Cairo, American University in Cairo, University of Freiburg [Freiburg], Freiburg Initiative in Systems Biology, Centre for Research and Technology Hellas (CERTH), Institut de Génomique d'Evry (IG), Université Paris-Saclay-Institut de Biologie François JACOB (JACOB), 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)), MArine Phototrophic Prokaryotes (MAPP), Adaptation et diversité en milieu marin (ADMM), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), 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 d'Évry-Val-d'Essonne (UEVE), 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), Charles University [Prague], Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR)-Centre National de la Recherche Scientifique (CNRS), Universitat Pompeu Fabra [Barcelona], Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Station biologique de Roscoff [Roscoff] (SBR), Institut de biologie de l'ENS Paris (UMR 8197/1024) (IBENS), 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), Sorbonne Université (SU)-Université des Antilles (UA)-Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS)-Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU)-Institut de Recherche pour le Développement (IRD), Institut de Recherche pour le Développement (IRD)-Institut Universitaire Européen de la Mer (IUEM), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Université de Brest (UBO)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS), Center for Research and Technology Hellas, Institut de Biologie François JACOB (JACOB), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay, Institut National de la Recherche Agronomique (INRA)-Université de Lille-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Département de Biologie - ENS Paris, École normale supérieure - Paris (ENS 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)-École normale supérieure - Paris (ENS 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), 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), Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE), Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Observatoire océanologique de Banyuls (OOB), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS Paris), Institut Universitaire Européen de la Mer (IUEM), Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Centre National de la Recherche Scientifique (CNRS)-Université de Brest (UBO), and Institut de Recherche pour le Développement (IRD)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0106 biological sciences, Transposable element, Genome evolution, [SDV]Life Sciences [q-bio], Molecular Sequence Data, Bacterial genome size, Biology, Chondrus, MESH: Base Sequence, MESH: RNA, Plant, Genes, Plant, 01 natural sciences, Genome, Evolution, Molecular, 03 medical and health sciences, MESH: Genes, Plant, 14. Life underwater, Gene, Genome size, MESH: Evolution, Molecular, 030304 developmental biology, Plant Proteins, Genetics, 0303 health sciences, Multidisciplinary, MESH: Molecular Sequence Data, Base Sequence, MESH: Plant Proteins, Archaeplastida, Biological Sciences, biology.organism_classification, MicroRNAs, RNA, Plant, MESH: MicroRNAs, MESH: Chondrus, 010606 plant biology & botany
Abstract: Red seaweeds are key components of coastal ecosystems and are economically important as food and as a source of gelling agents, but their genes and genomes have received little attention. Here we report the sequencing of the 105-Mbp genome of the florideophyte Chondrus crispus (Irish moss) and the annotation of the 9,606 genes. The genome features an unusual structure characterized by gene-dense regions surrounded by repeat-rich regions dominated by transposable elements. Despite its fairly large size, this genome shows features typical of compact genomes, e.g., on average only 0.3 introns per gene, short introns, low median distance between genes, small gene families, and no indication of large-scale genome duplication. The genome also gives insights into the metabolism of marine red algae and adaptations to the marine environment, including genes related to halogen metabolism, oxylipins, and multicellularity (microRNA processing and transcription factors). Particularly interesting are features related to carbohydrate metabolism, which include a minimalistic gene set for starch biosynthesis, the presence of cellulose synthases acquired before the primary endosymbiosis showing the polyphyly of cellulose synthesis in Archaeplastida, and cellulases absent in terrestrial plants as well as the occurrence of a mannosylglycerate synthase potentially originating from a marine bacterium. To explain the observations on genome structure and gene content, we propose an evolutionary scenario involving an ancestral red alga that was driven by early ecological forces to lose genes, introns, and intergenetic DNA; this loss was followed by an expansion of genome size as a consequence of activity of transposable elements.
Published: 2013

40. Biochemical and Structural Characterization of the Complex Agarolytic Enzyme System from the Marine Bacterium Zobellia galactanivorans

