Evidence for a common structural pattern in the polysaccharide sulphates of the Rhodophyceae, Nature, vol.205, pp.1060-1062, 1965. ,
Microorganisms living on macroalgae: diversity, interactions, and biotechnological applications, Appl. Microbiol. Biotechnol, vol.98, pp.2917-2935, 2014. ,
URL : https://hal.archives-ouvertes.fr/hal-00999506
The kappa-carrageenase of P. carrageenovora features a tunnelshaped active site: a novel insight in the evolution of Clan-B glycoside hydrolases, Structure, vol.9, pp.513-525, 2001. ,
The iota-carrageenase of Alteromonas fortis. A beta-helix foldcontaining enzyme for the degradation of a highly polyanionic polysaccharide, J. Biol. Chem, vol.276, pp.40202-40209, 2001. ,
Degradation of lambda-carrageenan by Pseudoalteromonas carrageenovora lambda-carrageenase: a new family of glycoside hydrolases unrelated to kappa-and iota-carrageenases, Biochem. J, vol.404, pp.105-114, 2007. ,
URL : https://hal.archives-ouvertes.fr/hal-00478659
Controlling carrageenan structure using a novel formylglycine-dependent sulfatase, an endo-4S-iotacarrageenan sulfatase, Mar. Biotechnol, vol.15, pp.265-274, 2013. ,
Enzyme-assisted preparation of furcellaran-like kappa-/beta-carrageenan, Mar. Biotechnol, vol.18, pp.133-143, 2016. ,
Environmental and gut bacteroidetes: the food connection, Front. Microbiol, vol.2, p.93, 2011. ,
URL : https://hal.archives-ouvertes.fr/hal-00925466
Substrate-controlled succession of marine bacterioplankton populations induced by a phytoplankton bloom, Science, vol.336, pp.608-611, 2012. ,
Habitat and taxon as driving forces of carbohydrate catabolism in marine heterotrophic bacteria: example of the model algaeassociated bacterium Zobellia galactanivorans DsijT, Environ. Microbiol, vol.18, pp.4610-4627, 2016. ,
Genetic evidence that outer membrane binding of starch is required for starch utilization by Bacteroides thetaiotaomicron, J. Bacteriol, vol.171, pp.3199-3204, 1989. ,
Biochemical evidence that starch breakdown by Bacteroides thetaiotaomicron involves outer membrane starch-binding sites and periplasmic starch-degrading enzymes, J. Bacteriol, vol.171, pp.3192-3198, 1989. ,
Functional genomic and metabolic studies of the adaptations of a prominent adult human gut symbiont, Bacteroides thetaiotaomicron, to the suckling period, J. Biol. Chem, vol.281, pp.36269-36279, 2006. ,
Automatic prediction of polysaccharide utilization loci in Bacteroidetes species, Bioinformatics, vol.31, pp.647-655, 2015. ,
URL : https://hal.archives-ouvertes.fr/hal-01438994
Specificity of polysaccharide use in intestinal bacteroides species determines diet-induced microbiota alterations, Cell, vol.141, pp.1241-1252, 2010. ,
A discrete genetic locus confers xyloglucan metabolism in select human gut Bacteroidetes, Nature, vol.506, pp.498-502, 2014. ,
Human gut Bacteroidetes can utilize yeast mannan through a selfish mechanism, Nature, vol.517, pp.165-169, 2015. ,
Complex pectin metabolism by gut bacteria reveals novel catalytic functions, Nature, vol.544, pp.65-70, 2017. ,
URL : https://hal.archives-ouvertes.fr/hal-01595600
Characterization of the first alginolytic operons in a marine bacterium: from their emergence in marine Flavobacteriia to their independent transfers to marine Proteobacteria and human gut Bacteroides, Environ. Microbiol, vol.14, pp.2379-2394, 2012. ,
Bacteria of the human gut microbiome catabolize red seaweed glycans with carbohydrate-active enzyme updates from extrinsic microbes, Proc. Natl Acad. Sci. USA, vol.109, pp.19786-19791, 2012. ,
The carbohydrate-active enzymes database (CAZy) in 2013, Nucleic Acids Res, vol.42, pp.490-495, 2014. ,
The kappacarrageenase of the marine bacterium Cytophaga drobachiensis. Structural and phylogenetic relationships within family-16 glycoside hydrolases, Mol. Biol. Evol, vol.15, pp.528-537, 1998. ,
iotaCarrageenases constitute a novel family of glycoside hydrolases, unrelated to that of kappa-carrageenases, J. Biol. Chem, vol.275, pp.35499-35505, 2000. ,
Identification of catalytic residues and mechanistic analysis of family GH82 iota-carrageenases, Biochemistry, vol.49, pp.7590-7599, 2010. ,
, Biology of the red algae, 1990.
