Meeting a Challenge: A View on Studying Transcriptional Control of Genes Involved in Plant Biomass Degradation in Aspergillus niger

Since the rapid developments in genome sequencing and transcriptome analysis technologies, the approaches to study the regulation of gene expression have tremendously changed. Whereas forward genetic screens have remained the most informative approaches, genome- and transcriptome-based methods have completely circumpassed more classical approaches in this field such as genetic linkage analysis and gene complementation studies. Functional analysis of gene regulation has enormously benefited from new gene knockout and overexpression strategies, most notably those based on nonhomologous end joining (NHEJ) mutants and CRISPR-cas technology. Also regarding transcriptional regulation of gene expression, new technologies, in particular RNAseq analysis, have completely taken over earlier transcript analysis methods like northern analysis and microarrays. With a combination of these new technologies, we have been able to address one of the challenges in fungal gene regulation, i.e., transcriptional control of pectin utilization in Aspergillus niger. Pectin degradation is an inherently complex system involving multiple different enzymatic activities, and traditional approaches have not led to the identification of the key factors involved in pectin degradation. However, using a combination of forward genetic screens, genome resequencing of mutant strains and targeted knockout, and overexpression strategies, followed by RNAseq-based transcriptome analysis, allowed the identification of two transcription factor genes, GaaR and GaaX. GaaR is a canonical Zn(II)2Cys6 transcriptional activator, whereas GaaX is a transcriptional repressor interacting with GaaR. Together, GaaR and GaaX consist of one of the more complex transcriptional regulation modules found in A. niger to date. However, genome mining has discovered the presence of similar paralogous modules in A. niger and many other fungi.