Biosynthetic Gene Content of the ‘Perfume Lichens’ Evernia prunastri and Pseudevernia furfuracea

Abstract

Lichen-forming fungi produce a vast number of unique natural products with a wide variety of biological activities and human uses. Although lichens have remarkable potential in natural product research and industry, the molecular mechanisms underlying the biosynthesis of lichen metabolites are poorly understood. Here we use genome mining and comparative genomics to assess biosynthetic gene clusters and their putative regulators in the genomes of two lichen-forming fungi, which have substantial commercial value in the perfume industry, Evernia prunastri and Pseudevernia furfuracea. We report a total of 80 biosynthetic gene clusters (polyketide synthases (PKS), non-ribosomal peptide synthetases and terpene synthases) in E. prunastri and 51 in P. furfuracea. We present an in-depth comparison of 11 clusters, which show high homology between the two species. A ketosynthase (KS) phylogeny shows that biosynthetic gene clusters from E. prunastri and P. furfuracea are widespread across the Fungi. The phylogeny includes 15 genomes of lichenized fungi and all fungal PKSs with known functions from the MIBiG database. Phylogenetically closely related KS domains predict not only similar PKS architecture but also similar cluster architecture. Our study highlights the untapped biosynthetic richness of lichen-forming fungi, provides new insights into lichen biosynthetic pathways and facilitates heterologous expression of lichen biosynthetic gene clusters.

Genome-Wide Analysis of Biosynthetic Gene Cluster Reveals Correlated Gene Loss with Absence of Usnic Acid in Lichen-Forming Fungi

“…2016 ). Genomic data sets are also increasing our knowledge of the presence and domain architecture of PKSs, which are key for the biosynthesis of fungal phenolics, at an unprecedented rate ( Calchera et al. 2019 ).…”

Cladonia uncialis as a valuable raw material of biosynthetic compounds against clinical strains of bacteria and fungi

“…The biosynthesis potential of C. uncialis and other lichens is still poorly explored due to the lack of any experimental evidence for definite linking biosynthetic gene clusters with secondary metabolites. Only recently, first attempts in the functional genome annotation have been carried out (Bertrand et al, 2018a;Calchera et al, 2019). Nevertheless, their importance as a natural source of polyketides from which a number of pharmacologically active substances is derived (Helfrich et al, 2014), would increase the intensity of ongoing research.…”

“…The C. uncialis genome was proposed to include enzymes for grayanic acid, patulin and betaenone biosynthesis, and the latter two were not found in other lichen species (Bertrand et al, 2018b). A recent genome mining study of other lichen species, Evernia prunastri and Pseudevernia furfuracea, reported 80 biosynthetic gene clusters in the first one and 51 in the latter (Calchera et al, 2019) that also included polyketide synthases, non-ribosomal peptide synthetases and terpene synthases.…”

A facile in vivo procedure to analyze metabolic pathways in intact lichens

“…More recently, gene clusters associated with the biosynthesis of secondary metabolites (e.g. polyketides) were identified in lichenizing fungi (Bertrand et al ., ; Dal Grande et al ., ; Wang et al ., ; Calchera et al ., ), and also for a gene cluster tentatively involved in the biosynthesis of usnic acid in Cladonia uncialis (Abdel‐Hameed et al ., ). This gene cluster encodes a putative nonreducing polyketide synthase named methylphloroacetophenone synthase, and a cytochrome P450 oxidase named methylphloroacetophenone oxidase.…”