Network Analysis Reveals Different Cellulose Degradation Strategies Across Trichoderma harzianum Strains Associated With XYR1 and CRE1.

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.

The synergistic actions of hydrolytic genes reveal the mechanism of Trichoderma harzianum for cellulose degradation.

Bioprospecting genes and proteins related to plant biomass degradation is an attractive approach for the identification of target genes for biotechnological purposes, especially those with potential applications in the biorefinery industry that can enhance second-generation ethanol production technology. Trichoderma harzianum is a potential candidate for cellulolytic enzyme prospection and production. Herein, the enzymatic activities, transcriptome, exoproteome, and coexpression networks of the T. harzianum strain CBMAI-0179 were examined under biomass degradation conditions. We identified differentially expressed genes (DEGs) and carbohydrate-active enzyme (CAZyme) genes related to plant biomass degradation and compared them with those of strains from congeneric species (T. harzianum IOC-3844 and T. atroviride CBMAI-0020). T. harzianum CBMAI-0179 harbors strain- and treatment-specific CAZyme genes and transcription factors. We detected important proteins related to biomass degradation, including ß-glucosidases, endoglucanases, cellobiohydrolases, lytic polysaccharide monooxygenases, endo-1,4-ß-xylanases and ß-mannanases. Based on coexpression networks, an enriched cluster with degradative enzymes was described, and the subnetwork of CAZymes revealed strong correlations among important secreted proteins and differentially expressed CAZyme genes. Our results provide valuable information for future studies on the genetic regulation of plant cell wall-degrading enzymes. This knowledge can be exploited for the improvement of enzymatic reactions in biomass degradation for bioethanol production.

Leader gene of Corynebacterium pseudotuberculosis may be useful in vaccines against caseous lymphadenitis of goats: a bioinformatics approach.

We conducted an in silico analysis to search for important genes in the pathogenesis of Caseous Lymphadenitis (CL), with prospects for use in formulating effective vaccines against this disease. For this, we performed a survey of proteins expressed by Corynebacterium pseudotuberculosis, using protein sequences collected from the NCBI GenPept database and the keywords "caseous lymphadenitis" and "Corynebacterium pseudotuberculosis" and "goats". A network was developed using the STRING 10 database, with a confidence score of 0.900. For every gene interaction identified, we summed the interaction score of each gene, generating a combined association score to obtain a single score named weighted number of links (WNL). Genes with the highest WNL were named "leader genes". Ontological analysis was extracted from the STRING database through Kyoto Encyclopedia of Genes and Genomes (KEGG) database. A search in the GenPept database revealed 2,124 proteins. By using and plotting with STRING 10, we then developed an in silico network model comprised of 1,243 genes/proteins interconnecting through 3,330 interactions. The highest WNL values were identified in the rplB gene, which was named the leader gene. Our ontological analysis shows that this protein acts effectively mainly on Metabolic pathways and Biosynthesis of secondary metabolites. In conclusion, the in silico analyses showed that rplB has good potential for vaccine development. However, functional assays are needed to make sure that this protein can potentially induce both humoral and cellular immune responses against C. pseudotuberculosis in goats.