DataSheet4_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.

哈茨木霉（Trichoderma harzianum）的基因表达严格受转录因子（transcription factors, TFs）XYR1与CRE1调控，是水解酶生产的潜在候选菌株。本研究针对哈茨木霉IOC-3844与哈茨木霉CBMAI-0179开展共表达网络分析，以探究这两株菌中转录因子的调控差异。此外，本研究还解析了木霉属内XYR1与CRE1蛋白序列的进化关系，并将哈茨木霉菌株的分析结果与寄生真菌深绿木霉（Trichoderma atroviride）CBMAI-0020的结果进行了对比。
尽管与cre1或xyr1共表达的转录本编码了碳水化合物活性酶（carbohydrate-active enzymes, CAZymes）、转录因子、转运蛋白及功能未知蛋白，但研究还鉴定出了其他与纤维素降解间接相关的蛋白。上述转录本分组的富集基因本体论（Gene Ontology, GO）条目在各菌株间存在显著差异，同时本研究鉴定出两类调控因子间相似度较高但存在菌株特异性差异的多条代谢通路。
此外，CRE1与XYR1的共表达子网在各菌株中呈现出不同的拓扑结构特征，提示两类调控因子在不同真菌中的调控作用存在差异。cre1与xyr1分组的核心节点（hub）包含尚未被注释的转录本，或已被报道与纤维素降解相关的转录本。邻接基因分析验证了cre1与xyr1共表达转录本的特征结果。最短路径分析显示，在纤维素降解条件下上调的CAZymes与两类调控因子关联最为紧密，同时本研究发现了这类信号通路间的全新靶标。
尽管本次评估的哈茨木霉菌株在系统发育上亲缘关系较近，且与XYR1和CRE1相关的氨基酸序列相似度极高，但与xyr1及cre1相关的转录本集合却存在差异，表明各哈茨木霉菌株针对纤维素降解采用了特异性的调控策略。更值得关注的是，本研究结果暗示在本次评估的哈茨木霉菌株中，XYR1与CRE1可间接调控纤维素降解相关蛋白的编码基因。深入理解真菌纤维素降解过程中的基础生物学特性，有助于将其酶类应用于多种生物技术场景，同时也为进一步研究同一物种内不同菌株间的差异奠定了基础。