Analysis of gene expression in Aspergillus niger using microarray technology

Aspergillus niger is an important industrial fungus. This organism is extensively used to produce large quantities of desired proteins owing to its efficient post-translational modification and secretory systems. At present, the production of foreign proteins by A. niger uses a gene-fusion strategy that is based mainly on the glucoamylase promoter. Detailed knowledge on the global expression pattern of this organism will help us develop other expression strategies.; Here the gene transcription profile of A. niger cultured under different conditions was assessed using microarrays. Microarray technology permits the simultaneous investigation of expression levels of thousands of genes. Protocols for the microarray experiments were specifically designed, executed and data were analyzed. Samples of DNA corresponding to 1,700 genes of A. niger were printed onto coated glass slides and hybridized with cDNA probes derived from RNA extracted from cells grown under diverse conditions. The growth media were supplemented with different carbon sources: minimal medium with glucose, maltose, xylose, xylan or wheat germ and complete medium.; Two types of data were generated from these experiments: genes that are differentially expressed under different growth conditions and genes that are highly expressed under these conditions. Eighty-eight genes were found to be differentially expressed and they were grouped using hierarchical and K-means clusterings. These data allow us to draw preliminary conclusions about the A. niger transcriptome under the various culture conditions. Of the 1,700 genes, 467 were considered highly expressed. By merging with the differentially expressed gene set, a total of 39 genes were shown to display both characteristics. In future experiments, the promoter of these genes could be used to increase the heterologous protein production in A. niger .