scholarly journals Histone Deacetylase Activity Regulates Chemical Diversity in Aspergillus

2007 ◽  
Vol 6 (9) ◽  
pp. 1656-1664 ◽  
Author(s):  
E. Keats Shwab ◽  
Jin Woo Bok ◽  
Martin Tribus ◽  
Johannes Galehr ◽  
Stefan Graessle ◽  
...  
Keyword(s):  
Small Molecules ◽  
Aspergillus Nidulans ◽  
Histone Deacetylase ◽  
Secondary Metabolite ◽  
Filamentous Fungi ◽  
Small Molecule ◽  
Transcriptional Activation ◽  
Hdac Inhibitors ◽  
Gene Clusters ◽  
Chemical Diversity

ABSTRACT Bioactive small molecules are critical in Aspergillus species during their development and interaction with other organisms. Genes dedicated to their production are encoded in clusters that can be located throughout the genome. We show that deletion of hdaA, encoding an Aspergillus nidulans histone deacetylase (HDAC), causes transcriptional activation of two telomere-proximal gene clusters—and subsequent increased levels of the corresponding molecules (toxin and antibiotic)—but not of a telomere-distal cluster. Introduction of two additional HDAC mutant alleles in a ΔhdaA background had minimal effects on expression of the two HdaA-regulated clusters. Treatment of other fungal genera with HDAC inhibitors resulted in overproduction of several metabolites, suggesting a conserved mechanism of HDAC repression of some secondary-metabolite gene clusters. Chromatin regulation of small-molecule gene clusters may enable filamentous fungi to successfully exploit environmental resources by modifying chemical diversity.

scholarly journals The histone deacetylase clr3 regulates secondary metabolite production and growth under oxidative stress conditions in Penicillium brasilianum

2020 ◽  
Author(s):  
Daniel Yuri Akiyama ◽  
Marina Campos Rocha ◽  
Jonas Henrique Costa ◽  
Iran Malavazi ◽  
Taícia Pacheco Fill
Keyword(s):  
Oxidative Stress ◽  
Histone Deacetylase ◽  
Secondary Metabolite ◽  
Filamentous Fungi ◽  
Gene Clusters ◽  
Stress Conditions ◽  
Biosynthetic Gene ◽  
Biosynthetic Gene Clusters ◽  
Metabolite Production ◽  
Penicillium Brasilianum

ABSTRACTMost of the biosynthetic gene clusters (BGCs) found in filamentous fungi are silent under standard laboratory cultivation conditions due to the lack of expression triggering stimuli, representing a considerable drawback in drug discovery. To access the full biosynthetic potential of these microbes, studies towards the activation of cryptic BGCs are essential. Histone acetylation status is an important regulator of chromatin structure which impacts in cell physiology and, therefore, expression of biosynthetic gene clusters in filamentous fungi. Histone deacetylases (HDACs) and histone acetyl-transferases (HATs) are responsible for maintaining and controlling this process under different cell conditions. In this study, clr3, a gene encoding a histone deacetylase in Penicillium brasilianum was deleted and associated phenotypic and metabolic changes evaluated. Results indicate reduced growth under oxidative stress conditions in the Δclr3 knockout strain. Also, the production of several secondary metabolites including austin-related meroterpenoids, brasiliamides, mycotoxins such as verruculogen and penicillic acid, as well as cyclodepsipeptides was reduced in the Δclr3 strain when compared to wild-type strain. Accordingly, addition of epigenetic modulators responsible for HDAC inhibition such as suberoylanilide hydroxamic acid (SAHA) and nicotinamide (NAA) to P. brasilianum growth media also culminated in reduction of secondary metabolite production. Mass Spectrometry Imaging (MSI) was applied to compare metabolite production and spatial distribution on the colony. Results suggest that Clr3 plays an important role in secondary metabolite biosynthesis in P. brasilianum, thus offering new strategies for regulation of natural product synthesis by assessing chromatin modification in P. brasilianum.

scholarly journals CRISPR-based transcriptional activation tool for silent genes in filamentous fungi

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
László Mózsik ◽  
Mirthe Hoekzema ◽  
Niels A. W. de Kok ◽  
Roel A. L. Bovenberg ◽  
Yvonne Nygård ◽  
...  
Keyword(s):  
Filamentous Fungi ◽  
Transcriptional Activation ◽  
Core Promoter ◽  
Crop Protection ◽  
Gene Clusters ◽  
Growth Conditions ◽  
Biosynthetic Gene ◽  
Biosynthetic Gene Clusters ◽  
Fluorescent Reporter ◽  
A Genome

