CAZyChip: dynamic assessment of exploration of glycoside hydrolases in microbial ecosystems

BMC Genomics

Research Article

Vincent Lombard¹  Bernard Henrissat²  Elisabeth Laville³  Anne Abot³  Adèle Lazuka³  Guillermina Hernandez-Raquet³  Gabrielle Potocki-Veronese³  Lucas Auer³  Sophie Lamarre³  Delphine Labourdette³  Gregory Arnal³  Lidwine Trouilh³  Claire Dumon³  Michael O’Donohue³  Véronique Anton Leberre⁴ 

[1] 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;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;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;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;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;

关键词: CAZymes detection;    Glycoside hydrolase;    Microarray;    Microbial functional diversity;    Plant cell wall degradation;    Transcriptomic analysis;   

DOI  :  10.1186/s12864-016-2988-4

 received in 2016-04-27, accepted in 2016-08-02,  发布年份 2016

来源: Springer

【 摘 要 】

BackgroundMicroorganisms 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.ResultsThis 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.ConclusionsThe 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.

【 授权许可】

CC BY   
© The Author(s). 2016