Table_7_Weighted Gene Co-expression Network Analysis Identifies Critical Genes for the Production of Cellulase and Xylanase in Penicillium oxalicum.DOCX

Genes involved in cellular processes undergo environment-dependent co-regulation, but the co-expression patterns of fungal cellulase and xylanase-encoding genes remain unclear. Here, we identified two novel carbon sources, methylcellulose and 2-hydroxyethyl cellulose, which efficiently induced the secretion of cellulases and xylanases in Penicillium oxalicum. Comparative transcriptomic analyses identified carbon source-specific transcriptional patterns, mainly including major cellulase and xylanase-encoding genes, genes involved in glycolysis/gluconeogenesis and the tricarboxylic acid cycle, and genes encoding transcription factors, transporters and G protein-coupled receptors. Moreover, the weighted correlation network analysis of time-course transcriptomes, generated 17 highly connected modules. Module MEivory, comprising 120 members, included major cellulase and xylanase-encoding genes, genes encoding the key regulators PoxClrB and PoxXlnR, and a cellodextrin transporter POX06051/CdtC, which were tightly correlated with the filter-paper cellulase, carboxymethylcellulase and xylanase activities in P. oxalicum. An expression kinetic analysis indicated that members in MEivory were activated integrally by carbon sources, but their expressional levels were carbon source- and/or induction duration-dependent. Three uncharacterized regulatory genes in MEivory were identified, which regulate the production of cellulases and xylanases in P. oxalicum. These findings provide insights into the mechanisms associated with the synthesis and secretion of fungal cellulases and xylanases, and a guide for P. oxalicum application in biotechnology.

参与细胞生命活动的基因存在环境依赖性的共调控现象，但目前真菌纤维素酶（cellulase）与木聚糖酶（xylanase）编码基因的共表达模式仍未明确。本研究鉴定出两种新型碳源（carbon source）——甲基纤维素（methylcellulose）与2-羟乙基纤维素（2-hydroxyethyl cellulose），二者可在草酸青霉（Penicillium oxalicum）中高效诱导纤维素酶与木聚糖酶的分泌。通过比较转录组分析（comparative transcriptomic analyses），我们鉴定出碳源特异性的转录谱特征，主要涵盖核心纤维素酶与木聚糖酶编码基因、参与糖酵解/糖异生（glycolysis/gluconeogenesis）及三羧酸循环（tricarboxylic acid cycle）的基因，以及编码转录因子、转运蛋白与G蛋白偶联受体（G protein-coupled receptors）的基因。此外，对时间序列转录组（time-course transcriptomes）开展加权共表达网络分析（weighted correlation network analysis），共得到17个高度连通的基因模块。其中包含120个成员的MEivory模块，涵盖核心纤维素酶与木聚糖酶编码基因、关键调控因子PoxClrB和PoxXlnR的编码基因，以及纤维二糖转运蛋白（cellodextrin transporter）POX06051/CdtC的编码基因；该模块的基因表达水平与草酸青霉的滤纸纤维素酶（filter-paper cellulase）、羧甲基纤维素酶（carboxymethylcellulase）及木聚糖酶活性显著相关。表达动力学分析（expression kinetic analysis）结果显示，MEivory模块的所有成员均可被碳源整体激活，但其表达水平受碳源种类和/或诱导时长的调控。我们在该模块中鉴定出3个未被功能注释的调控基因（uncharacterized regulatory genes），它们可调控草酸青霉的纤维素酶与木聚糖酶合成。本研究结果为解析真菌纤维素酶与木聚糖酶的合成与分泌机制提供了新的理论见解，同时为草酸青霉在生物技术领域的应用提供了重要指导。