Author: François Thomas, Mirjam Czjzek, Tristan Barbeyron, William Helbert, Gurvan Michel, Thomas Bernard, Gaëlle Correc, Murielle Jam, Jan-Hendrik Hehemann, Végétaux marins et biomolécules, Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-GOEMAR-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Biologie Intégrative des Modèles Marins (LBI2M), Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS), and Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Models, Molecular, Glycoside Hydrolases, Stereochemistry, [SDV]Life Sciences [q-bio], Crystallography, X-Ray, complex mixtures, 7. Clean energy, Biochemistry, Enzyme catalysis, Structure-Activity Relationship, 03 medical and health sciences, chemistry.chemical_compound, Bacterial Proteins, Hydrolase, natural sciences, Glycoside hydrolase, Molecular Biology, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, chemistry.chemical_classification, 0303 health sciences, biology, 030306 microbiology, fungi, food and beverages, Active site, Bacteroidetes, Cell Biology, biochemical phenomena, metabolism, and nutrition, biology.organism_classification, Protein Structure, Tertiary, Agar, Enzyme, chemistry, Galactose, Protein Structure and Folding, biology.protein, Flavobacteriaceae, Bacteria
Abstract: Zobellia galactanivorans is an emerging model bacterium for the bioconversion of algal biomass. Notably, this marine Bacteroidetes possesses a complex agarolytic system comprising four β-agarases and five β-porphyranases, all belonging to the glycoside hydrolase family 16. Although β-agarases are specific for the neutral agarobiose moieties, the recently discovered β-porphyranases degrade the sulfated polymers found in various quantities in natural agars. Here, we report the biochemical and structural comparison of five β-porphyranases and β-agarases from Z. galactanivorans. The respective degradation patterns of two β-porphyranases and three β-agarases are analyzed by their action on defined hybrid oligosaccharides. In light of the high resolution crystal structures, the biochemical results allowed a detailed mapping of substrate specificities along the active site groove of the enzymes. Although PorA displays a strict requirement for C6-sulfate in the -2- and +1-binding subsites, PorB tolerates the presence of 3-6-anhydro-l-galactose in subsite -2. Both enzymes do not accept methylation of the galactose unit in the -1 subsite. The β-agarase AgaD requires at least four consecutive agarose units (DP8) and is highly intolerant to modifications, whereas for AgaB oligosaccharides containing C6-sulfate groups at the -4, +1, and +3 positions are still degraded. Together with a transcriptional analysis of the expression of these enzymes, the structural and biochemical results allow proposition of a model scheme for the agarolytic system of Z. galactanivorans.
Published: 2012

41. Evolution and Diversity of Plant Cell Walls: From Algae to Flowering Plants

Author: David S. Domozych, Gurvan Michel, Bernard Kloareg, Dagmar B. Stengel, Zoë A. Popper, Maria G. Tuohy, William G.T. Willats, Cécile Hervé, Végétaux marins et biomolécules, Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-GOEMAR-Centre National de la Recherche Scientifique (CNRS), and ~
Subjects: 0106 biological sciences, Physiology, Arabinogalactan proteins, Plant Science, Red algae, Cell Communication, Environment, Photosynthesis, Phaeophyta, 01 natural sciences, Cell wall, 03 medical and health sciences, Algae, Cell Wall, Chlorophyta, Botany, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Plastid, Xyloglucan, Molecular Biology, Phylogeny, 030304 developmental biology, Plant Proteins, 0303 health sciences, Genome, biology, Ecology, Cell Biology, 15. Life on land, Plants, biology.organism_classification, Mannan, Biological Evolution, Immunity, Innate, Brown algae, Multicellular organism, Rhodophyta, Multicellularity, Green algae, 010606 plant biology & botany
Abstract: International audience; 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.
Published: 2011

42. Chlorophyll-binding proteins revisited - a multigenic family of light-harvesting and stress proteins from a brown algal perspective

