Deletion of the epigenetic regulator GcnE in Aspergillus niger FGSC A1279 activates the production of multiple polyketide metabolites

Epigenetic modification is an important regulatory mechanism in the biosynthesis of secondary metabolites in Aspergillus species, which have been considered to be the treasure trove of new bioactive secondary metabolites. In this study, we reported that deletion of the epigenetic regulator gcnE, a histone acetyltransferase in the SAGA/ADA complex, resulted in the production of 12 polyketide secondary metabolites in A. niger FGSC A1279, which was previously not known to produce toxins or secondary metabolites. Chemical workup and structural elucidation by 1D/2D NMR and high resolution electrospray ionization mass (HR-ESIMS) yielded the novel compound nigerpyrone (1) and five known compounds: carbonarone A (2), pestalamide A (3), funalenone (4), aurasperone E (5), and aurasperone A (6). Based on chemical information and the literature, the biosynthetic gene clusters of funalenone (4), aurasperone E (5), and aurasperone A (6) were located on chromosomes of A. niger FGSC A1279. This study found that inactivation of GcnE activated the production of secondary metabolites in A. niger. The biosynthetic pathway for nigerpyrone and its derivatives was identified and characterized via gene knockout and complementation experiments. A biosynthetic model of this group of pyran-based fungal metabolites was proposed. [Abstract copyright: Crown Copyright © 2018. Published by Elsevier GmbH. All rights reserved.

Truncation of the transcriptional repressor protein Cre1 in Trichoderma reesei Rut-C30 turns it into an activator

Abstract Background The filamentous fungus Trichoderma reesei (T. reesei) is a natural producer of cellulolytic and xylanolytic enzymes and is therefore industrially used. Many industries require high amounts of enzymes, in particular cellulases. Strain improvement strategies by random mutagenesis yielded the industrial ancestor strain Rut-C30. A key property of Rut-C30 is the partial release from carbon catabolite repression caused by a truncation of the repressor Cre1 (Cre1-96). In the T. reesei wild-type strain a full cre1 deletion leads to pleiotropic effects and strong growth impairment, while the truncated cre1-96 enhances cellulolytic activity without the effect of growth deficiencies. However, it is still unclear which function Cre1-96 has in Rut-C30. Results In this study, we deleted and constitutively expressed cre1-96 in Rut-C30. We found that the presence of Cre1-96 in Rut-C30 is crucial for its cellulolytic and xylanolytic performance under inducing conditions. In the case of the constitutively expressed Cre1-96, the cellulase activity could further be improved approximately twofold. The deletion of cre1-96 led to growth deficiencies and morphological abnormalities. An in silico domain prediction revealed that Cre1-96 has all necessary properties that a classic transactivator needs. Consequently, we investigated the cellular localization of Cre1-96 by fluorescence microscopy using an eYFP-tag. Cre1-96 is localized in the fungal nuclei under both, inducing and repressing conditions. Furthermore, chromatin immunoprecipitation revealed an enrichment of Cre1-96 in the upstream regulatory region of the main transactivator of cellulases and xylanases, Xyr1. Interestingly, transcript levels of cre1-96 show the same patterns as the ones of xyr1 under inducing conditions. Conclusions The findings suggest that the truncation turns Cre1 into an activating regulator, which primarily exerts its role by approaching the upstream regulatory region of xyr1. The conversion of repressor proteins to potential activators in other biotechnologically used filamentous fungi can be applied to increase their enzyme production capacities

KdmB, a Jumonji Histone H3 Demethylase, Regulates Genome-Wide H3K4 Trimethylation and Is Required for Normal Induction of Secondary Metabolism in Aspergillus nidulans.

Histone posttranslational modifications (HPTMs) are involved in chromatin-based regulation of fungal secondary metabolite biosynthesis (SMB) in which the corresponding genes-usually physically linked in co-regulated clusters-are silenced under optimal physiological conditions (nutrient-rich) but are activated when nutrients are limiting. The exact molecular mechanisms by which HPTMs influence silencing and activation, however, are still to be better understood. Here we show by a combined approach of quantitative mass spectrometry (LC-MS/MS), genome-wide chromatin immunoprecipitation (ChIP-seq) and transcriptional network analysis (RNA-seq) that the core regions of silent A. nidulans SM clusters generally carry low levels of all tested chromatin modifications and that heterochromatic marks flank most of these SM clusters. During secondary metabolism, histone marks typically associated with transcriptional activity such as H3 trimethylated at lysine-4 (H3K4me3) are established in some, but not all gene clusters even upon full activation. KdmB, a Jarid1-family histone H3 lysine demethylase predicted to comprise a BRIGHT domain, a zinc-finger and two PHD domains in addition to the catalytic Jumonji domain, targets and demethylates H3K4me3 in vivo and mediates transcriptional downregulation. Deletion of kdmB leads to increased transcription of about ~1750 genes across nutrient-rich (primary metabolism) and nutrient-limiting (secondary metabolism) conditions. Unexpectedly, an equally high number of genes exhibited reduced expression in the kdmB deletion strain and notably, this group was significantly enriched for genes with known or predicted functions in secondary metabolite biosynthesis. Taken together, this study extends our general knowledge about multi-domain KDM5 histone demethylases and provides new details on the chromatin-level regulation of fungal secondary metabolite production

KdmA, a histone H3 demethylase with bipartite function, differentially regulates primary and secondary metabolism in Aspergillus nidulans

