Transcriptome analysis of Aspergillus niger xlnR and xkiA mutants grown on corn Stover and soybean hulls reveals a highly complex regulatory network

Abstract

BackgroundEnzymatic plant biomass degradation by fungi is a highly complex process and one of the leading challenges in developing a biobased economy. Some industrial fungi (e.g. Aspergillus niger) have a long history of use with respect to plant biomass degradation and for that reason have become ‘model’ species for this topic. A. niger is a major industrial enzyme producer that has a broad ability to degrade plant based polysaccharides. A. niger wild-type, the (hemi-)cellulolytic regulator (xlnR) and xylulokinase (xkiA1) mutant strains were grown on a monocot (corn stover, CS) and dicot (soybean hulls, SBH) substrate. The xkiA1 mutant is unable to utilize the pentoses D-xylose and L-arabinose and the polysaccharide xylan, and was previously shown to accumulate inducers for the (hemi-)cellulolytic transcriptional activator XlnR and the arabinanolytic transcriptional activator AraR in the presence of pentoses, resulting in overexpression of their target genes. The xlnR mutant has reduced growth on xylan and down-regulation of its target genes. The mutants therefore have a similar phenotype on xylan, but an opposite transcriptional effect. D-xylose and L-arabinose are the most abundant monosaccharides after D-glucose in nearly all plant-derived biomass materials. In this study we evaluated the effect of the xlnR and xkiA1 mutation during growth on two pentose-rich substrates by transcriptome analysis.ResultsParticular attention was given to CAZymes, metabolic pathways and transcription factors related to the plant biomass degradation. Genes coding for the main enzymes involved in plant biomass degradation were down-regulated at the beginning of the growth on CS and SBH. However, at a later time point, significant differences were found in the expression profiles of both mutants on CS compared to SBH.ConclusionThis study demonstrates the high complexity of the plant biomass degradation process by fungi, by showing that mutant strains with fairly straightforward phenotypes on pure mono- and polysaccharides, have much less clear-cut phenotypes and transcriptomes on crude plant biomass.

Effect of Oligosaccharide Degree of Polymerization on the Induction of Xylan-Degrading Enzymes by Fusarium oxysporum f. sp. Lycopersici

“…Hence, the concentration of the compound also dictates whether it acts as inducer or not. This was confirmed in A. niger , whereby a low concentration of d -xylose induced xylanases, whereas a higher one repressed them through CreA [ 48 ]. CreA is a C2H2 finger domain that functions as a transcription repressor of CAZymes in filamentous fungi, such as A. niger and Aspergillus nidulans [ 49 , 50 ].…”

The Transcription Factor VpxlnR Is Required for the Growth, Development, and Virulence of the Fungal Pathogen Valsa pyri

“…The main functions of xlnR orthologues in Aspergillus spp. are to regulate xylose and other polysaccharides ( van Peij et al, 1998 ; Hasper et al, 2004 ; Noguchi et al, 2011 ; Ishikawa et al, 2018 ; Khosravi et al, 2019 ). However, AnxlnR was not involved in glucose or sucrose utilization.…”

Isolation of Potential Extracellular Cellulase Producer and Determination of Cellulase Production Efficiency with Various Raw Substrates

“…According to the carbohydrate active enzymes database (CAZy) all cellulase are found in 12 GH families. 12,13 Main five types of cellulase are endocellulase (EC 3.2.1.4), exocellulase (EC 3.2.1.91), cellobiases (EC 3.2.1.21), oxidative cellulases and cellulose phosphorylases. Each of these five cellulases carries out a specific type of degradation reaction.…”