TNO Quality of Life, Zeist, The Netherlands.
Fungal Genet Biol. 2010 Jun;47(6):539-50. doi: 10.1016/j.fgb.2010.03.005. Epub 2010 Mar 27.
The fungus Aspergillus niger has been studied in considerable detail with respect to various industrial applications. Although its central metabolic pathways are established relatively well, the mechanisms that control the adaptation of its metabolism are understood rather poorly. In this study, clustering of co-expressed genes has been performed on the basis of DNA microarray data sets from two experimental approaches. In one approach, low amounts of inducer caused a relatively mild perturbation, while in the other approach the imposed environmental conditions including carbon source starvation caused severe perturbed stress. A set of conserved genes was used to construct gene co-expression networks for both the individual and combined data sets. Comparative analysis revealed the existence of modules, some of which are present in all three networks. In addition, experimental condition-specific modules were identified. Module-derived consensus expression profiles enabled the integration of all protein-coding A. niger genes to the co-expression analysis, including hypothetical and poorly conserved genes. Conserved sequence motifs were detected in the upstream region of genes that cluster in some modules, e.g., the binding site for the amino acid metabolism-related transcription factor CpcA as well as for the fatty acid metabolism-related transcription factors, FarA and FarB. Moreover, not previously described putative transcription factor binding sites were discovered for two modules: the motif 5'-CGACAA is overrepresented in the module containing genes encoding cytosolic ribosomal proteins, while the motif 5'-GGCCGCG is overrepresented in genes related to 'gene expression', such as RNA helicases and translation initiation factors.
黑曲霉（Aspergillus niger）的各种工业应用已得到相当详细的研究。尽管其中心代谢途径已经相对较好地建立，但控制其代谢适应的机制理解得相当差。在这项研究中，基于两个实验方法的 DNA 微阵列数据集进行了共表达基因聚类。在一种方法中，少量诱导剂引起相对温和的扰动，而在另一种方法中，所施加的环境条件包括碳源饥饿会导致严重的扰动应激。一组保守基因用于构建两个单独和组合数据集的基因共表达网络。比较分析揭示了模块的存在，其中一些存在于所有三个网络中。此外，还确定了特定于实验条件的模块。模块衍生的共识表达谱使所有编码 A. niger 的蛋白质编码基因都可以整合到共表达分析中，包括假设和保守性较差的基因。在某些模块中聚类的基因的上游区域中检测到保守的序列基序，例如与氨基酸代谢相关的转录因子 CpcA 以及与脂肪酸代谢相关的转录因子 FarA 和 FarB 的结合位点。此外，还发现了两个模块中以前未描述的假定转录因子结合位点：在包含编码细胞质核糖体蛋白的基因的模块中，5'-CGACAA 基序过度表达，而在与“基因表达”相关的基因中，如 RNA 解旋酶和翻译起始因子，5'-GGCCGCG 基序过度表达。
