Structural, phylogenetic and expression analysis of genes producing lignin degrading enzymes in the basidiomycete Cyathus bulleri and their effect on the release of reducing sugars from agro-residues

Abstract

One of the major impediments in the use of agricultural by-products, including rice husk and wheat straw, as a raw material for biofuel production is the availability of a suitable biological method for delignification. The current physical, chemical and physico-chemical methods are harsh, expensive and are accompanied by the release of toxic end-products such as furan derivatives, weak carboxylic acids and phenolic compounds. The aim of this study was to explore the lignin degrading enzymes of Cyathus bulleri, an avid lignin degrader, for their use in delignification of agricultural by-products. A total of 13 laccase (Lcc) encoding and 6 manganese peroxidase or MnP (MnP) encoding genes were identified in the draft genome of C. bulleri. The Lcc genes could be sub-divided in to 3 classes based on their structural organization whereas no common structures were identified in the MnPs. Similarity at the genomic level for all laccases (except Lcc12) indicated their evolution as a result of gene duplication and these appeared to be very closely related based on the phylogenetic relationship. All the copper binding domains and the heme signature sequences were conserved in the laccases and the MnPs respectively. A transmembrane helix was predicted at the C-terminus of Lcc12 suggesting its localization on the mycelial surface. A temporal analysis of the transcription of Lcc and MnP genes was carried out on wheat bran (WB) and the data indicated Lcc1 to be transcribed the most on Day 4 while Lcc12 was transcribed during later stages of growth. The crude culture filtrate obtained from WB-grown fungus released reducing sugars from rice husk (∼18.5 mg/g of rice husk) and wheat straw (∼9.5 mg/g of WS) indicating effective delignification as well as saccharification of these materials.