Composition and Expression of Genes Encoding Carbohydrate-Active Enzymes in the Straw-Degrading Mushroom Volvariella volvacea

Yong-Sun Bahn,Bingzhi Chen,Youjin Deng,Fu Gui,Shaojie Li,Baogui Xie,Xianyun Sun,Yongxin Tao,Mengying Lin

doi:10.1371/journal.pone.0058780

Abstract

Volvariella volvacea is one of a few commercial cultivated mushrooms mainly using straw as carbon source. In this study, the genome of V. volcacea was sequenced and assembled. A total of 285 genes encoding carbohydrate-active enzymes (CAZymes) in V. volvacea were identified and annotated. Among 15 fungi with sequenced genomes, V. volvacea ranks seventh in the number of genes encoding CAZymes. In addition, the composition of glycoside hydrolases in V. volcacea is dramatically different from other basidiomycetes: it is particularly rich in members of the glycoside hydrolase families GH10 (hemicellulose degradation) and GH43 (hemicellulose and pectin degradation), and the lyase families PL1, PL3 and PL4 (pectin degradation) but lacks families GH5b, GH11, GH26, GH62, GH93, GH115, GH105, GH9, GH53, GH32, GH74 and CE12. Analysis of genome-wide gene expression profiles of 3 strains using 3′-tag digital gene expression (DGE) reveals that 239 CAZyme genes were expressed even in potato destrose broth medium. Our data also showed that the formation of a heterokaryotic strain could dramatically increase the expression of a number of genes which were poorly expressed in its parental homokaryotic strains.

Highlights

Volvariella volvacea (Bull.: Fr.) Singer, commonly known as the straw mushroom and the Chinese mushroom, is an important, edible, straw-degrading basidomycete fungus of the tropics and subtropics
By comparison with 14 other filamentous fungi, we discovered some features in the composition of carbohydrate-active enzymes (CAZymes) in this fungus
By searching the predicted amino acid sequences of V. volvacea genes against the Carbohydrate-Active Enzyme database (CAZy), we identified totally 285 CAZymes encoded by the genome of V. volvacea, including 191 glycoside hydrolases, 44 glycosyltransferases, 19 polysaccharide lyases and 31 carbohydrate esterases

Summary

Introduction

Volvariella volvacea (Bull.: Fr.) Singer, commonly known as the straw mushroom and the Chinese mushroom, is an important, edible, straw-degrading basidomycete fungus of the tropics and subtropics. The annual yield of the fungus was about 437,200 tons in 2008 [1]. The cultivation of V. volvacea uses about 4 million tons of straw per year in China, accounting for approximately 2% of the annual straw yield in China and its cultivation residues are a source of organic fertilizer with high quality for crops. A clear grasp of the mechanism of lignocellulose degradation is important for breeding for increased straw degradation efficiency and biological efficiency, and generally to expand their immense biotechnological potential. These objectives have given impetus to the quest to sequence its genome and to characterize its gene expression. Genome sequence information of mushrooms will help to increase the understanding of the biology, evolution, and biomedical implications of the entire fungal kingdom

Methods

Results

Conclusion