Author: Thierry Tonon, Catherine Boyen, Jonas Collén, Gurvan Michel, and Simon M. Dittami
Subjects: Models, Molecular, Chlorophyll b, Evolution, Molecular Sequence Data, Light-Harvesting Protein Complexes, Chlorophyll c, Phaeophyta, Evolution, Molecular, chemistry.chemical_compound, Stress, Physiological, Botany, QH359-425, Amino Acid Sequence, Phylogeny, Ecology, Evolution, Behavior and Systematics, Binding Sites, biology, Endosymbiosis, Ectocarpus siliculosus, Sequence Analysis, DNA, Ectocarpus, biology.organism_classification, Protein Structure, Tertiary, chemistry, Evolutionary biology, Multigene Family, Chlorophyll, Green algae, Chlorophyll Binding Proteins, Research Article
Abstract: Background Chlorophyll-binding proteins (CBPs) constitute a large family of proteins with diverse functions in both light-harvesting and photoprotection. The evolution of CBPs has been debated, especially with respect to the origin of the LI818 subfamily, members of which function in non-photochemical quenching and have been found in chlorophyll a/c-containing algae and several organisms of the green lineage, but not in red algae so far. The recent publication of the Ectocarpus siliculosus genome represents an opportunity to expand on previous work carried out on the origin and function of CBPs. Results The Ectocarpus genome codes for 53 CBPs falling into all major families except the exclusively green family of chlorophyll a/b binding proteins. Most stress-induced CBPs belong to the LI818 family. However, we highlight a few stress-induced CBPs from Phaeodactylum tricornutum and Chondrus crispus that belong to different sub-families and are promising targets for future functional studies. Three-dimensional modeling of two LI818 proteins revealed features common to all LI818 proteins that are likely to interfere with their capacity to bind chlorophyll b and lutein, but may enable binding of chlorophyll c and fucoxanthin. In the light of this finding, we examined the possibility that LI818 proteins may have originated in a chlorophyll c/fucoxanthin containing organism and compared this scenario to three alternatives: an independent evolution of LI818 proteins in different lineages, an ancient origin together with the first CBPs, before the separation of the red and the green lineage, or an origin in the green lineage and a transfer to an ancestor of haptophytes and heterokonts during a cryptic endosymbiosis event. Conclusions Our findings reinforce the idea that the LI818 family of CBPs has a role in stress response. In addition, statistical analyses of phylogenetic trees show an independent origin in different eukaryotic lineages or a green algal origin of LI818 proteins to be highly unlikely. Instead, our data favor an origin in an ancestral chlorophyll a/c-containing organism and a subsequent lateral transfer to some green algae, although an origin of LI818 proteins in a common ancestor of red and green algae cannot be ruled out.
Published: 2010

43. MARINE-EXPRESS: taking advantage of high throughput cloning and expression strategies for the post-genomic analysis of marine organisms

Author: Isabel Morgado, Catherine Boyen, Mirjam Czjzek, Deborah M. Power, Claire Geslin, Didier Flament, Christiane Herve, Etienne Rebuffet, Alexandra Jeudy, Gurvan Michel, Yann Chevolot, Agnès Groisillier, Margherita Branno, Hervé Moreau, Pierre Francois Pluchon, Végétaux marins et biomolécules, Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-GOEMAR-Centre National de la Recherche Scientifique (CNRS), Laboratoire de microbiologie des environnements extrêmophiles (LM2E), Centre National de la Recherche Scientifique (CNRS)-Université de Brest (UBO)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), INL - Chimie et Nanobiotechnologies (INL - C&N), Institut des Nanotechnologies de Lyon (INL), Centre National de la Recherche Scientifique (CNRS)-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA)-École Centrale de Lyon (ECL), Université de Lyon-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-École supérieure de Chimie Physique Electronique de Lyon (CPE)-Centre