Abstract
The biomass-degrading fungus Trichoderma reesei has been considered a model for cellulose degradation, and it is the primary source of the industrial enzymatic cocktails used in second-generation (2G) ethanol production. However, although various studies and advances have been conducted to understand the cellulolytic system and the transcriptional regulation of T. reesei, the whole set of genes related to lignocellulose degradation has not been completely elucidated. In this study, we inferred a weighted gene co-expression network analysis based on the transcriptome dataset of the T. reesei RUT-C30 strain aiming to identify new target genes involved in sugarcane bagasse breakdown. In total, ~70% of all the differentially expressed genes were found in 28 highly connected gene modules. Several cellulases, sugar transporters, and hypothetical proteins coding genes upregulated in bagasse were grouped into the same modules. Among them, a single module contained the most representative core of cellulolytic enzymes (cellobiohydrolase, endoglucanase, β-glucosidase, and lytic polysaccharide monooxygenase). In addition, functional analysis using Gene Ontology (GO) revealed various classes of hydrolytic activity, cellulase activity, carbohydrate binding and cation:sugar symporter activity enriched in these modules. Several modules also showed GO enrichment for transcription factor activity, indicating the presence of transcriptional regulators along with the genes involved in cellulose breakdown and sugar transport as well as other genes encoding proteins with unknown functions. Highly connected genes (hubs) were also identified within each module, such as predicted transcription factors and genes encoding hypothetical proteins. In addition, various hubs contained at least one DNA binding site for the master activator Xyr1 according to our in silico analysis. The prediction of Xyr1 binding sites and the co-expression with genes encoding carbohydrate active enzymes and sugar transporters suggest a putative role of these hubs in bagasse cell wall deconstruction. Our results demonstrate a vast range of new promising targets that merit additional studies to improve the cellulolytic potential of T. reesei strains and to decrease the production costs of 2G ethanol.
Highlights
Over the previous years, the development of new sustainable alternatives to fossil fuels has become critical to mitigate greenhouse gas emissions and to avoid the exhaustion of natural sources
The data were imported into the Weighted Correlation Network Analysis (WGCNA) package, and a softpower β of 26 (R2 = 0.85) was chosen to fit the scale independence to a scale-free topology and taking into account the connectivity between the genes based on their expression (Data Sheet 2A)
The T. reesei gene co-expression network analysis grouped several differentially expressed genes into modules based on their expression patterns in steam-exploded sugarcane bagasse
Summary
The development of new sustainable alternatives to fossil fuels has become critical to mitigate greenhouse gas emissions and to avoid the exhaustion of natural sources. Bagasse is used to produce steam and energy in the sugar-ethanol biorefineries, and the straw is left on the soil to prevent erosion and enhance the organic carbon content (da Rosa, 2013; Pereira et al, 2015; Lisboa et al, 2017). These residues have already been used as feedstocks for 2G ethanol in Brazilian industrial plants (GranBio and Raízen), and they have a high potential to be explored more thoroughly in an integrated process with 1G ethanol technology (Junqueira et al, 2017; Lynd et al, 2017)
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