AbstractFilamentous fungi are historically known to be a rich reservoir of bioactive compounds that are applied in a myriad of fields ranging from crop protection to medicine. The surge of genomic data available shows that fungi remain an excellent source for new pharmaceuticals. However, most of the responsible biosynthetic gene clusters are transcriptionally silent under laboratory growth conditions. Therefore, generic strategies for activation of these clusters are required. Here, we present a genome-editing-free, transcriptional regulation tool for filamentous fungi, based on the CRISPR activation (CRISPRa) methodology. Herein, a nuclease-defective mutant of Cas9 (dCas9) was fused to a highly active tripartite activator VP64-p65-Rta (VPR) to allow for sgRNA directed targeted gene regulation. dCas9-VPR was introduced, together with an easy to use sgRNA “plug-and-play” module, into a non-integrative AMA1-vector, which is compatible with several filamentous fungal species. To demonstrate its potential, this vector was used to transcriptionally activate a fluorescent reporter gene under the control of the penDE core promoter in Penicillium rubens. Subsequently, we activated the transcriptionally silent, native P. rubens macrophorin biosynthetic gene cluster by targeting dCas9-VPR to the promoter region of the transcription factor macR. This resulted in the production of antimicrobial macrophorins. This CRISPRa technology can be used for the rapid and convenient activation of silent fungal biosynthetic gene clusters, and thereby aid in the identification of novel compounds such as antimicrobials.

scholarly journals Deletion of the Histone Deacetylase HdaA in Endophytic Fungus Penicillium chrysogenum Fes1701 Induces the Complex Response of Multiple Bioactive Secondary Metabolite Production and Relevant Gene Cluster Expression

Molecules ◽  
2020 ◽  
Vol 25 (16) ◽  
pp. 3657 ◽  
Author(s):  
Zhuang Ding ◽  
Haibo Zhou ◽  
Xiao Wang ◽  
Huiming Huang ◽  
Haotian Wang ◽  
...  
Keyword(s):  
Histone Deacetylase ◽  
Secondary Metabolite ◽  
Endophytic Fungus ◽  
Penicillium Chrysogenum ◽  
Gene Clusters ◽  
Transcriptional Analysis ◽  
Secondary Metabolite Production ◽  
Metabolite Production ◽  
Epigenetic Regulator ◽  
Relevant Gene

Epigenetic regulation plays a critical role in controlling fungal secondary metabolism. Here, we report the pleiotropic effects of the epigenetic regulator HdaA (histone deacetylase) on secondary metabolite production and the associated biosynthetic gene clusters (BGCs) expression in the plant endophytic fungus Penicillium chrysogenum Fes1701. Deletion of the hdaA gene in strain Fes1701 induced a significant change of the secondary metabolite profile with the emergence of the bioactive indole alkaloid meleagrin. Simultaneously, more meleagrin/roquefortine-related compounds and less chrysogine were synthesized in the ΔhdaA strain. Transcriptional analysis of relevant gene clusters in ΔhdaA and wild strains indicated that disruption of hdaA had different effects on the expression levels of two BGCs: the meleagrin/roquefortine BGC was upregulated, while the chrysogine BGC was downregulated. Interestingly, transcriptional analysis demonstrated that different functional genes in the same BGC had different responses to the disruption of hdaA. Thereinto, the roqO gene, which encodes a key catalyzing enzyme in meleagrin biosynthesis, showed the highest upregulation in the ΔhdaA strain (84.8-fold). To our knowledge, this is the first report of the upregulation of HdaA inactivation on meleagrin/roquefortine alkaloid production in the endophytic fungus P. chrysogenum. Our results suggest that genetic manipulation based on the epigenetic regulator HdaA is an important strategy for regulating the productions of secondary metabolites and expanding bioactive natural product resources in endophytic fungi.

scholarly journals Accurate prediction of secondary metabolite gene clusters in filamentous fungi

2012 ◽  
Vol 110 (1) ◽  
pp. E99-E107 ◽  
Author(s):  
M. R. Andersen ◽  
J. B. Nielsen ◽  
A. Klitgaard ◽  
L. M. Petersen ◽  
M. Zachariasen ◽  
...  
Keyword(s):  
Secondary Metabolite ◽  
Filamentous Fungi ◽  
Gene Clusters ◽  
Accurate Prediction

scholarly journals Histone deacetylase inhibitors suppress IL-2–mediated gene expression prior to induction of apoptosis

Blood ◽  
2000 ◽  
Vol 96 (4) ◽  
pp. 1490-1495 ◽  
Author(s):  
Yuko Koyama ◽  
Masaaki Adachi ◽  
Masuo Sekiya ◽  
Mutsuhiro Takekawa ◽  
Kohzoh Imai
Keyword(s):  
Gene Expression ◽  
Histone Deacetylase ◽  
Transcriptional Activation ◽  
Histone Deacetylase Inhibitors ◽  
Trichostatin A ◽  
Hdac Inhibitors ◽  
K562 Cells ◽  
Histone Hyperacetylation ◽  
Induced Apoptosis ◽  
Do So

Histone deacetylase (HDAC) inhibitors can induce transcriptional activation of a number of genes and induce cellular differentiation as histone acetylation levels increase. Although these inhibitors induce apoptosis in several cell lines, the precise mechanism by which they do so remains obscure. This study shows that HDAC inhibitors, sodium butyrate and trichostatin A (TSA), abrogate interleukin (IL)-2–mediated gene expression in IL-2–dependent cells. The HDAC inhibitors readily induced apoptosis in IL-2–dependent ILT-Mat cells and BAF-B03 transfectants expressing the IL-2 receptor βc chain, whereas they induced far less apoptosis in cytokine-independent K562 cells. However, these inhibitors similarly increased acetylation levels of histones in both cells. Although histone hyperacetylation is believed to lead to transcriptional activation, the results showed an abrogation of IL-2–mediated induction of c-myc,bag-1, and LC-PTP gene expression. This observed abrogation of gene expression occurred prior to phosphatidylserine externalization, a process that occurs in early apoptotic cells. Considering the biologic role played by IL-2–mediated gene expression in cell survival, these data suggest that its abrogation may contribute to the apoptotic process induced by HDAC inhibitors.