Matching the diversity of sulfated biomolecules: creation of a classification database for sulfatases reflecting their substrate specificity, PLoS ONE, vol.11, p.164846, 2016. ,
URL : https://hal.archives-ouvertes.fr/hal-01409013
Characterization of a novel beta-L-arabinofuranosidase in Bifidobacterium longum: functional elucidation of a DUF1680 protein family member, J. Biol. Chem, vol.289, pp.5240-5249, 2014. ,
Alpha-N-acetylgalactosaminidase from infant-associated bifidobacteria belonging to novel glycoside hydrolase family 129 is implicated in alternative mucin degradation pathway, J. Biol. Chem, vol.287, pp.693-700, 2012. ,
Evolution and diversity of plant cell walls: from algae to flowering plants, Annu. Rev. Plant Biol, vol.62, pp.567-590, 2011. ,
URL : https://hal.archives-ouvertes.fr/hal-01117618
Comparison of the structures of hybrid ?-/?-carrageenans extracted from Furcellaria lumbricalis and Tichocarpus crinitus, Carbohydr. Polym, vol.88, pp.31-36, 2012. ,
URL : https://hal.archives-ouvertes.fr/hal-02108474
The use of polyacrylamide-gel electrophoresis for the highresolution separation of reducing saccharides labelled with the fluorophore 8aminonaphthalene-1,3,6-trisulphonic acid. Detection of picomolar quantities by an imaging system based on a cooled charge-coupled device, Biochem. J, vol.270, pp.705-713, 1990. ,
The novel catabolic pathway of 3,6-anhydro-L-galactose, the main component of red macroalgae, in a marine bacterium, Environ. Microbiol, vol.17, pp.1677-1688, 2015. ,
Metabolic pathway of 3,6-anhydro-Dgalactose in carrageenan-degrading microorganisms, Appl. Microbiol. Biotechnol, vol.100, pp.4109-4121, 2016. ,
Purification, crystallization and structural elucidation of D-galactaro-1,4-lactone cycloisomerase from Agrobacterium tumefaciens involved in pectin degradation, Acta. Crystallogr. Sect. F Struct. Biol. Cryst. Commun, vol.72, pp.36-41, 2016. ,
Genetic analyses unravel the crucial role of a horizontally acquired alginate lyase for brown algal biomass degradation by Zobellia galactanivorans, Environ. Microbiol, vol.19, pp.2164-2181, 2017. ,
Biochemical and structural characterization of the complex agarolytic enzyme system from the marine bacterium Zobellia galactanivorans, J. Biol. Chem, vol.287, pp.30571-30584, 2012. ,
URL : https://hal.archives-ouvertes.fr/hal-02108464
The nonphosphorylative Entner-Doudoroff pathway in the thermoacidophilic euryarchaeon Picrophilus torridus involves a novel 2-keto-3-deoxygluconate-specific aldolase, J. Bacteriol, vol.192, pp.964-974, 2010. ,
Plant carbohydrate scavenging through tonB-dependent receptors: a feature shared by phytopathogenic and aquatic bacteria, PLoS ONE, vol.2, p.224, 2007. ,
Transfer of carbohydrate-active enzymes from marine bacteria to Japanese gut microbiota, Nature, vol.464, pp.908-912, 2010. ,
