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. 2016 Aug 23;17(1):671.
doi: 10.1186/s12864-016-2988-4.

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

Anne Abot  1   2   3 , Gregory Arnal  1   2   3 , Lucas Auer  1   2   3 , Adèle Lazuka  1   2   3 , Delphine Labourdette  1   2   3 , Sophie Lamarre  1   2   3 , Lidwine Trouilh  1   2   3 , Elisabeth Laville  1   2   3 , Vincent Lombard  4   5   6 , Gabrielle Potocki-Veronese  1   2   3 , Bernard Henrissat  4   5   6   7 , Michael O'Donohue  1   2   3 , Guillermina Hernandez-Raquet  1   2   3 , Claire Dumon  1   2   3 , Véronique Anton Leberre  8   9   10   11
Affiliations

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

Anne Abot et al. BMC Genomics. .

Abstract

Background: 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.

Results: 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.

Conclusions: 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.

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

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Figures

Fig. 1
Fig. 1
Heatmaps of log base 2 intensity signal of targeted probes for GHs cloned in plasmids samples. Each horizontal line represents a probe, and each vertical line represents an individual sample. Genes that were overexpressed are in red, whereas genes weakly expressed are in green. The color intensity indicates the degree of variation in expression
Fig. 2
Fig. 2
Heatmaps of log base 2 intensity signal of targeted probes for GHs cloned in fosmids a samples from termite microbiota labeled with cyanine 3 (left panel) or labeled with cyanine 5 (right panel), b samples from human microbiota and c samples from cattle rumen microbiota. Each horizontal line represents a probe, and each vertical line represents an individual sample. Genes that were overexpressed are in red, whereas genes weakly expressed are in green. The color intensity indicates the degree of variation in expression
Fig. 3
Fig. 3
Expressed GH family known to be implicated in plant cell wall (PCW) degradation in day 3 and 5. For details see Additional file 6: Table S4
See this image and copyright information in PMC

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