Journal Article

Expression-based clustering of CAZyme-encoding genes of Aspergillus niger

De Vries, Ronald P., Gruben, Birgit S., Mäkelä, Miia R., Kowalczyk, Joanna E., Zhou, Miaomiao, Benoit-Gelber, Isabelle

2017

Overview

Background The Aspergillus niger genome contains a large repertoire of genes encoding carbohydrate active enzymes (CAZymes) that are targeted to plant polysaccharide degradation enabling A. niger to grow on a wide range of plant biomass substrates. Which genes need to be activated in certain environmental conditions depends on the composition of the available substrate. Previous studies have demonstrated the involvement of a number of transcriptional regulators in plant biomass degradation and have identified sets of target genes for each regulator. In this study, a broad transcriptional analysis was performed of the A. niger genes encoding (putative) plant polysaccharide degrading enzymes. Microarray data focusing on the initial response of A. niger to the presence of plant biomass related carbon sources were analyzed of a wild-type strain N402 that was grown on a large range of carbon sources and of the regulatory mutant strains Δ xlnR , Δ araR , Δ amyR , Δ rhaR and Δ galX that were grown on their specific inducing compounds. Results The cluster analysis of the expression data revealed several groups of co-regulated genes, which goes beyond the traditionally described co-regulated gene sets. Additional putative target genes of the selected regulators were identified, based on their expression profile. Notably, in several cases the expression profile puts questions on the function assignment of uncharacterized genes that was based on homology searches, highlighting the need for more extensive biochemical studies into the substrate specificity of enzymes encoded by these non-characterized genes. The data also revealed sets of genes that were upregulated in the regulatory mutants, suggesting interaction between the regulatory systems and a therefore even more complex overall regulatory network than has been reported so far. Conclusions Expression profiling on a large number of substrates provides better insight in the complex regulatory systems that drive the conversion of plant biomass by fungi. In addition, the data provides additional evidence in favor of and against the similarity-based functions assigned to uncharacterized genes.

• Publisher: BioMed Central,BioMed Central Ltd,Springer Nature B.V,BMC
• Subject: AmyR / Analysis / Animal Genetics and Genomics / Aspergillus / Aspergillus niger / Biodegradation / Biomass / Biomedical and Life Sciences / Carbohydrates / Carbon / Carbon sources / CAZy genes / Cellulose / Cluster analysis / Clustering / DNA microarrays / Environmental conditions / Enzymes / Eukaryote microbial genomics / Fungi / GalX / Gene expression / Genes / Genetic aspects / Genomes / Genomics / Homology / Life Sciences / Metabolism / Microarrays / Microbial Genetics and Genomics / Physiological aspects / Plant biomass / Plant biomass degradation / Plant Genetics and Genomics / Polysaccharides / Proteomics / Regulators / Research Article / Substrate specificity / Substrates / Target recognition / Transcription / Transcriptional regulators / XlnR