Abstract
Trichoderma harzianum, whose gene expression is tightly controlled by the transcription factors (TFs) XYR1 and CRE1, is a potential candidate for hydrolytic enzyme production. Here, we performed a network analysis of T. harzianum IOC-3844 and T. harzianum CBMAI-0179 to explore how the regulation of these TFs varies between these strains. In addition, we explored the evolutionary relationships of XYR1 and CRE1 protein sequences among Trichoderma spp. The results of the T. harzianum strains were compared with those of Trichoderma atroviride CBMAI-0020, a mycoparasitic species. Although transcripts encoding carbohydrate-active enzymes (CAZymes), TFs, transporters, and proteins with unknown functions were coexpressed with cre1 or xyr1, other proteins indirectly related to cellulose degradation were identified. The enriched GO terms describing the transcripts of these groups differed across all strains, and several metabolic pathways with high similarity between both regulators but strain-specific differences were identified. In addition, the CRE1 and XYR1 subnetworks presented different topology profiles in each strain, likely indicating differences in the influences of these regulators according to the fungi. The hubs of the cre1 and xyr1 groups included transcripts not yet characterized or described as being related to cellulose degradation. The first-neighbor analyses confirmed the results of the profile of the coexpressed transcripts in cre1 and xyr1. The analyses of the shortest paths revealed that CAZymes upregulated under cellulose degradation conditions are most closely related to both regulators, and new targets between such signaling pathways were discovered. Although the evaluated T. harzianum strains are phylogenetically close and their amino acid sequences related to XYR1 and CRE1 are very similar, the set of transcripts related to xyr1 and cre1 differed, suggesting that each T. harzianum strain used a specific regulation strategy for cellulose degradation. More interestingly, our findings may suggest that XYR1 and CRE1 indirectly regulate genes encoding proteins related to cellulose degradation in the evaluated T. harzianum strains. An improved understanding of the basic biology of fungi during the cellulose degradation process can contribute to the use of their enzymes in several biotechnological applications and pave the way for further studies on the differences across strains of the same species.
Highlights
Lignocellulosic biomass is a complex recalcitrant structure that requires a consortium of carbohydrate-active enzymes (CAZymes) for its complete depolymerization
To represent the evolutionary relationships of catabolite repressor 1 (CRE1) and xylanase regulator 1 (XYR1) among T. harzianum IOC-3844 (Th3844), T. harzianum CBMAI-0179 (Th0179), and T. atroviride CBMAI-0020 (Ta0020), a phylogenetic analysis was performed while considering their amino acid sequences (Figure 1)
The importance of XYR1 and CRE1 in the expression of CAZyme-encoding genes and other proteins required for lignocellulose degradation is evident, the transcriptional regulation mediated by both proteins in T. harzianum strains remains poorly explored (Delabona et al, 2017; Delabona et al, 2021)
Summary
Lignocellulosic biomass is a complex recalcitrant structure that requires a consortium of carbohydrate-active enzymes (CAZymes) for its complete depolymerization. Due to their unique ability to secrete these proteins efficiently, filamentous fungi, such as Trichoderma spp. and Aspergillus spp., are widely explored for the industrial production of CAZymes (de Assis et al, 2015; Bischof et al, 2016). In the genus Trichoderma, Trichoderma reesei is the primary fungal industrial source of cellulases and hemicellulases (Martinez et al, 2008), while Trichoderma harzianum and Trichoderma atroviride have been widely explored by examining their biocontrol capacity against plant pathogenic fungi (Medeiros et al, 2017; Saravanakumar et al, 2017). In the genus Trichoderma, XYR1 evolved by vertical gene transfer (Druzhinina et al, 2018)
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