Transcriptome analysis of A. nidulans growing in different carbon sources

Aspergillus nidulans is a model organism for aspergilli, an important group of filamentous fungi that encompasses human and plant pathogens, as well as industrial cell factories. Aspergilli have a highly diversified metabolism and both in connection with their biotechnological application as well as their interaction with other cells (humans or plants), it is valuable to understand how their metabolism is regulated. We therefore performed genome-wide transcription analysis of A. nidulans grown on three different carbon sources (glucose, glycerol, and ethanol) with the objective to identify global regulatory structures. We furthermore reconstructed the complete metabolic network of this organism, and this resulted in linking of 666 genes with metabolic functions, as well as assigning metabolic roles to 472 genes that had not been annotated earlier. Through combinations of the reconstructed metabolic network and the transcription data, we identified subnetwork structures that pointed to coordinated regulation of genes involved in many different parts of the metabolism. Keywords: carbon sources, metabolism, comparative genomics Aspergillus was grown in three different carbon sources - glucose, ethanol and glycerol. Cultivations were run in triplicate, and each biological replicate was load on a different chip. Therefore, we analyzed nine arrays (3 carbon sources x 3 biological replicates).

构巢曲霉（Aspergillus nidulans）是曲霉属（Aspergillus）的模式生物，曲霉属是一类重要的丝状真菌类群，既包含人类与植物致病菌，也涵盖工业细胞工厂。曲霉属物种的代谢多样性极高，无论从其生物技术应用场景，还是其与人类、植物细胞的互作关系出发，解析其代谢调控机制均具有重要研究价值。
为此，我们对以三种不同碳源（葡萄糖、甘油及乙醇）培养的构巢曲霉开展了全基因组转录分析，旨在识别其全局调控网络结构。此外，我们还重构了该物种的完整代谢网络，最终将666个基因与代谢功能建立关联，并为此前未被注释的472个基因赋予了代谢功能定位。通过整合重构的代谢网络与转录组数据，我们识别出多个子网络结构，这些结构提示代谢多个通路中的基因存在协同调控现象。
关键词：碳源、代谢、比较基因组学
本实验以三种不同碳源（葡萄糖、乙醇及甘油）培养构巢曲霉。所有培养均设置三次生物学重复，且每个生物学重复样本均加载至不同的基因芯片。因此，我们共分析了9组芯片数据（3种碳源 × 3次生物学重复）。