A Candidate Gene Cluster for the Bioactive Natural Product Gyrophoric Acid in Lichen-Forming Fungi

Abstract

Natural products of lichen-forming fungi are structurally diverse and have a variety of medicinal properties. Despite this, they have limited implementation in industry mostly because the corresponding genes are unknown for most of their natural products. Here, we implement a long-read sequencing and bioinformatic approach to identify the putative biosynthetic gene cluster of the bioactive natural product gyrophoric acid (GA). Using 15 high-quality genomes representing nine GA-producing species of the lichen-forming fungal genus Umbilicaria, we identify the most likely GA cluster and investigate the cluster gene organization and composition across the nine species. Our results show that GA clusters are promiscuous within Umbilicaria, and only three genes are conserved across species, including the polyketide synthase (PKS) gene. In addition, our results suggest that the same cluster codes for different, but structurally similar compounds, namely, GA, umbilicaric-, and hiascic acid, bringing new evidence that lichen metabolite diversity is also generated through regulatory mechanisms at the molecular level. Ours is the first study to identify the most likely GA cluster and, thus, provides essential information to open new avenues for biotechnological approaches to producing and modifying GA and similar lichen-derived compounds. GA PKS is the first tridepside PKS to be identified. IMPORTANCE The implementation of natural products in the pharmaceutical industry relies on the possibility of modifying the natural product (NP) pathway to optimize yields and pharmacological effects. Characterization of genes and pathways underlying natural product biosynthesis is a major bottleneck for exploiting the medicinal properties of the natural products. Genome mining is a promising and relatively cost- and time-effective approach to utilize unexplored NP resources for drug discovery. In this study, we identify the most likely gene cluster for the lichen-forming fungal depside gyrophoric acid in nine Umbilicaria species. This compound shows cytotoxic and antiproliferative properties against several cancer cell lines and is also a broad-spectrum antimicrobial agent. This information paves the way for generating GA analogs with modified properties by selective activation/deactivation of genes.

Keywords: PKS phylogeny; Umbilicaria; biosynthetic genes; depsides; fungi; genome mining; genomics; lichen compounds; long-read sequencing; microbial biotechnology; nonreducing PKSs; pharmaceutically relevant natural products; secondary metabolites.

FIG 1

Chemical structures and nomenclature. Structure of a lichen depside, atranorin, GA, and other depsides produced by Umbilicaria spp.

FIG 2

NR-PKS phylogeny of lichen-forming fungi. This is a maximum-likelihood tree based on amino acid sequences of NR-PKSs from nine Umbilicaria spp., six Cladonia spp., Dermatocarpon miniatum, Stereocaulon alpinum, and Pseudevernia furfuracea. Branches in bold indicate bootstrap support >70%. Green color clades represent the PKSs common to all nine Umbilicaria spp. used in this study. PKS groups are based on Kim et al. (17).

FIG 3

(A) Gyrophoric acid cluster from Umbilicaria deusta as predicted by antiSMASH. Colored boxes indicate genes. Genes in gray represent genes coding for unknown proteins as predicted by the antiSMASH. (B) Putative functions of the genes of the gyrophoric acid cluster based on InterProScan and NCBI CDS search. The numbers correspond to the gene numbers of U. deusta in panel A.

FIG 4

Synteny plots based on tBLASTn showing the homology and synteny between the putative gyrophoric acid clusters U. deusta and other Umbilicaria spp. (A) and between the gyrophoric acid cluster from U. deusta and the grayanic acid cluster from Cladonia grayi, the olivetoric acid cluster from Pseudevernia furfuracea, and the orsellinic acid cluster from Aspergillus nidulans (B). All of the PKSs are highly homologous to the GA PKS and have the same domains as the GA PKS: SAT-KS-AT-PT-ACP-ACP-TE.

FIG 5

CORASON-based PKS phylogeny to elucidate evolutionary relationships and cluster organization of the GA cluster in Umbilicaria spp. The bar plot below depicts the percentage of Umbilicaria species in which a particular gene is present. The color of the genes is white when the homology to the genes of the other gyrophoric acid clusters is low.