Comparative metabolism of cellulose, sophorose and glucose in Trichoderma reeseiusing high-throughput genomic and proteomic analyses

Abstract

BackgroundThe filamentous fungus Trichoderma reesei is a major producer of lignocellulolytic enzymes utilized by bioethanol industries. However, to achieve low cost second generation bioethanol production on an industrial scale an efficient mix of hydrolytic enzymes is required for the deconstruction of plant biomass. In this study, we investigated the molecular basis for lignocellulose-degrading enzyme production T. reesei during growth in cellulose, sophorose, and glucose.ResultsWe examined and compared the transcriptome and differential secretome (2D-DIGE) of T. reesei grown in cellulose, sophorose, or glucose as the sole carbon sources. By applying a stringent cut-off threshold 2,060 genes were identified as being differentially expressed in at least one of the respective carbon source comparisons. Hierarchical clustering of the differentially expressed genes identified three possible regulons, representing 123 genes controlled by cellulose, 154 genes controlled by sophorose and 402 genes controlled by glucose. Gene regulatory network analyses of the 692 genes differentially expressed between cellulose and sophorose, identified only 75 and 107 genes as being specific to growth in sophorose and cellulose, respectively. 2D-DIGE analyses identified 30 proteins exclusive to sophorose and 37 exclusive to cellulose. A correlation of 70.17% was obtained between transcription and secreted protein profiles.ConclusionsOur data revealed new players in cellulose degradation such as accessory proteins with non-catalytic functions secreted in different carbon sources, transporters, transcription factors, and CAZymes, that specifically respond in response to either cellulose or sophorose.

Defining the genome-wide role of CRE1 during carbon catabolite repression in Trichoderma reesei using RNA-Seq analysis

“…BGL2 produces substantial amounts of sophorose and cellobiose from glucose through the transglycosylation reaction (Saloheimo et al, 2002). This finding reinforces the fact that sophorose and cellobiose can act as a cellulase inducers in T. reesei (Dos Santos Castro et al, 2014) and shows that the transglycosylation reaction is under the control of CRE1-mediated CCR. On the other hand, in relation to cellulose, the detection of genes related to oxidative metabolism at the top of the list (Table 1) suggests that when T. reesei is growing in this complex carbon source, where glucose availability is limited by the cellulose degradation rate, the cells may be under constant semi-starvation conditions, which would induce stress-related metabolism, leading to the expression of genes that encode cellulases and hemicellulases.…”

Deciphering the Cis-Regulatory Elements for XYR1 and CRE1 Regulators in Trichoderma reesei

“…For this, we used RNA-seq data from T. reesei cells grown on cellulose, sophorose and glucose as sole carbon sources [45]. Raw sequence data and count data for all samples are available at Gene Expression Omnibus (GEO database) under the accession number GSE53629.…”

Involvement of Trichoderma harzianum Epl-1 Protein in the Regulation of Botrytis Virulence- and Tomato Defense-Related Genes

“…The structure of CP proteins resembles that of expansins, which do not have an enzymatic function. Furthermore, expansin-like proteins are important in the degradation of the plant cell wall by inducing the opening of physical spaces required for the action of cellulolytic enzymes (Baccelli et al, 2014; Castro et al, 2014). Like expansins, CP proteins also bind carbohydrates, which suggest that CP proteins have a similar function and that these proteins can induce the opening of physical spaces in structural components of the fungal cell wall, such as in chitin polymers (Frischmann et al, 2013; Baccelli et al, 2014; Bonazza et al, 2015).…”