Epigenome manipulation as a pathway to new natural product scaffolds and their congeners

Abstract

The covalent modification of chromatin is an important control mechanism used by fungi to modulate the transcription of genes involved in secondary metabolite production. To date, both molecular-based and chemical approaches targeting histone and DNA posttranslational processes have shown great potential for rationally directing the activation and/or suppression of natural-product-encoding gene clusters. In this Highlight, the organization of the fungal epigenome is summarized and strategies for manipulating chromatin-related targets are presented. Applications of these techniques are illustrated using several recently published accounts in which chemical-epigenetic methods and mutant studies were successfully employed for the de novo or enhanced production of structurally diverse fungal natural products (e.g., anthraquinones, cladochromes, lunalides, mycotoxins, and nygerones).

Fig. 1

Outline illustrating the flow of genetic information leading to secondary metabolite biosynthesis in fungi and how these events are impacted by epigenetic processes.

Fig. 2

Amino acid sequences of histone subunits H2A (A), H2B (B), H3 (C), and H4 (D) for the fungi (from top to bottom) Aspergillus niger, Coprinus cinereus, Phanerochaete chrysosporium, Aspergillus clavatus, Neosartorya fischeri, Fusarium graminearum, Magnaporthe grisea, Neurospora crassa, Saccharomyces cerevisiae, and Ustilago maydis. The sequences of human histones were included for comparisons to illustrate the substantial conservation of their primary structures. Pair-wise identities for the listed histone subunit sequences are 69%, 80%, 92%, and 94% for H2A, H2B, H3, and H4, respectively. Color-coding of the amino acid residues is as follows: bright green = identical residues; olive-green = highly conserved, but non-identical residues; orange = modest conservation of residues, and white = residue conservation is low or the residue is not present. Alignments were performed in Geneious v4.7 using sequence data available from GenBank and the Broad Institute Fungal Genome Initiative database.

Fig. 3

Illustration showing the association of DNA with histones, as well as common posttranslational modifications that influence these interactions. Several epigenetic modifications that alter DNA and histones include (clockwise from the bottom left): methylation of histones and DNA, biotinylation, citrullination, ADP-ribosylation, phosphorylation, acetylation, glycosylation, ubiquitination, and sumoylation.

Fig. 4

Acetylation of lysine residues found in histone tails and their interactions with DNA.

Fig. 5

Example small-molecule inhibitors and their respective epigenetic targets.

Fig. 6

Chromatograms of the reverse-phase-separated dichloromethane extracts of A. niger ATCC 1015 cultures treated with 7 showing the impact of HDAC inhibition on secondary metabolite diversity (UV traces at 210 nm were collected one and two weeks after addition of 10 μM of 7 or vehicle alone).