The regulatory and transcriptional landscape associated with carbon utilization in a filamentous fungus

Abstract

Filamentous fungi, such asNeurospora crassa, are very efficient in deconstructing plant biomass by the secretion of an arsenal of plant cell wall-degrading enzymes, by remodeling metabolism to accommodate production of secreted enzymes, and by enabling transport and intracellular utilization of plant biomass components. Although a number of enzymes and transcriptional regulators involved in plant biomass utilization have been identified, how filamentous fungi sense and integrate nutritional information encoded in the plant cell wall into a regulatory hierarchy for optimal utilization of complex carbon sources is not understood. Here, we performed transcriptional profiling ofN. crassaon 40 different carbon sources, including plant biomass, to provide data on how fungi sense simple to complex carbohydrates. From these data, we identified regulatory factors inN. crassaand characterized one (PDR-2) associated with pectin utilization and one with pectin/hemicellulose utilization (ARA-1). Using in vitro DNA affinity purification sequencing (DAP-seq), we identified direct targets of transcription factors involved in regulating genes encoding plant cell wall-degrading enzymes. In particular, our data clarified the role of the transcription factor VIB-1 in the regulation of genes encoding plant cell wall-degrading enzymes and nutrient scavenging and revealed a major role of the carbon catabolite repressor CRE-1 in regulating the expression of major facilitator transporter genes. These data contribute to a more complete understanding of cross talk between transcription factors and their target genes, which are involved in regulating nutrient sensing and plant biomass utilization on a global level.

Effects of codon usage on gene expression are promoter context dependent

“…In contrast, non-constitutively expressed genes showed much lower correlations (Figure 1C ). For Neurospora , we analyzed mRNA-seq (FPKM > 1) results from 71 samples that were grown under different nutrient conditions ( 42 ) ( Supplementary Table S2 ). Constitutive genes were defined as those up- or down-regulated by >2-fold in fewer than seven samples.…”

CreA-mediated repression of gene expression occurs at low monosaccharide levels during fungal plant biomass conversion in a time and substrate dependent manner

“…However, this regulation is strongly carbon source dependent and predominantly occurs at the early stage of fungal growth on lignocellulose. The further comparison of CreA regulon between A. niger and A. nidulans during their growth on crude plant biomass, and the previously identified cellulose-related CreA/CRE1 regulons in Trichoderma reesei ( Antonieto et al, 2014 ), Penicillium oxalicum ( Li et al, 2015 ), and Neurospora crassa ( Sun and Glass, 2011 , Wu et al, 2020 ) showed that a common set of genes were regulated by CreA across different species. In addition, the analysis of binding sites of different TFs in promoter sequences of CreA-regulated genes revealed potential co-regulation between CreA and other important lignocellulose and starch degradation related TFs, such as XlnR ( de Vries et al, 2002a , van Peij et al, 1998 ), AraR ( Battaglia et al, 2014 , Ishikawa et al, 2018 ), RhaR ( Kowalczyk et al, 2017 ), GaaR ( Alazi et al, 2016 , Martens-Uzunova and Schaap, 2008 ) and AmyR ( Tani et al, 2001 ) associated with cellulose, hemicellulose, pectin and starch degradation.…”

Diversity of Cellulase-Producing Filamentous Fungi From Tibet and Transcriptomic Analysis of a Superior Cellulase Producer Trichoderma harzianum LZ117

“…The transcript levels of the homologue of cdt1 and cdt2 genes, Th_75576 and Th_130330 respectively, in T. harzianum LZ117 were also similar to that in K223452, so did the transcript of cltb homologous gene (Th_101977). Cre-1-mediated CCR in N. crassa acts through sugar transporter, transcription factor, sugar catabolism, and PCWDE genes to regulate plant cell wall degradation (Wu et al, 2020). In our results, down-regulation of cre1 did not correlate with enhanced expressions of the master sugar transporters such as cdt1, cdt2, which demonstrate that regulatory mechanism underlying Cre1-mediated CCR might be varied between different fungal species.…”