Microarray analysis of laeA deletion and overexpression A.
Reconstructing fungal natural product biosynthetic pathways
Thus, manipulation of laeA expression levels will be of benefit to identify previously unknown metabolites in fungi. Efforts to uncover the mechanism of the global regulator LaeA revealed that some subtelomeric secondary metabolite clusters were located in heterochromatic regions of the genome. Importantly, gene transcription of telomere-proximal gene clusters and the level of the corresponding molecular generation are controlled by epigenetic regulation such as histone deacetylation.
Deletion of hdaA histone deacetylase or treatment with a histone deacetylase HDAC inhibitor in Aspergillus nidulans resulted in the transcriptional activation of sterigmatocystin 12 and penicillin 1 gene clusters, both located in subtelomeres [ 23 ]. Cichewicz et al. Treatment of Cladosporium cladosporioides with 5-azacytidine a DNA methyltransferase inhibitor stimulated the production of several oxylipins including 9 Z ,12 Z hydroxyoctadeca-9,dienoic acid 15 , its methyl ester 16 , and a glycerol conjugate 17 Figure 6.
Frontiers | Association of fungal secondary metabolism and sclerotial biology | Microbiology
In contrast, administration of suberoylanilide hydroxamic acid an HDAC inhibitor yielded production of a complex series of perylenequinones including cladochromes 18 — 23 and calphostin B Treatment of a Diatrype species with 5-azacytidine elicited the formation of lunalides A 25 and B 26 [ 24 ]. The Cichewicz group also isolated nygerone A 27 from Aspergillus niger when culturing with suberoylanilide hydroxamic acid [ 25 ].
These results demonstrate the potential of triggering cryptic metabolites through chemical epigenetic methodology. Unlocking fungal cryptic secondary metabolites via addition of DNA methyltransferase and histone deacetylase HDAC inhibitors to the culture medium. Accruing evidence linking chromatin modifications with secondary metabolite cluster regulation led us to examine the hypothesis that additional chromatin modifying proteins were important in their regulation.
CclA , an ortholog of bre2 in S. Chemical profiling followed by genetic analysis led to the identification of two NR-PKS gene clusters, one cluster responsible for monodictyphenone 28 , emodin 29 and emodin derivatives 30 — 33 , and a second encoding the enzymes for FA 34 and B 35 Figure 7 [ 29 ]. One non-activated gene nearby, however, was associated with only reduced levels of di- and trimethylation at H3K4 but not H3K9.
Thus, strongly reduced levels of di- and trimethylation at H3K4 and H3K9 are required for de-repression during secondary metabolism. Since not all secondary metabolite gene clusters contain pathway specific activators, modification of the chromatin landscape provides another means to active cryptic gene clusters [ 29 ]. Histone proteins are substrates for a wide array of modifications including acetylation, methylation, phosphorylation, and ubiquitination.
SUMO is a small ubiquitin-like protein that is added posttranslationally to a number of proteins in the cell.
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The aromatic nature of asperthecin 38 suggested an NR-PKS is responsible for its biosynthesis and the pathway was established through a series of knockout genetic analysis Figure 8B [ 31 ]. However, the mechanisms underlying SUMO regulation of secondary metabolism remains elusive; it may occur at different levels of regulation, including chromatin modification of the gene cluster, transcription factor modification, or the consequences of the effects on growth or primary metabolism. A Unlocking fungal cryptic secondary metabolites via deletion of SumO protein. B Proposed biosynthetic pathway of asperthecin 38 generated from genetic and chemical analysis.
With an ever-increasing number of complete genome sequences at hand, many novel gene clusters have now been identified. However, the corresponding secondary metabolites remain elusive, and researchers worldwide are working together to annotate gene function in the post-genomic era [ 32 ]. This review presents that, given exciting new approaches for identifying novel natural products, the next frontier of natural product discovery will be a synergistic combination of genomics, molecular genetics, biochemistry, and natural product chemistry to mine the fungal metabolome for useful natural products.
Clearly, natural product chemistry and molecular genetics have a new interrelationship. Collaborations between mycologists, geneticists, biochemists and chemists are essential to facilitate the discovery of novel natural products and the genes involved in their biosynthesis, which in the end will benefit the commercial search of enzymatic reactions [ 33 ]. The OSMAC approach, co-culture experiments [ 25 ], specific regulator activation, and epigenetic regulation will continue to play crucial roles for discovering cryptic novel natural products.
