Transcriptional profiling of biomass degradation-related genes during Trichoderma reesei growth on different carbon sources

To identify all the gene products involved in cellulosic biomass degradation, we employed RNA sequencing technology to perform a genome-wide comparison of gene expression during growth of Trichoderma reesei QM9414 on cellulose or glucose. Due to their important role in lignocellulose decomposition, we focused on CAZymes and other secreted proteins. In total, 122 CAZymes showed at least a two-fold change in mRNA abundance, and 97 of those were highly induced by cellulose. Compared to the well-characterized cellulases and hemicellulases, a majority of the other upregulated CAZymes showed lower transcriptional levels. In addition, 64 secreted proteins, including oxidoreductases, exhibited at least two-fold upregulation on cellulose medium. To better understand the potential roles of low-abundance CAZymes in cellulose breakdown, we compared the expression patterns of 25 glycoside hydrolase genes under different conditions via real-time PCR. Substantial differences for the 25 genes were observed for individual strains grown on different carbon sources, and between QM9414 and RUTC30 when grown on the same carbon source. Moreover, we identified 3 genes that are coregulated with known cellulases. Collectively, this study highlights a comprehensive transcriptional profile for biomass degradation-related proteins and provides a first step toward the identification of candidates to construct optimized enzyme cocktails.