Discovery and structural characterization of a novel glycosidase family of marine origin, Environ. Microbiol, vol.13, pp.1253-1270, 2011. ,
Polysaccharide utilization loci: fuelling microbial communities, J. Bacteriol ,
MARINE-EXPRESS: taking advantage of high throughput cloning and expression strategies for the post-genomic analysis of marine organisms, Microb. Cell Fact, vol.9, p.45, 2010. ,
URL : https://hal.archives-ouvertes.fr/hal-00609166
Protein production by auto-induction in high density shaking cultures, Protein Expr. Purif, vol.41, pp.207-234, 2005. ,
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, Acta Crystallogr. D, vol.71, pp.209-223, 2015. ,
URL : https://hal.archives-ouvertes.fr/hal-01140143
Protein identification and analysis tools on the ExPASy Server, The Proteomics Protocols Handbook, 2005. ,
Expression, purification, crystallization and preliminary x-ray analysis of the kappa-carrageenase from Pseudoalteromonas carrageenovora, Acta Crystallogr. D, vol.55, pp.918-920, 1999. ,
Expression, purification, crystallization and preliminary X-ray analysis of the iota-carrageenase from Alteromonas fortis, Acta Crystallogr. D, vol.56, pp.766-768, 2000. ,
An extremely thermostable aldolase from Sulfolobus solfataricus with specificity for non-phosphorylated substrates, Biochem. J, vol.343, pp.563-570, 1999. ,
The Rossmann Fourier autoindexing algorithm in MOSFLM, Acta Crystallogr. D, vol.55, pp.1690-1695, 1999. ,
DOI : 10.1107/s0907444999009506
URL : http://journals.iucr.org/d/issues/1999/10/00/ba0024/ba0024.pdf
Recent changes to the MOSFLM package for processing film and image plate data, Jnt. CCP4/ESF-EACBM Newslett. Protein Crystallogr, vol.26, 1992. ,
An introduction to data reduction: space-group determination, scaling and intensity statistics, Acta Crystallogr. D, vol.67, pp.282-292, 2011. ,
DOI : 10.1107/s090744491003982x
URL : http://journals.iucr.org/d/issues/2011/04/00/ba5158/ba5158.pdf
Scaling and assessment of data quality, Acta Crystallogr. D, vol.62, pp.72-82, 2006. ,
, Collaborative Computational Project Number 4. The CCP4 suite: programs for protein crystallography, Acta Crystallogr. D, vol.50, pp.760-763, 1994.
Substructure solution with SHELXD, Acta Crystallogr. D, vol.58, pp.1772-1779, 2002. ,
CRANK: new methods for automated macromolecular crystal structure solution, Structure, vol.12, pp.1753-1761, 2004. ,
DOI : 10.1107/s0108767304099702
URL : http://journals.iucr.org/a/issues/2004/a1/00/a31223/a31223.pdf
MOLREP: an automated program for molecular replacement, J. Appl. Crystallogr, vol.30, pp.1022-1025, 1997. ,
DOI : 10.1107/s0021889897006766
REFMAC5 dictionary: organization of prior chemical knowledge and guidelines for its use, Acta Crystallogr. D, vol.60, pp.2184-2195, 2004. ,
Features and development of Coot, Acta Crystallogr. D, vol.66, pp.486-501, 2010. ,
, Acta Crystallogr. D, vol.66, pp.125-132, 2010.
