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Open Access Highly Accessed Research article

Carbohydrate-active enzymes from the zygomycete fungus Rhizopus oryzae: a highly specialized approach to carbohydrate degradation depicted at genome level

Evy Battaglia1, Isabelle Benoit1, Joost van den Brink2, Ad Wiebenga2, Pedro M Coutinho3, Bernard Henrissat3* and Ronald P de Vries12*

Author Affiliations

1 Microbiology & Kluyver Centre for Genomics of Industrial Fermentation, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands

2 Fungal Physiology, CBS-KNAW, Uppsalalaan 8, 3584 CT, Utrecht, The Netherlands

3 Architecture et Fonction des Macromolécules Biologiques, UMR6098, CNRS and Universités d'Aix-Marseille I & II, Case 932, 163 Av de Luminy, 13288 Marseille cedex 9, France

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BMC Genomics 2011, 12:38  doi:10.1186/1471-2164-12-38

Published: 17 January 2011

Abstract

Background

Rhizopus oryzae is a zygomycete filamentous fungus, well-known as a saprobe ubiquitous in soil and as a pathogenic/spoilage fungus, causing Rhizopus rot and mucomycoses.

Results

Carbohydrate Active enzyme (CAZy) annotation of the R. oryzae identified, in contrast to other filamentous fungi, a low number of glycoside hydrolases (GHs) and a high number of glycosyl transferases (GTs) and carbohydrate esterases (CEs). A detailed analysis of CAZy families, supported by growth data, demonstrates highly specialized plant and fungal cell wall degrading abilities distinct from ascomycetes and basidiomycetes. The specific genomic and growth features for degradation of easily digestible plant cell wall mono- and polysaccharides (starch, galactomannan, unbranched pectin, hexose sugars), chitin, chitosan, β-1,3-glucan and fungal cell wall fractions suggest specific adaptations of R. oryzae to its environment.

Conclusions

CAZy analyses of the genome of the zygomycete fungus R. oryzae and comparison to ascomycetes and basidiomycete species revealed how evolution has shaped its genetic content with respect to carbohydrate degradation, after divergence from the Ascomycota and Basidiomycota.