title: A trispecies Aspergillus microarray: comparative transcriptomics of three Aspergillus species.
abstract: The full-genome sequencing of the filamentous fungi Aspergillus nidulans, Aspergillus niger, and Aspergillus oryzae has opened possibilities for studying the cellular physiology of these fungi on a systemic level. As a tool to explore this, we are making available an Affymetrix GeneChip developed for transcriptome analysis of any of the three above-mentioned aspergilli. Transcriptome analysis of triplicate batch cultivations of all three aspergilli on glucose and xylose media was used to validate the performance of the microarray. Gene comparisons of all three species and cross-analysis with the expression data identified 23 genes to be a conserved response across Aspergillus sp., including the xylose transcriptional activator XlnR. A promoter analysis of the up-regulated genes in all three species indicates the conserved XlnR-binding site to be 5'-GGNTAAA-3'. The composition of the conserved gene-set suggests that xylose acts as a molecule, indicating the presence of complex carbohydrates such as hemicellulose, and triggers an array of degrading enzymes. With this case example, we present a validated tool for transcriptome analysis of three Aspergillus species and a methodology for conducting cross-species evolutionary studies within a genus using comparative transcriptomics.
authors.affiliation: Center for Microbial Biotechnology, BioCentrum-DTU, Technical University of Denmark, DK-2800 Kgs Lyngby, Denmark.
authors.forename: Mikael R
authors.initials: MR
authors.lastname: Andersen
authors.forename: Wanwipa
authors.initials: W
authors.lastname: Vongsangnak
authors.forename: Gianni
authors.initials: G
authors.lastname: Panagiotou
authors.forename: Margarita P
authors.initials: MP
authors.lastname: Salazar
authors.forename: Linda
authors.initials: L
authors.lastname: Lehmann
authors.forename: Jens
authors.initials: J
authors.lastname: Nielsen
mesh_terms: D001230:Aspergillus / Q000145:classification* / Q000235:genetics* / Q000378:metabolism; D015536:Down-Regulation; D005656:Fungal Proteins / Q000235:genetics / Q000378:metabolism; D020869:Gene Expression Profiling; D015966:Gene Expression Regulation, Fungal; D020411:Oligonucleotide Array Sequence Analysis; D015534:Trans-Activators / Q000235:genetics / Q000378:metabolism; D015854:Up-Regulation
chemical_list: D005656:Fungal Proteins; D015534:Trans-Activators; C115443:XlnR protein, Aspergillus