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

Anne Abot,Lidwine Trouilh,Lucas Auer,Sophie Lamarre,Michael O’Donohue,Adèle Lazuka,Gregory Arnal,Elisabeth Laville,Claire Dumon,Bernard Henrissat,Delphine Labourdette,Véronique Anton Leberre,Vincent Lombard,Gabrielle Potocki-Veronese,Guillermina Hernandez-Raquet

doi:10.1186/s12864-016-2988-4

Abstract

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.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-2988-4) contains supplementary material, which is available to authorized users.

Highlights

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 degradation of polysaccharides such as cellulose, chitin, starch and glycogen is an essential feature of carbon cycle in the biosphere, a process that requires the contribution of various microorganisms that together deploy an arsenal of carbohydrate-degrading enzymes
Among the key plant cell wall (PCW)-degrading enzymes that are produced by microorganisms, the glycoside hydrolases (GH) and the carbohydrate esterases (CE) belong to a wide class of enzymes that modify, synthesize or hydrolyze carbohydrates: Carbohydrate Active enZymes, or CAZymes

Summary

Introduction

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). Plant cell walls (PCWs) are composed of a composite network of macromolecules, including polysaccharides and lignin. The CAZymes are prominent and highly diverse and have been identified in all taxa, representing typically 1–5 % of the predicted coding sequences in their genomes [39]. These proteins are expressed by microorganisms inhabiting almost all ecological niches (e.g., soil, marine environment and digestive tracts), where they participate in carbon cycling. The strategies of carbohydrate-degradation are often different at both the level of the microbial community and of individual microorganisms [30]

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