Although epigenetic approaches might have serious drawbacks, chiefly because targeting some histone-modifying complexes for loss-of-function could have negative effects on other cellular processes, continued development of genome mining tools will make these cryptic systems a potentially invaluable resource for the discovery of new chemical entities. Mol Plant Pathol , 20 6 , 29 Mar Front Microbiol , , 15 Nov Org Biomol Chem , 16 27 , 01 Jul Cited by: 5 articles PMID: Nat Prod Rep , 34 7 , 01 Jul Mar Drugs , 15 4 , 23 Mar To arrive at the top five similar articles we use a word-weighted algorithm to compare words from the Title and Abstract of each citation.
Chiang YM 1 ,. Lee KH ,.
Sanchez JF ,. Keller NP ,. Wang CC.
Affiliations 1 author 1. Share this article Share with email Share with twitter Share with linkedin Share with facebook. Free full text. Nat Prod Commun. This suggests that fine-scale sampling of fungal genomes can reveal broader evolutionary patterns. However, it is possible that an intact DEP cluster is not essential for depudecin production.
Furthermore, depudecin-like compounds could be synthesized by the 22 clusters containing a functional DEP5 along with either a functional DEP2 1 cluster or DEP4 21 clusters. The relatively high frequency of DEP pseudogenes and partial DEP clusters among the fungal genomes examined provides evidence that frequent degeneration of the cluster has occurred, which in turn suggests sporadic selection for depudecin production.
In recent years, there have been a number of reports of HGT of SM gene clusters between distantly related fungi Khaldi et al. By utilizing evidence from fungal genomes, the current study provides a more detailed understanding of the tempo or frequency of this birth and death process of a gene cluster that is weakly selected.
First, DEP3 and DEP6 might confer resistance to depudecin or depudecin-like metabolites produced by other fungi that occupy the same habitat. For example, the DEP3 -encoded transporter may export additional metabolic products, while the DEP6 -encoded transcription factor may interact with other regulatory proteins thereby exposing deleterious mutations in these regulators for remediation, thus impacting broader regulatory networks.
Rather, there is evidence for the presence of DEP3 homologs in other clusters that include a different transcription factor. Overall, DEP3 exhibited low fidelity to the DEP cluster, and among the genomes examined there are at least two other transcription factor genes physically linked to it tables 3 and 4 , indicating that the DEP3 -encoded transporter has an especially non-specific or modular function.
Unlocking Fungal Cryptic Natural Products
The presence of DEP3 adjacent to putative SM biosynthetic genes in genomes that do not include other DEP genes suggests that in some fungi DEP3 has relocated to other gene clusters, which may have allowed it to persist in organisms that do not produce depudecin. Fourth, selective gene retention may have resulted from physiological constraints imposed on the metabolic pathway. In this scenario, toxic biosynthetic intermediates accumulate due to deletion or mutation of an enzyme-encoding gene, regulator, or transporter, favoring the repeated loss of enzymes that catalyze formation of the intermediates Slot and Rokas ; Campbell et al.
Additionally, the deletion analysis performed here revealed that F. This result is similar to the finding that the ABC transporter gene FUM19 in the gene cluster responsible for synthesis of fumonisin mycotoxins is not required for resistance to fumonisins Proctor et al.
However, these tests were likely performed on haploid strains, and it is possible that retention of DEP3 and DEP6 is driven by selection imposed on a heterokaryon, or that DEP3 aids in intracellular depudecin resistance, but that there is redundancy in depudecin i. Thus, there is no evidence that gene loss in the DEP cluster leads to a decrease in fitness resulting from accumulation of toxic metabolites. Further experimentation on phenotypic changes induced by depudecin in various genetic backgrounds is needed to better understand how this SM affects fungal fitness.
Here we show that the gene cluster responsible for depudecin synthesis occurs broadly but discontinuously among species of Pezizomycotina, and that HGT and gene loss have contributed to this pattern of distribution, as predicted by the selfish cluster model. These observations provide broader insight into evolution of SM gene clusters.
Both of these benefits could increase the likelihood that cluster-encoded transporters and proteins that regulate transporter expression are preferentially repurposed for other functions. Such repurposing could lead to incorporation of the corresponding genes into other gene clusters and subsequent HGT of the genes as part of the remodeled clusters. When observations were noted for these genomes, we refer to them only by taxonomic class.
In the C. Protein translations for all complete homologs of each DEP gene that lacked in-frame stop codons were combined into a single file, aligned using mafft v.