title: CAZyChip: dynamic assessment of exploration of glycoside hydrolases in microbial ecosystems.
abstract: Microorganisms constitute a reservoir of enzymes involved in environmental carbon cycling and degradation of plant polysaccharides through their production of a vast variety of Glycoside Hydrolases (GH). The CAZyChip was developed to allow a rapid characterization at transcriptomic level of these GHs and to identify enzymes acting on hydrolysis of polysaccharides or glycans.
  
  
  
  This DNA biochip contains the signature of 55,220 bacterial GHs available in the CAZy database. Probes were designed using two softwares, and microarrays were directly synthesized using the in situ ink-jet technology. CAZyChip specificity and reproducibility was validated by hybridization of known GHs RNA extracted from recombinant E. coli strains, which were previously identified by a functional metagenomic approach. The GHs arsenal was also studied in bioprocess conditions using rumen derived microbiota.
  
  
  
  The CAZyChip appears to be a user friendly tool for profiling the expression of a large variety of GHs. It can be used to study temporal variations of functional diversity, thereby facilitating the identification of new efficient candidates for enzymatic conversions from various ecosystems.
authors.affiliation: Université de Toulouse, INSA, UPS, INP; LISBP, 135 Avenue de Rangueil, F-31077, Toulouse, France.|INRA, UMR792 Ingénierie des Systèmes Biologiques et des Procédés, F-31400, Toulouse, France.|CNRS, UMR5504, F-31400, Toulouse, France.
authors.forename: Anne
authors.initials: A
authors.lastname: Abot
authors.affiliation: Université de Toulouse, INSA, UPS, INP; LISBP, 135 Avenue de Rangueil, F-31077, Toulouse, France.|INRA, UMR792 Ingénierie des Systèmes Biologiques et des Procédés, F-31400, Toulouse, France.|CNRS, UMR5504, F-31400, Toulouse, France.
authors.forename: Gregory
authors.initials: G
authors.lastname: Arnal
authors.affiliation: Université de Toulouse, INSA, UPS, INP; LISBP, 135 Avenue de Rangueil, F-31077, Toulouse, France.|INRA, UMR792 Ingénierie des Systèmes Biologiques et des Procédés, F-31400, Toulouse, France.|CNRS, UMR5504, F-31400, Toulouse, France.
authors.forename: Lucas
authors.initials: L
authors.lastname: Auer
authors.affiliation: Université de Toulouse, INSA, UPS, INP; LISBP, 135 Avenue de Rangueil, F-31077, Toulouse, France.|INRA, UMR792 Ingénierie des Systèmes Biologiques et des Procédés, F-31400, Toulouse, France.|CNRS, UMR5504, F-31400, Toulouse, France.
authors.forename: Adèle
authors.initials: A
authors.lastname: Lazuka
authors.affiliation: Université de Toulouse, INSA, UPS, INP; LISBP, 135 Avenue de Rangueil, F-31077, Toulouse, France.|INRA, UMR792 Ingénierie des Systèmes Biologiques et des Procédés, F-31400, Toulouse, France.|CNRS, UMR5504, F-31400, Toulouse, France.
authors.forename: Delphine
authors.initials: D
authors.lastname: Labourdette
authors.affiliation: Université de Toulouse, INSA, UPS, INP; LISBP, 135 Avenue de Rangueil, F-31077, Toulouse, France.|INRA, UMR792 Ingénierie des Systèmes Biologiques et des Procédés, F-31400, Toulouse, France.|CNRS, UMR5504, F-31400, Toulouse, France.
authors.forename: Sophie
authors.initials: S
authors.lastname: Lamarre
authors.affiliation: Université de Toulouse, INSA, UPS, INP; LISBP, 135 Avenue de Rangueil, F-31077, Toulouse, France.|INRA, UMR792 Ingénierie des Systèmes Biologiques et des Procédés, F-31400, Toulouse, France.|CNRS, UMR5504, F-31400, Toulouse, France.
authors.forename: Lidwine
authors.initials: L
authors.lastname: Trouilh
