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

Abstract

BackgroundThe 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 ΔxlnR, ΔaraR, ΔamyR, ΔrhaR and ΔgalX that were grown on their specific inducing compounds.ResultsThe 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.ConclusionsExpression 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.Electronic supplementary materialThe online version of this article (10.1186/s12864-017-4164-x) contains supplementary material, which is available to authorized users.

Colonies of the fungus Aspergillus niger are highly differentiated to adapt to local carbon source variation

“…The part of the colony exposed to WB displayed the highest xylanase expression and production Hemicellulolytic and cellulolytic transcripts and enzymes are activated by the transcriptional activator XlnR in response to the presence of D-xylose in A. niger (Gruben et al, 2017), which is an abundant building block of the WB xylan (Table 1). The total expression of these transcripts in W2 was approximately fivefold higher than in S2 or G2 (Fig.…”

“…GO terms were considered enriched when P value <0.05, the number of A. niger proteins annotated with the GO term >2 and the number of proteins annotated with the GO term in the list of significantly higher or lower expressed or transcripts >1. The PBD CAZy substrate and enzyme annotations were based on the studies by Benoit et al (2015b), Gruben et al (2017), and Kowalczyk et al (2017)).…”

Evolutionary adaptation of Aspergillus niger for increased ferulic acid tolerance

“…The function of the induced LPMOs have not been characterized, however, it has been shown that LPMOs from AA9 catalyze oxidative cleavage of b-(1-4)-xylosyl bonds in xylan and b-(1-4)-glucosyl bonds in cellulose (Frommhagen et al 2015(Frommhagen et al , 2017Brenelli et al 2018). Both induced LPMOs have been predicted to act on cellulose (Borin et al 2017) and one of them (NRRL3_3929) has been suggested to be regulated by AraR (Gruben et al 2017). The transcriptional profile of the FAE encoding genes correlated with previous observations (de Vries et al 2002;Dilokpimol et al 2017).…”

Mutation of a Conserved Alanine Residue in Transcription Factor AraR Leads to Hyperproduction of α‐l‐Arabinofuranosidases in Penicillium oxalicum

“…Deletion of araR dramatically reduced the α‐ l ‐arabinofuranosidase activity of A. niger and the transcription abundances of α‐L‐arabinofuranosidase–encoding genes . Another transcription factor XlnR, which is a close homolog of AraR, controls not only the expression of xylanolytic genes but also the expression of some α‐ l ‐arabinofuranosidase genes . In addition, AraR and XlnR activate the expression of genes in the pentose catabolic pathway and participate in the control of genes in the pentose phosphate pathway, the oxidoreductive d ‐galactose catabolic pathway, and pectin degradation …”