National de la Recherche Scientifique (CNRS)-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-École supérieure de Chimie Physique Electronique de Lyon (CPE), Centro de Ciências do Mar [Faro] (CCMAR), Universidade do Algarve (UAlg), Cellular and Developmental Biology, Stazione Zoologica Anton Dohrn (SZN), Modèles en biologie cellulaire et évolutive (MBCE), Observatoire océanologique de Banyuls (OOB), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS), École Centrale de Lyon (ECL), Université de Lyon-Université de Lyon-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-École Supérieure de Chimie Physique Électronique de Lyon (CPE)-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-École Centrale de Lyon (ECL), and Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Pyrococcus abyssi, MESH: High-Throughput Screening Assays, Archaeal Proteins, Recombinant Fusion Proteins, ved/biology.organism_classification_rank.species, lcsh:QR1-502, MESH: Sea Bream, Bioengineering, Computational biology, MESH: Flavobacteriaceae, Biology, Genome, Applied Microbiology and Biotechnology, lcsh:Microbiology, Microbiology, 03 medical and health sciences, Plasmid, Marine bacteriophage, Bacterial Proteins, MESH: Plasmids, MESH: Recombinant Fusion Proteins, Animals, MESH: Animals, MESH: Cloning, Molecular, Cloning, Molecular, Model organism, Gene, MESH: Pyrococcus abyssi, MESH: Bacterial Proteins, 030304 developmental biology, Cloning, 0303 health sciences, Expression vector, ved/biology, Research, 030302 biochemistry & molecular biology, Computational Biology, Eukaryota, MESH: Archaeal Proteins, Sea Bream, High-Throughput Screening Assays, MESH: Eukaryota, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Flavobacteriaceae, Function (biology), Plasmids, Biotechnology, MESH: Computational Biology
Abstract: Background The production of stable and soluble proteins is one of the most important steps prior to structural and functional studies of biological importance. We investigated the parallel production in a medium throughput strategy of genes coding for proteins from various marine organisms, using protocols that involved recombinatorial cloning, protein expression screening and batch purification. This strategy was applied in order to respond to the need for post-genomic validation of the recent success of a large number of marine genomic projects. Indeed, the upcoming challenge is to go beyond the bioinformatic data, since the bias introduced through the genomes of the so called model organisms leads to numerous proteins of unknown function in the still unexplored world of the oceanic organisms. Results We present here the results of expression tests for 192 targets using a 96-well plate format. Genes were PCR amplified and cloned in parallel into expression vectors pFO4 and pGEX-4T-1, in order to express proteins N-terminally fused to a six-histidine-tag and to a GST-tag, respectively. Small-scale expression and purification permitted isolation of 84 soluble proteins and 34 insoluble proteins, which could also be used in refolding assays. Selected examples of proteins expressed and purified to a larger scale are presented. Conclusions The objective of this program was to get around the bottlenecks of soluble, active protein expression and crystallization for post-genomic validation of a number of proteins that come from various marine organisms. Multiplying the constructions, vectors and targets treated in parallel is important for the success of a medium throughput strategy and considerably increases the chances to get rapid access to pure and soluble protein samples, needed for the subsequent biochemical characterizations. Our set up of a medium throughput strategy applied to genes from marine organisms had a mean success rate of 44% soluble protein expression from marine bacteria, archaea as well as eukaryotic organisms. This success rate compares favorably with other protein screening projects, particularly for eukaryotic proteins. Several purified targets have already formed the base for experiments aimed at post-genomic validation.
Published: 2010

