Transcription analysis using high-density micro-arrays of Aspergillus nidulans wild-type and creA mutant during growth on glucose or ethanol

Here, we describe how the recently published Aspergillus nidulans genome sequence [Galagan, J.E., Calvo, S.E., Cuomo, C., Li-Jun, M., Wortman, J.R., et al., 2005. Sequencing of Aspergillus nidulans and comparative analysis with A. fumigatus and A. oryzae. Nature 438 (7071), 1105–1115] was used to design a high-density oligo array with probes for 3278 selected genes using the Febit Geniom® One array system. For this purpose, the program OligoWiz II was used to design 24,125 probes to cover the 3278 selected genes. Subsequently, the Febit system was used to investigate carbon catabolite repression by comparing the gene expression of a creA deleted mutant strain with a reference strain grown either with glucose or ethanol as the sole carbon source. In order to identify co-regulated genes and genes influenced by either the carbon source or CreA, the most significantly regulated genes (p ⩽ 0.01) were grouped in eight clusters based on their expression profile. Analysis of the clusters allowed identification of numerous genes that are presumably not regulated by CreA, or alternatively are either directly or indirectly regulated by CreA. Surprisingly, we found evidence that more than 25% of the genes (54 out of the 200 significantly regulated) that are repressed by glucose are not completely de-repressed during growth on ethanol, as deletion of the creA resulted in increased expression of the genes in question even during growth on ethanol. Thus, the expression profiles obtained in the eight clusters indicate that the carbon catabolite repression is not a simple on/off switch but a more complex system not only dependent on the presence or absence of CreA but also on the carbon source.