Strategies Shaping the Transcription of Carbohydrate-Active Enzyme Genes in Aspergillus nidulans

Abstract

Understanding the coordinated regulation of the hundreds of carbohydrate-active enzyme (CAZyme) genes occurring in the genomes of fungi has great practical importance. We recorded genome-wide transcriptional changes of Aspergillus nidulans cultivated on glucose, lactose, or arabinogalactan, as well as under carbon-starved conditions. We determined both carbon-stress-specific changes (weak or no carbon source vs. glucose) and carbon-source-specific changes (one type of culture vs. all other cultures). Many CAZyme genes showed carbon-stress-specific and/or carbon-source-specific upregulation on arabinogalactan (138 and 62 genes, respectively). Besides galactosidase and arabinan-degrading enzyme genes, enrichment of cellulolytic, pectinolytic, mannan, and xylan-degrading enzyme genes was observed. Fewer upregulated genes, 81 and 107 carbon stress specific, and 6 and 16 carbon source specific, were found on lactose and in carbon-starved cultures, respectively. They were enriched only in galactosidase and xylosidase genes on lactose and rhamnogalacturonanase genes in both cultures. Some CAZyme genes (29 genes) showed carbon-source-specific upregulation on glucose, and they were enriched in β-1,4-glucanase genes. The behavioral ecological background of these characteristics was evaluated to comprehensively organize our knowledge on CAZyme production, which can lead to developing new strategies to produce enzymes for plant cell wall saccharification.

Keywords: Aspergillus nidulans; arabinogalactan; carbohydrate-active enzyme; carbon limitation; carbon starvation; sterigmatocystin production; transcriptomics; utilization of lactose.

Figure 1

Growing and metabolic activity of the studied A. nidulans THS30 cultures. Changes in the MTT-reducing activity (A) and DCM (B) of the strain were characterized in cultures growing on glucose (●), in the absence of any carbon source (○), on lactose (■), or on arabinogalactan (□). Mean ± SD values calculated from three biological replicates are presented. The MTT-reducing activity of 12 h cultures was significantly higher (Student’s t-test, p < 0.05) than that of the 4 h cultures. The DCM of the 12 h glucose, lactose, or arabinogalactan-containing cultures was significantly higher (Student’s t-test, p < 0.05) than that of the 0 h cultures. ^{g, l, a, s}—Significant difference (Student’s t-test, p < 0.05) from the data of cultures containing glucose, lactose, arabinogalactan, or no carbon source, respectively.

Figure 2

Distribution of carbon-stress-responsive (A) and culture-specific (B) genes among the cultures. Figures represent the number of upregulated/downregulated genes. Note, the three sets in (A) contain carbon-stress-responsive genes, and the intersection of the three sets contains the general stress response genes (using glucose-containing cultures as reference). The upregulated general stress response genes are identical with the downregulated glucose-specific genes and the downregulated general stress response genes are identical with the upregulated glucose-specific genes (B).

Figure 3

Distribution of carbon-stress-responsive (A) and culture-specific (B) transcription factor genes among the cultures. Figures represent the number of upregulated/downregulated transcription factor genes.

Figure 4

Production of sterigmatocystin by carbon-stressed A. nidulans THS30 cultures. A representative photo on the results of a TLC is presented. Mycelial samples were taken 12 h (carbon-stressed cultures) or 4 h (glucose-containing cultures) after the mycelia, grown on glucose, were transferred into fresh media. A—glucose-containing cultures; B—carbon-starved cultures; C—sterigmatocystin standard; D—lactose-containing cultures; E—arabinogalactan-containing cultures.