44. The cell wall polysaccharide metabolism of the brown alga Ectocarpus siliculosus. Insights into the evolution of extracellular matrix polysaccharides in Eukaryotes

Author: Gurvan Michel, J. Mark Cock, Bernard Kloareg, Delphine Scornet, Thierry Tonon, Végétaux marins et biomolécules, Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-GOEMAR-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Biologie Intégrative des Modèles Marins (LBI2M), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Station biologique de Roscoff [Roscoff] (SBR), and Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0106 biological sciences, Alginates, Physiology, [SDV]Life Sciences [q-bio], Plant Science, Cellulase, Eukaryote evolution, Phaeophyta, Polysaccharide, brown algae, 01 natural sciences, Evolution, Molecular, Cell wall, 03 medical and health sciences, Polysaccharides, Botany, alginate, Phylogeny, 030304 developmental biology, chemistry.chemical_classification, 0303 health sciences, biology, Ectocarpus siliculosus, Ectocarpus, multicellularity, biology.organism_classification, cellulose, Biosynthetic Pathways, Extracellular Matrix, Brown algae, Multicellular organism, Biochemistry, chemistry, Horizontal gene transfer, biology.protein, adaptation to terrestrial environment, cell wall, sulfated fucans, 010606 plant biology & botany
Abstract: International audience; 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.
Published: 2010

45. Central and storage carbon metabolism of the brown alga Ectocarpus siliculosus: insights into the origin and evolution of storage carbohydrates in Eukaryotes

Author: Thierry Tonon, Gurvan Michel, Delphine Scornet, Bernard Kloareg, J. Mark Cock, Laboratoire de Biologie Intégrative des Modèles Marins (LBI2M), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff (SBR), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Station biologique de Roscoff [Roscoff] (SBR), and Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0106 biological sciences, Physiology, Plant Science, Phaeophyta, brown algae, 01 natural sciences, Carbon Cycle, Evolution, Molecular, 03 medical and health sciences, chemistry.chemical_compound, Laminarin, Phylogenetics, Botany, Symbiosis, β-1, Phylogeny, trehalose, 030304 developmental biology, Eukaryotic evolution, 0303 health sciences, Genome, biology, Glycogen, Ectocarpus siliculosus, starch, mannitol, Ectocarpus, [SDV.BV.BOT]Life Sciences [q-bio]/Vegetal Biology/Botanics, biology.organism_classification, Trehalose, Carbon, Chromalveolate, Brown algae, 3-glucan, Biochemistry, chemistry, glycogen, Horizontal gene transfer, Carbohydrate Metabolism, 010606 plant biology & botany
Abstract: International audience; Brown algae exhibit a unique carbon (C) storage metabolism. The photoassimilate d‐fructose 6‐phosphate is not used to produce sucrose but is converted into d‐mannitol. These seaweeds also store C as β‐1,3‐glucan (laminarin), thus markedly departing from most living organisms, which use α‐1,4‐glucans (glycogen or starch).Using a combination of bioinformatic and phylogenetic approaches, we identified the candidate genes for the enzymes involved in C storage in the genome of the brown alga Ectocarpus siliculosus and traced their evolutionary origins.Ectocarpus possesses a complete set of enzymes for synthesis of mannitol, laminarin and trehalose. By contrast, the pathways for sucrose, starch and glycogen are completely absent.The synthesis of β‐1,3‐glucans appears to be a very ancient eukaryotic pathway. Brown algae inherited the trehalose pathway from the red algal progenitor of phaeoplasts, while the mannitol pathway was acquired by lateral gene transfer from Actinobacteria. The starch metabolism of the red algal endosymbiont was entirely lost in the ancestor of Stramenopiles. In light of these novel findings we question the validity of the ‘Chromalveolate hypothesis’.
Published: 2010

