BackgroundLignocellulolytic fungal cells suffer endoplasmic reticulum (ER) stress during lignocellulase synthesis; however, an understanding of this integrated process on a genome-wide scale remains poor. Here, we undertook a systematic investigation of this process in Neurospora crassa (N. crassa) using transcriptomic analysis coupled with genetic screens.ResultsA set of 766 genes was identified as the ER stress response targets (ESRTs) in N. crassa under cellulose utilization conditions. Among these, the expression of 223 and 186 genes showed dependence on IRE-1 and HAC-1, respectively. A total of 527 available mutants for ESRT genes were screened, 249 of which exhibited ER stress susceptibility, including 100 genes with unknown function. Disruption of ire-1 or hac-1 in N. crassa did not affect transcriptional induction of lignocellulase genes by cellulose but severely affected secretion of the corresponding enzymes. A global investigation of transcription factors (TFs) discovered three novel regulators (RES-1, RES-2, RRG-2) involved in lignocellulase secretion. Production of lignocellulases in Δres-1 increased by more than 30% in comparison to wild type (WT), while secretion decreased by nearly 30% in strains Δres-2 and Δrrg-2. Transcriptional profiling of the three TF mutants suggests they are deeply involved in lignocellulase secretion and ER stress response.ConclusionsHere, we determined the transcriptional scope of the ER stress response during lignocellulase synthesis in the model cellulolytic fungus N. crassa. Through genome-wide mutant screening and analysis, dozens of novel genes were discovered to be involved in the process. The findings of this work will be useful for strain improvement to facilitate lignocellulase and biomass-based chemical production.Electronic supplementary materialThe online version of this article (doi:10.1186/s13068-015-0248-5) contains supplementary material, which is available to authorized users.

Heterochromatin is a distinctive chromatin structure that is essential for chromosome segregation, genome stability and regulation of gene expression. H3K9 methylation (H3K9me), a hallmark of heterochromatin, is deposited by the Su(var)3-9 family of proteins; however, the mechanism by which H3K9 methyltransferases bind and methylate the nucleosome is poorly understood. In this work we determined the interaction of Clr4, the fission yeast H3K9 methyltransferase, with nucleosomes using nuclear magnetic resonance, biochemical and genetic assays. Our study shows that the Clr4 chromodomain binds the H3K9me3 tail and that both, the chromodomain and the disordered region connecting the chromodomain and the SET domain, bind the nucleosome core. We show that interaction of the disordered region with the nucleosome core is independent of H3K9me and contributes to H3K9me in vitro and in vivo. Moreover, we show that those interactions with the nucleosome core are contributing to de novo deposition of H3K9me and to establishment of heterochromatin.

Fungal degradation of lignocellulosic biomass requires various (hemi-)cellulases and is an important part of the natural carbon cycle.Although induction of cellulases has been described for some saprobic filamentous fungi, the regulation of cellulase transcription is complex and many aspects are still poorly understood. Here, we identified and characterized the novel cellulase regulation factor NcCLR-4 in Neurospora crassa and its ortholog MtCLR-4 in Myceliophthora thermophila. Deletion of CLR-4 resulted in similarly defective cellulolytic enzyme production and activities. Transcriptome analyses of ΔNcclr-4/ΔMtclr-4 revealed the downregulation of genes encoding (hemi-)cellulases and pivotal regulators (clr-1, clr-2 and xyr-1) and key genes in the cAMP signaling pathway such as adenylate cyclase Nccr-1. Intracellular cAMP levels were markedly lower in ΔNcclr-4/ΔMtclr-4 than in wildtype during cellulose utilization. In electrophoretic mobility shift (EMSA) and DNase I footprinting assays, NcCLR-4/MtCLR-4 can directly bound to the promoters of Nccr-1/Mtcr-1 (encoding adenylyl cyclase). EMSAs also demonstrated that NcCLR-4/ MtCLR-4 could directly bound to clr-1 (encoding a key cellulase regulator), Mtclr-2 and Mtxyr-1 (encoding biomass deconstruction regulators). These findings about the novel cellulase expression regulators NcCLR-4 and MtCLR-4 enrich our understanding of how cellulose degradation is regulated and provide new targets for engineering fungi to deconstruct plant biomass in biorefineries.