Integration, scaling, space-group assignment and post-refinement, Acta Crystallogr. D, vol.66, pp.133-144, 2010. ,
DOI : 10.1107/s0907444909047374
URL : http://journals.iucr.org/d/issues/2010/02/00/dz5178/dz5178.pdf
Phaser crystallographic software, J. Appl. Crystallogr, vol.40, pp.658-674, 2007. ,
Exploiting structure similarity in refinement: automated NCS and target-structure restraints in BUSTER, Acta Crystallogr. D, vol.68, pp.368-380, 2012. ,
Performance evaluation on a wide set of matrix-assisted laser desorption ionization matrices for the detection of oligosaccharides in a highthroughput mass spectrometric screening of carbohydrate depolymerizing enzymes, Rapid Commun. Mass. Spectrom, vol.25, pp.2059-2070, 2011. ,
URL : https://hal.archives-ouvertes.fr/hal-01967556
Studies on marine bacteria I The cultural requirements of heterotrophic aerobes, J Mar Res, vol.4, pp.42-75, 1941. ,
Evaluation of reference genes for realtime quantitative PCR in the marine flavobacterium Zobellia galactanivorans, J. Microbiol. Methods, vol.84, pp.61-66, 2011. ,
Quality control and preprocessing of metagenomic datasets, Bioinformatics, vol.27, pp.863-864, 2011. ,
DOI : 10.1093/bioinformatics/btr026
URL : https://academic.oup.com/bioinformatics/article-pdf/27/6/863/646767/btr026.pdf
Fast gapped-read alignment with Bowtie 2, Nat. Methods, vol.9, pp.357-359, 2012. ,
DOI : 10.1038/nmeth.1923
URL : http://europepmc.org/articles/pmc3322381?pdf=render
The sequence alignment/map format and SAMtools, Bioinformatics, vol.25, pp.2078-2079, 2009. ,
DOI : 10.1093/bioinformatics/btp352
URL : https://academic.oup.com/bioinformatics/article-pdf/25/16/2078/531810/btp352.pdf
Transcriptomic profiling of the oyster pathogen Vibrio splendidus opens a window on the evolutionary dynamics of the small RNA repertoire in the Vibrio genus, RNA, vol.18, pp.2201-2219, 2012. ,
URL : https://hal.archives-ouvertes.fr/hal-00757205
Artemis: sequence visualization and annotation, Bioinformatics, vol.16, pp.944-945, 2000. ,
DOI : 10.1093/bioinformatics/16.10.944
URL : https://academic.oup.com/bioinformatics/article-pdf/16/10/944/598346/160944.pdf
HTSeq-a Python framework to work with high-throughput sequencing data, Bioinformatics, vol.31, pp.166-1669, 2015. ,
DOI : 10.1093/bioinformatics/btu638
URL : https://academic.oup.com/bioinformatics/article-pdf/31/2/166/7000027/btu638.pdf
SARTools: A DESeq2-and Edger-based R pipeline for comprehensive differential analysis of RNA-Seq data, PLoS ONE, vol.11, p.157022, 2016. ,
URL : https://hal.archives-ouvertes.fr/hal-01344179
MicroScope in 2017: an expanding and evolving integrated resource for community expertise of microbial genomes, Nucleic Acids Res, vol.45, pp.517-528, 2016. ,
MAFFT multiple sequence alignment software version 7: improvements in performance and usability, Mol. Biol. Evol, vol.30, pp.772-780, 2013. ,
DOI : 10.1093/molbev/mst010
URL : https://academic.oup.com/mbe/article-pdf/30/4/772/6420419/mst010.pdf
Block Mapping and Gathering with Entropy): a new software for selection of phylogenetic informative regions from multiple sequence alignments, BMC Evol. Biol, vol.10, p.210, 2010. ,
ProtTest 3: fast selection of best-fit models of protein evolution, Bioinformatics, vol.27, pp.1164-1165, 2011. ,
New algorithms and methods to estimate maximumlikelihood phylogenies: assessing the performance of PhyML 3.0, Syst. Biol, vol.59, pp.307-321, 2010. ,
URL : https://hal.archives-ouvertes.fr/lirmm-00511784
Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees, Nucleic Acids Res, vol.44, pp.242-245, 2016. ,
performed the mass spectrometry experiments. G.C. produced and purified the furcellaran oligosaccharides. M.M. performed the site-directed mutagenesis of ZGAL_3152. K.A.S. synthesized initial potential substrates for ZGAL_3152 and ,