46. The Ectocarpus genome and the independent evolution of multicellularity in brown algae

Author: Jean-Marc Aury, Frithjof C. Küpper, Diego Miranda-Saavedra, John H. F. Bothwell, Claire Jubin, Chris Bowler, Bernhard Gschloessl, James W. Tregear, Andrés Ritter, Andrew E. Allen, Carolyn A. Napoli, Ludovic Delage, Bernard Kloareg, Takahiro Yamagishi, Pi Nyvall-Collén, Svenja Heesch, Julia Morales, Gaelle Samson, Kei Kimura, Ga Youn Cho, Grigoris D. Amoutzias, Yves Van de Peer, Simon M. Dittami, Kenny Billiau, Julie Poulain, François Artiguenave, Sylvie Doulbeau, Marek Eliáš, Bank Beszteri, Carl J. Carrano, Daniel Lang, Florian Maumus, Stefan A. Rensing, Jonathan H. Badger, Béatrice Segurens, Martina Strittmatter, Sylvie Rousvoal, Hervé Moreau, Patrice Lerouge, Colin Brownlee, Betsy Read, Akira F. Peters, J. Mark Cock, Corinne Da Silva, Declan C. Schroeder, Catherine Boyen, Pierre Rouzé, Eric Bonnet, Jonas Collén, Susana M. Coelho, Aude Le Bail, Kamel Jabbari, David R. Nelson, Thierry Tonon, Pascal J. Lopez, Véronique Anthouard, Hadi Quesneville, Manoj P. Samanta, Delphine Scornet, Klaus Valentin, Nicolas Delaroque, Bénédicte Charrier, Cindy Martens, Peter von Dassow, Martin Lohr, Garry Farnham, Chikako Nagasato, Claire M. M. Gachon, Gurvan Michel, Lieven Sterck, Philippe Potin, Erwan Corre, Catherine Leblanc, Taizo Motomura, Cyril Pommier, Patrick Wincker, Hiroshi Kawai, Publica, Végétaux marins et biomolécules, Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-GOEMAR-Centre National de la Recherche Scientifique (CNRS), Department of Plant Systems Biology, State University of Ghent, J Craig Venter Institute, Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), 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 Paris-Saclay, Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung (AWI), Marine Biological Association, Institut de biologie de l'ENS Paris (UMR 8197/1024) (IBENS), Département de Biologie - 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), San Diego State University (SDSU), Phophorylation de protéines et Pathologies Humaines (P3H), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff (SBR), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Fraunhofer Institute for Cell Therapy and Immunology (IZI), Diversité et adaptation des plantes cultivées (UMR DIAPC), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Université Montpellier 2 - Sciences et Techniques (UM2), Charles University [Prague], Scottish Association for Marine Science (SAMS), Kobe University, Institute of Algological Research [Muroran], Hokkaido University, Fakultät für Biologie = Faculty of Biology [Freiburg], Albert-Ludwigs-Universität Freiburg, Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Glycobiologie et Matrice Extracellulaire Végétale (Glyco-MEV), Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-Normandie Université (NU), Johannes Gutenberg - Universität Mainz (JGU), École normale supérieure - Paris (ENS Paris), Institut de biologie de l'Ecole Normale Supérieure (IBENS), École normale supérieure - Paris (ENS Paris)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Department of Haematology, University of Cambridge [UK] (CAM), Mer et santé (MS), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Observatoire océanologique de Banyuls (OOB), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), University of Arizona, The University of Tennessee Health Science Center [Memphis] (UTHSC), Unité de Recherche Génomique Info (URGI), Institut National de la Recherche Agronomique (INRA), California State University [Los Angeles] (CAL STATE LA), Laboratoire de Biotechnologie et Chimie Marines (LBCM), Université de Bretagne Sud (UBS)-Université de Brest (UBO)-Institut Universitaire Européen de la Mer (IUEM), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD), Systemix Institute, Savelli, Bruno, Center for Plant Systems Biology (PSB Center), Vlaams Instituut voor Biotechnologie [Ghent, Belgique] (VIB), J. Craig Venter Institute, 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 de biologie de l'ENS Paris (IBENS), 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)-Centre National de la Recherche Scientifique (CNRS)-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)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Adaptation et diversité en milieu marin (AD2M), Fraunhofer Institute for Cell Therapy and Immunology (Fraunhofer IZI), Fraunhofer (Fraunhofer-Gesellschaft), Charles University [Prague] (CU), Hokkaido University [Sapporo, Japan], Johannes Gutenberg - Universität Mainz = Johannes Gutenberg University (JGU), Université Paris sciences et lettres (PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-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)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS Paris), Université Montpellier 2 - Sciences et Techniques (UM2)-Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-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)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC), and Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Département de Biologie - ENS Paris
Subjects: 0106 biological sciences, Lineage (evolution), Molecular Sequence Data, Phaeophyta, 01 natural sciences, Genome, Evolution, Molecular, 03 medical and health sciences, Algae, [SDV.BDD] Life Sciences [q-bio]/Development Biology, Botany, BIOLOGIE CELLULAIRE, Animals, 14. Life underwater, [SDV.BDD]Life Sciences [q-bio]/Development Biology, flore marine, Phylogeny, Organism, ComputingMilieux_MISCELLANEOUS, phéophycées, 030304 developmental biology, 0303 health sciences, Multidisciplinary, biology, Ectocarpus siliculosus, Algal Proteins, Eukaryota, Pigments, Biological, Ectocarpus, 15. Life on land, biology.organism_classification, Biological Evolution, Brown algae, Multicellular organism, Evolutionary biology, algues brunes, Biologie, Signal Transduction, 010606 plant biology & botany
Abstract: Brown algae (Phaeophyceae) are complex photosynthetic organisms with a very different evolutionary history to green plants, to which they are only distantly related. These seaweeds are the dominant species in rocky coastal ecosystems and they exhibit many interesting adaptations to these, often harsh, environments. Brown algae are also one of only a small number of eukaryotic lineages that have evolved complex multicellularity (Fig. 1). We report the 214 million base pair (Mbp) genome sequence of the filamentous seaweed Ectocarpus siliculosus (Dillwyn) Lyngbye, a model organism for brown algae, closely related to the kelps (Fig. 1). Genome features such as the presence of an extended set of light-harvesting and pigment biosynthesis genes and new metabolic processes such as halide metabolism help explain the ability of this organism to cope with the highly variable tidal environment. The evolution of multicellularity in this lineage is correlated with the presence of a rich array of signal transduction genes. Of particular interest is the presence of a family of receptor kinases, as the independent evolution of related molecules has been linked with the emergence of multicellularity in both the animal and green plant lineages. The Ectocarpus genome sequence represents an important step towards developing this organism as a model species, providing the possibility to combine genomic and genetic approaches to explore these and other aspects of brown algal biology further. © 2010 Macmillan Publishers Limited. All rights reserved.
Published: 2010