Aspergillus nidulans kdmA encodes a member of the KDM4 family of jumonji histone demethylase proteins, highly similar to metazoan orthologues both within functional domains and in domain architecture. This family of proteins exhibits demethylase activity towards lysines 9 and 36 of histone H3 and plays a prominent role in gene expression and chromosome structure in many species. Mass spectrometry mapping of A. nidulans histones revealed that around 3% of bulk histone H3 carried trimethylated H3K9 (H3K9me3) but more than 90% of histones carried either H3K36me2 or H3K36me3. KdmA functions as H3K36me3 demethylase and has roles in transcriptional regulation. Genetic manipulation of KdmA levels is tolerated without obvious effect in most conditions, but strong phenotypes are evident under various conditions of stress. Transcriptome analysis revealed that - in submerged early and late cultures - between 25% and 30% of the genome is under KdmA influence respectively. Transcriptional imbalance in the kdmA deletion mutant may contribute to the lethal phenotype observed upon exposure of mutant cells to low-density visible light on solid medium. Although KdmA acts as transcriptional co-repressor of primary metabolism genes, it is required for full expression of several genes involved in biosynthesis of secondary metabolites

Impact of a Novel PagR-like Transcriptional Regulator on Cereulide Toxin Synthesis in Emetic Bacillus cereus

The emetic type of foodborne disease caused by Bacillus cereus is produced by the small peptide toxin cereulide. The genetic locus encoding the Ces nonribosomal peptide synthetase (CesNRPS) multienzyme machinery is located on a 270 kb megaplasmid, designated pCER270, which shares its backbone with the Bacillus anthracis toxin plasmid pXO1. Although the ces genes are plasmid-borne, the chromosomally encoded pleiotropic transcriptional factors CodY and AbrB are key players in the control of ces transcription. Since these proteins only repress cereulide synthesis during earlier growth phases, other factors must be involved in the strict control of ces expression and its embedment in the bacterial life cycle. In silico genome analysis revealed that pCER270 carries a putative ArsR/SmtB family transcription factor showing high homology to PagR from B. anthracis. As PagR plays a crucial role in the regulation of the protective antigen gene pagA, which forms part of anthrax toxin, we used a gene-inactivation approach, combined with electrophoretic mobility shift assays and a bacterial two-hybrid system for dissecting the role of the PagR homologue PagRBc in the regulation of cereulide synthesis. Our results highlight that the plasmid-encoded transcriptional regulator PagRBc plays an important role in the complex and multilayered process of cereulide synthesis

Levels of H3K4me3 are increased in <i>kdmBΔ</i> histones.

<p>MS/MS Base Peak Chromatograms (BPC) of tryptic histone digests analysing peptides T₃-R₈ of histone H3 show the different variants of methylated K4 and their ratios in the wild type (WT) and the <i>kdmBΔ</i> strain.</p

The catalytic domain of JMJD2 and JARID- JmjC family demethylases.

<p><b>A</b>. Sequence alignment of JmjC domains of JMJD2 and JARID demethylases from human (Hs), <i>A</i>. <i>nidulans</i> (An) and <i>S</i>. <i>cerevisiae</i> (Sc). Conserved residues responsible for the catalytic activity are marked in yellow (α-ketoglutarate binding site) and blue (Fe²⁺ binding site). Specificity-determining residues for H3K9K36me2/3 are marked in green [<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1006222#pgen.1006222.ref061" target="_blank">61</a>, <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1006222#pgen.1006222.ref062" target="_blank">62</a>]. <b>B</b>. Domain composition of JARID group H3K4me2/3 demethylases from human, <i>A</i>. <i>nidulans</i> and <i>S</i>. <i>cerevisiae</i>. KdmB possesses conserved histidine and glutamate as well as phenylalanine, asparagine and lysine residues responsible for Fe²⁺ ion chelating and α-ketoglutarate binding respectively, which are found in all catalytically active JmjC demethylases.</p

H3K4me3 localizes to actively transcribed genes.

<p><b>A.</b> The metaplot depicts the enrichment pattern of H3K4 trimethylation (H3K4me3), H3K36 trimethylation (H3K36me3), and H3K9/K14 acetylation (H3Ac) for all genes on chromosome 4 in wild type actively growing cells (17h cultures). All genes are aligned to the predicted ATG (position 0) and analysed for a 2 kb window starting with 500 bp of their 5´UTR and promoter sequences (-500) followed by 1500 bp of their coding region (indicated positions within coding region 500, 1000 and 1500 bp). Counts were binned in 10-bp windows and averaged. <b>B.</b> The scatter plots shows the relationship between the average expression level and H3K4me3 enrichment. Values on the x-axis represent the average expression level of each gene determined by RNA-seq from both 17 and 48h cultures (see <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1006222#sec012" target="_blank">methods</a>; log₂ RPKM). On the y axis, normalized and H3K4me3 levels averaged over the whole gene (log₂ RPKM) are shown for each of these genes. Grey dots represent constitutively expressed genes), and genes differentially expressed in the two tested conditions (with a p-value of p ≤0.001) are represented as black or red dots where the latter indicate differentially expressed genes involved in SM biosynthesis.</p

Genome viewer image presenting the chromatin landscape of chromosome IV in wild type (WT) and <i>kdmB</i> deletion (<i>kdmB</i>Δ) cells grown in liquid shake cultures for 17 hours (primary metabolism).

<p>RNA-seq represents transcriptional activity of the locus. A control ChIP (No Antibody) was performed to detect non-specific ChIP-seq signals.</p