scholarly journals Repression of Salmonella Host Cell Invasion by Aromatic Small Molecules from the Human Fecal Metabolome

2017 ◽  
Vol 83 (19) ◽  
Author(s):  
Rafael J. M. Peixoto ◽  
Eduardo S. Alves ◽  
Melody Wang ◽  
Rosana B. R. Ferreira ◽  
Alessandra Granato ◽  
...  
Keyword(s):  
Biological Activity ◽  
Small Molecules ◽  
Host Cell ◽  
Small Molecule ◽  
Cell Invasion ◽  
Salmonella Enterica ◽  
Chemical Diversity ◽  
Host Cell Invasion ◽  
Human Gut ◽  
Content Type

ABSTRACT The human microbiome is a collection of microorganisms that inhabit every surface of the body that is exposed to the environment, generally coexisting peacefully with their host. These microbes have important functions, such as producing vitamins, aiding in maturation of the immune system, and protecting against pathogens. We have previously shown that a small-molecule extract from the human fecal microbiome has a strong repressive effect on Salmonella enterica serovar Typhimurium host cell invasion by modulating the expression of genes involved in this process. Here, we describe the characterization of this biological activity. Using a series of purification methods, we obtained fractions with biological activity and characterized them by mass spectrometry. These experiments revealed an abundance of aromatic compounds in the bioactive fraction. Selected compounds were obtained from commercial sources and tested with respect to their ability to repress the expression of hilA, the gene encoding the master regulator of invasion genes in Salmonella. We found that the aromatic compound 3,4-dimethylbenzoic acid acts as a strong inhibitor of hilA expression and of invasion of cultured host cells by Salmonella. Future studies should reveal the molecular details of this phenomenon, such as the signaling cascades involved in sensing this bioactive molecule. IMPORTANCE Microbes constantly sense and adapt to their environment. Often, this is achieved through the production and sensing of small extracellular molecules. The human body is colonized by complex communities of microbes, and, given their biological and chemical diversity, these ecosystems represent a platform where the production and sensing of molecules occur. In previous work, we showed that small molecules produced by microbes from the human gut can significantly impair the virulence of the enteric pathogen Salmonella enterica. Here, we describe a specific compound from the human gut that produces this same effect. The results from this work not only shed light on an important biological phenomenon occurring in our bodies but also may represent an opportunity to develop drugs that can target these small-molecule interactions to protect us from enteric infections and other diseases.

scholarly journals Cross Talk between Histone Deacetylase 4 and STAT6 in the Transcriptional Regulation of Arginase 1 during Mouse Dendritic Cell Differentiation

2014 ◽  
Vol 35 (1) ◽  
pp. 63-75 ◽  
Author(s):  
Quan Yang ◽  
Jianyang Wei ◽  
Limei Zhong ◽  
Maohua Shi ◽  
Pan Zhou ◽  
...  
Keyword(s):  
Histone Deacetylase ◽  
Cross Talk ◽  
Transcriptional Activation ◽  
Hdac Inhibitors ◽  
Ectopic Expression ◽  
Suppressor Cells ◽  
Dendritic Cell Differentiation ◽  
Arginase 1 ◽  
Histone Deacetylase 4 ◽  
Macrophage Colony

l-Arginine andl-arginine-metabolizing enzymes play important roles in the biology of some types of myeloid cells, including macrophage and myeloid-derived suppressor cells. In this study, we found evidence that arginase 1 (Arg1) is required for the differentiation of mouse dendritic cells (DCs). Expression of Arg1 was robustly induced during monocyte-derived DC differentiation. Ectopic expression of Arg1 significantly promoted monocytic DC differentiation in a granulocyte-macrophage colony-stimulating factor culture system and also facilitated the differentiation of CD8α+conventional DCs in the presence of Flt3 ligand. Knockdown of Arg1 reversed these effects. Mechanistic studies showed that the induced expression of Arg1 in differentiating DCs was caused by enhanced recruitment of histone deacetylase 4 (HDAC4) to the Arg1 promoter region, which led to a reduction in the acetylation of both the histone 3 and STAT6 proteins and subsequent transcriptional activation of Arg1. Further investigation identified a novel STAT6 binding site within the Arg1 promoter that mediated its regulation by STAT6 and HDAC4. These observations suggest that the cross talk between HDAC4 and STAT6 is an important regulatory mechanism of Arg1 transcription in DCs. Moreover, overexpression of Arg1 clearly abrogated the ability of HDAC inhibitors to suppress DC differentiation. In conclusion, we show that Arg1 is a novel regulator of myeloid DC differentiation.

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