47. Description of Maribacter forsetii sp nov., a marine Flavobacteriaceae isolated from North Sea water, and emended description of the genus Maribacter

Author: Gurvan Michel, Margarete Schüler, Rudolf Amann, Flavien Carpentier, Stéphane L'Haridon, Tristan Barbeyron, Végétaux marins et biomolécules, Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-GOEMAR-Centre National de la Recherche Scientifique (CNRS), Laboratoire de microbiologie des environnements extrêmophiles (LM2E), Centre National de la Recherche Scientifique (CNRS)-Université de Brest (UBO)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Max Planck Institute for Biological Cybernetics, Max-Planck-Gesellschaft, Max Planck Institute for Marine Microbiology, and Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)
Subjects: MESH: Carbohydrate Metabolism, MESH: Flavobacteriaceae, Germany, RNA, Ribosomal, 16S, MESH: Phylogeny, Phylogeny, [SDV.EE]Life Sciences [q-bio]/Ecology, environment, 0303 health sciences, Ecology, Fatty Acids, General Medicine, MESH: Fatty Acids, MESH: RNA, Ribosomal, 16S, RNA, Bacterial, Phenotype, Carbohydrate Metabolism, Taxonomy (biology), MESH: Genes, Bacterial, MESH: RNA, Bacterial, Flavobacteriaceae, DNA, Bacterial, MESH: Terminology as Topic, Molecular Sequence Data, education, Biology, MESH: Phenotype, Microbiology, MESH: Sequence Homology, Nucleic Acid, 03 medical and health sciences, Species Specificity, Phylogenetics, Sequence Homology, Nucleic Acid, Terminology as Topic, Botany, MESH: Species Specificity, Seawater, North sea, MESH: Germany, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, MESH: Molecular Sequence Data, 030306 microbiology, MESH: Seawater, Ribosomal RNA, 16S ribosomal RNA, biology.organism_classification, MESH: DNA, Bacterial, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Genes, Bacterial, Genus Maribacter, Bacteria
Abstract: This is an author manuscript that has been accepted for publication in International Journal of Systematic and Evolutionary Microbiology, copyright Society for General Microbiology, but has not been copy-edited, formatted or proofed. Cite this article as appearing in International Journal of Systematic and Evolutionary Microbiology. This version of the manuscript may not be duplicated or reproduced, other than for personal use or within the rule of 'Fair Use of Copyrighted Materials' (section 17, Title 17, US Code), without permission from the copyright owner, Society for General Microbiology. The Society for General Microbiology disclaims any responsibility or liability for errors or omissions in this version of the manuscript or in any version derived from it by any other parties. The final copy-edited, published article, which is the version of record, can be found at http://mic.sgmjournals.org, and is freely available without a subscription.; International audience; Three rod-shaped, Gram-negative, chemo-organotrophic, heterotrophic, strictly aerobic, gliding bacterial strains, KT02ds18-4, KT02ds18-5 and KT02ds18-6T, were isolated from North Sea surface waters near the island of Helgoland, Germany. Their taxonomic position was investigated by a polyphasic approach. The three strains were light yellow, oxidase- and catalase-positive, and grew optimally at 25 degrees C, at pH 7.5, and in the presence of 2.5 % (w/v) NaCl. The Chargaff's coefficient was 34.2-34.4 mol%. The three strains shared >90 % DNA-DNA relatedness and an identical 16S rRNA gene sequence. Comparative 16S rRNA gene sequence analysis allocated the three strains to the genus Maribacter in the family Flavobacteriaceae, with similarities of 97.0-97.4 % to five of the recognized Maribacter species. Their low level of DNA-DNA relatedness (
Published: 2008

48. Alpha-agarases define a new family of glycoside hydrolases, distinct from beta-agarase families

Author: Murielle Jam, Tristan Barbeyron, Mirjam Czjzek, Philippe Potin, Gurvan Michel, Didier Flament, Bernard Kloareg, Végétaux marins et biomolécules, Station biologique de Roscoff [Roscoff] (SBR), and Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-GOEMAR-Centre National de la Recherche Scientifique (CNRS)
Subjects: MESH: Sequence Analysis, DNA, Hydrolases, Amino Acid Motifs, MESH: Amino Acid Sequence, Applied Microbiology and Biotechnology, MESH: Amino Acid Motifs, Glycoside hydrolase, Cloning, Molecular, Peptide sequence, Genetics, chemistry.chemical_classification, 0303 health sciences, Ecology, biology, Agarase, MESH: Molecular Weight, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Biochemistry, Biotechnology, DNA, Bacterial, Repetitive Sequences, Amino Acid, Glycoside Hydrolases, MESH: Alteromonas, Sequence analysis, Molecular Sequence Data, Gene product, O-Glycosidases, 03 medical and health sciences, MESH: Glycoside Hydrolases, MESH: Cloning, Molecular, Amino Acid Sequence, Enzymology and Protein Engineering, Alteromonas, Glycosidases, Gene, 030304 developmental biology, Binding Sites, MESH: Molecular Sequence Data, MESH: Repetitive Sequences, Amino Acid, 030306 microbiology, Glycoside, Sequence Analysis, DNA, biology.organism_classification, MESH: DNA, Bacterial, Molecular Weight, MESH: Binding Sites, chemistry, Enzyme, biology.protein, Food Science
Abstract: The gene encoding the α-agarase from “ Alteromonas agarilytica ” (proposed name) has been cloned and sequenced. The gene product (154 kDa) is unrelated to β-agarases and instead belongs to a new family of glycoside hydrolases (GH96). The α-agarase also displays a complex modularity, with the presence of five thrombospondin type 3 repeats and three carbohydrate-binding modules.
Published: 2007

