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.

Fig. 1.

Histograms of gene expression values. The distribution of log²-transformed gene expression values of the genes of the three Aspergillus sp. in three experiments. Each column shows an experiment where cRNA from the noted organism was hybridized to the chip. Each row shows the distribution for genes from a specific organism. The analysis was done with the statistical software R (31).

Fig. 2.

Summary of fermentation parameters. For each of the Aspergillus sp., a profile of a representative replicate is shown. (□): Sugar concentration (g/liter). (▵): Biomass concentration (g dry weight/liter). The vertical line shows the average time of sampling for transcriptome analysis. Time, sampling time for transcriptome analysis; Biomass, biomass concentration at the sampling time; μ_max, maximum specific growth rate. For all three values are shown average and standard deviation for the three replicates.

Fig. 3.

Venn diagram of differentially expressed genes. The gray circles contain the genes that are significantly differentially expressed and conserved in all three Aspergillus species. The numbers on a white background are not conserved in all three species, but still differentially expressed in a single species.