DataSheet6_Network Analysis Reveals Different Cellulose Degradation Strategies Across Trichoderma harzianum Strains Associated With XYR1 and CRE1.xlsx

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.

木霉属真菌（Trichoderma harzianum）的基因表达受到转录因子（TFs）XYR1和CRE1的严格调控，该真菌具有生产水解酶的潜力。本研究对T. harzianum IOC-3844和T. harzianum CBMAI-0179进行了网络分析，以探究不同菌株间这些转录因子的调控差异。此外，我们还研究了XYR1和CRE1蛋白序列在木霉属中的进化关系。将T. harzianum菌株的结果与真菌寄生种T. atroviride CBMAI-0020的结果进行了比较。尽管编码碳水化合物活性酶（CAZymes）、转录因子、转运蛋白和功能未知的蛋白的转录本与cre1或xyr1共表达，但还鉴定出与纤维素降解间接相关的其他蛋白。描述这些转录组GO术语的富集分析在所有菌株中均有所不同，且在两种调控因子之间存在高度相似性的代谢途径以及菌株特异性差异均被发现。此外，CRE1和XYR1子网络在每个菌株中的拓扑结构也呈现不同的特征，这可能是由于真菌对这些调控因子影响的差异。CRE1和XYR1组的枢纽包括尚未表征或描述为与纤维素降解相关的转录本。邻域分析证实了cre1和xyr1中共同表达转录本的概况。最短路径分析揭示了在纤维素降解条件下上调的CAZymes与两种调控因子最为密切，并发现了此类信号通路间的新靶点。尽管评估的T. harzianum菌株在系统发育上相近，且其与XYR1和CRE1相关的氨基酸序列非常相似，但与xyr1和cre1相关的转录本集却存在差异，这表明每个T. harzianum菌株都采用了特定的纤维素降解调控策略。更有趣的是，我们的发现可能表明XYR1和CRE1间接调控编码与纤维素降解相关的蛋白的基因在评估的T. harzianum菌株中。对纤维素降解过程中真菌基本生物学的深入了解，有助于其酶在多种生物技术应用中的利用，并为同一物种不同菌株间差异的进一步研究铺平道路。