49. Structural Evidence for the Evolution of Xyloglucanase Activity from Xyloglucan Endo-Transglycosylases: Biological Implications for Cell Wall Metabolism[W]

Author: Harry Brumer, Martin J. Baumann, Mirjam Czjzek, Jens M. Eklöf, Tuula T. Teeri, Åsa M. Kallas, and Gurvan Michel
Subjects: DNA, Complementary, Glycoside Hydrolases, Molecular Sequence Data, Static Electricity, Oligosaccharides, Plant Science, Biology, Nasturtium, Crystallography, X-Ray, Catalysis, Protein Structure, Secondary, Substrate Specificity, Cell wall, Evolution, Molecular, chemistry.chemical_compound, Structure-Activity Relationship, Tropaeolum, Cell Wall, Glycoside hydrolase, Xyloglucan:xyloglucosyl transferase, Cloning, Molecular, Glucans, Research Articles, Phylogeny, Plant Proteins, chemistry.chemical_classification, Cell Biology, Xyloglucan endotransglucosylase, biology.organism_classification, Recombinant Proteins, Tropaeolum majus, Xyloglucan, Kinetics, Enzyme, chemistry, Biochemistry, Mutagenesis, Chromatography, Gel, Mutant Proteins, Xylans, Gene Deletion
Abstract: High-resolution, three-dimensional structures of the archetypal glycoside hydrolase family 16 (GH16) endo-xyloglucanases Tm-NXG1 and Tm-NXG2 from nasturtium (Tropaeolum majus) have been solved by x-ray crystallography. Key structural features that modulate the relative rates of substrate hydrolysis to transglycosylation in the GH16 xyloglucan-active enzymes were identified by structure–function studies of the recombinantly expressed enzymes in comparison with data for the strict xyloglucan endo-transglycosylase Ptt-XET16-34 from hybrid aspen (Populus tremula × Populus tremuloides). Production of the loop deletion variant Tm-NXG1-ΔYNIIG yielded an enzyme that was structurally similar to Ptt-XET16-34 and had a greatly increased transglycosylation:hydrolysis ratio. Comprehensive bioinformatic analyses of XTH gene products, together with detailed kinetic data, strongly suggest that xyloglucanase activity has evolved as a gain of function in an ancestral GH16 XET to meet specific biological requirements during seed germination, fruit ripening, and rapid wall expansion.
Published: 2007

50. Site-directed mutagenesis of the active site region in the quinate/shikimate 5-dehydrogenase YdiB of Escherichia coli

Author: Miroslaw Cygler, Allan Matte, Guy Nadeau, Robert Menard, Holger A. Lindner, and Gurvan Michel
Subjects: Protein Conformation, Quinic Acid, Dehydrogenase, Plasma protein binding, Biochemistry, Catalysis, Protein structure, 5'-guanylic acid, Escherichia coli, Shikimate pathway, pharmaceutical, Site-directed mutagenesis, Molecular Biology, Aspartic Acid, Cofactor binding, Binding Sites, biology, Escherichia coli Proteins, Lysine, Mutagenesis, Active site, Cell Biology, Alcohol Oxidoreductases, Kinetics, Mutagenesis, Site-Directed, biology.protein, mutagenesis, Protein Binding
Abstract: YdiB and its paralog AroE are members of the quinate/shikimate 5-dehdrogenase family. Enzymes from this family function in the shikimate pathway that is essential for survival of microorganisms and plants and represent potential drug targets. Recent YdiB and AroE crystal structures revealed the presence of a NAD(P)-binding and a catalytic domain. We carried out site-directed mutagenesis of 8 putative active site residues in YdiB from Escherichia coli and analyzed structural and kinetic properties of the mutant enzymes. Our data indicate critical roles for an invariant lysine and aspartate residue in substrate binding and allowed us to differentiate between two previously proposed models for the binding of the substrate in the active site. Comparison of several YdiB and AroE structures led us to conclude that, upon cofactor binding and domain closure, the 2 identified binding residues are repositioned to bind to the substrate. Although the lysine residue contributes to some extent to the stabilization of the transition state, we did not identify any residue as catalytically essential. This indicates that catalysis does not operate through a general acid-base mechanism, as thought originally. Our improved understanding of the medically and agriculturally important quinate/shikimate 5-dehydrogenase family at the molecular level may prove useful in the development of novel herbicides and antimicrobial agents.
Published: 2004

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