authors.affiliation: Université de Toulouse, INSA, UPS, INP; LISBP, 135 Avenue de Rangueil, F-31077, Toulouse, France.|INRA, UMR792 Ingénierie des Systèmes Biologiques et des Procédés, F-31400, Toulouse, France.|CNRS, UMR5504, F-31400, Toulouse, France.
authors.forename: Elisabeth
authors.initials: E
authors.lastname: Laville
authors.affiliation: Centre National de la Recherche Scientifique, UMR 7257, F-13288, Marseille, France.|Architecture et Fonction des Macromolécules Biologiques, Aix-Marseille University, F-13288, Marseille, France.|INRA, USC 1408 AFMB, F-13288, Marseille, France.
authors.forename: Vincent
authors.initials: V
authors.lastname: Lombard
authors.affiliation: Université de Toulouse, INSA, UPS, INP; LISBP, 135 Avenue de Rangueil, F-31077, Toulouse, France.|INRA, UMR792 Ingénierie des Systèmes Biologiques et des Procédés, F-31400, Toulouse, France.|CNRS, UMR5504, F-31400, Toulouse, France.
authors.forename: Gabrielle
authors.initials: G
authors.lastname: Potocki-Veronese
authors.affiliation: Centre National de la Recherche Scientifique, UMR 7257, F-13288, Marseille, France.|Architecture et Fonction des Macromolécules Biologiques, Aix-Marseille University, F-13288, Marseille, France.|INRA, USC 1408 AFMB, F-13288, Marseille, France.|Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia.
authors.forename: Bernard
authors.initials: B
authors.lastname: Henrissat
authors.affiliation: Université de Toulouse, INSA, UPS, INP; LISBP, 135 Avenue de Rangueil, F-31077, Toulouse, France.|INRA, UMR792 Ingénierie des Systèmes Biologiques et des Procédés, F-31400, Toulouse, France.|CNRS, UMR5504, F-31400, Toulouse, France.
authors.forename: Michael
authors.initials: M
authors.lastname: O'Donohue
authors.affiliation: Université de Toulouse, INSA, UPS, INP; LISBP, 135 Avenue de Rangueil, F-31077, Toulouse, France.|INRA, UMR792 Ingénierie des Systèmes Biologiques et des Procédés, F-31400, Toulouse, France.|CNRS, UMR5504, F-31400, Toulouse, France.
authors.forename: Guillermina
authors.initials: G
authors.lastname: Hernandez-Raquet
authors.affiliation: Université de Toulouse, INSA, UPS, INP; LISBP, 135 Avenue de Rangueil, F-31077, Toulouse, France.|INRA, UMR792 Ingénierie des Systèmes Biologiques et des Procédés, F-31400, Toulouse, France.|CNRS, UMR5504, F-31400, Toulouse, France.
authors.forename: Claire
authors.initials: C
authors.lastname: Dumon
authors.affiliation: Université de Toulouse, INSA, UPS, INP; LISBP, 135 Avenue de Rangueil, F-31077, Toulouse, France. leberre@insa-toulouse.fr.|INRA, UMR792 Ingénierie des Systèmes Biologiques et des Procédés, F-31400, Toulouse, France. leberre@insa-toulouse.fr.|CNRS, UMR5504, F-31400, Toulouse, France. leberre@insa-toulouse.fr.|Laboratoire d'Ingénierie des Systèmes Biologiques et des Procédés (LISBP), UMR INSA/CNRS 5504/INRA 792, INSA Batiment Bio 5, 135, avenue de Rangueil, F-31077, Toulouse cedex 4, France. leberre@insa-toulouse.fr.
authors.forename: Véronique Anton
authors.identifier: 0000-0002-3282-5133
authors.initials: VA
authors.lastname: Leberre
mesh_terms: D001426:Bacterial Proteins / Q000235:genetics; D002473:Cell Wall / Q000378:metabolism; D030541:Databases, Genetic; D004926:Escherichia coli / Q000235:genetics; D015964:Gene Expression Regulation, Bacterial; D006026:Glycoside Hydrolases / Q000235:genetics*; D054892:Metagenome; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D010944:Plants / Q000378:metabolism; D011134:Polysaccharides / Q000378:metabolism; D017423:Sequence Analysis, RNA / Q000379:methods*
chemical_list: D001426:Bacterial Proteins; D011134:Polysaccharides; D006026:Glycoside Hydrolases
keywords: CAZymes detection; Glycoside hydrolase; Microarray; Microbial functional diversity; Plant cell wall degradation; Transcriptomic analysis