Final Report Summary - PROFITS (Bridging the world of fungi and dementia)
We also performed a gene co-expression network analysis for A. niger to functionally annotate uncharacterized genes of A. niger. Although its genome sequence is known since almost 10 years, only 2% of the predicted 14,000 genes of A. niger are characterized. Gene co-expression network analysis is based on the assumption that genes with shared expression profiles are tightly connected and are predicted to function in the same regulatory and/or functional pathway (“guilt-by-association” approach). We thus identified genes with a consistent, correlated expression pattern across ~280 microarray data covering 155 phenotypically diverse samples or experimental conditions for A. niger. The functional modules predicted by the gene co-expression network for the 14,000 genes of A. niger were investigated for gene content and validated based on published data for the function of known secretory pathway genes. These analyses supported the biological relevance of these modules, suggesting that the co-expression network obtained presents a valuable predictive tool for functional annotation of A. niger genes.
In addition to this in silico meta-analysis of trancriptomic data for A. niger, the PROFITS projects aimed at establishing and analyzing specific secretion stress transcriptome data by forced expression of AD related proteins and peptides in A. niger. In doing so, the tetracycline/doxycycline-inducible TetON promoter system for A. niger was exploited and used to express the fibrillogenic amyloid peptide Aß, its precursor protein APP and the intracellular tangle forming Tau protein in A. niger. To ensure entry of Aß peptides into the secretory pathway, expression constructs were designed as such, that the Aß peptide was N-terminally fused to the glucoamylase A, serving as a carrier protein, which is a strongly secreted homologous protein of A. niger. APP and Tau proteins have not been fused to intend intracellular expression.