Biosynthesis Most of the core genes coding for enzymes that act in a discrete pathway for the biosynthesis of a specific secondary metabolite are located in physical vicinity in the fungal genome. This grouping of functionally linked genes into biosynthetic gene clusters (BGC) is a distinctive feature of fungal secondary metabolism.
The central part of a secondary BGC typically codes for a backbone-generating enzyme such as polyketide synthase (PKS), non ribosomal peptide synthetase (NRPS), hybrid NRPS-PKS, dimethylallyl tryptophan synthase, or terpene cyclase. PKS and NRPS core enzymes consist of multiple domains that progressively assemble the metabolite backbone. Their genes show high diversity and discontinuous distribution across fungal genomes, respectively, and evolve rapidly. In addition, accessory enzymes involved in chemical modification of the generated product to generate the final compound, transporters for product export, and transcription factors for cluster regulation may be encoded by cluster-resident genes (Fig. 1). Although secondary BGC often are self-contained units for the biosynthesis of a specific substance, this is not necessarily always the case. There is no standard composition of these gene clusters but diversity regarding structure, content and size even among different strains of the same fungal species. Some clusters for example encode multiple backbone genes while others lack certain genes such as those coding for transcription factors that regulate biosynthetic gene expression. The penicillin biosynthesis cluster of Penicillium chrysogenum exemplifies the latter case.
Fig1. Scheme of a prototypical secondary metabolism gene cluster and its subtelomeric localization on the chromosome.
A pathway-specific regulator is absent from the gene cluster; instead, penicillin production is subject to regulation by a network of global regulatory proteins that are responding to diverse nutritional and environmental cues and simultaneously govern various cellular processes including metabolism and development. The biosynthesis of a given secondary metabolite may also involve more than one gene cluster. This is the case for cephalosporin production by Acremonium chrysogenum, to which two clusters are contributing (Martin et al., 2014; Zeilinger et al., 2015).
A further hallmark of many fungal secondary BGC is their enrichment near to the ends of chromosomes, at subtelomeric regions. As the areas adjacent to the telomeres contain densely packed nucleosomes which renders them transcriptionally silent, these secondary BGC are subject to chromatin-level control. Nucleosome repositioning as well as DNA and histone modifications are involved in their transcriptional activation, which occurs in response to pleiotropic environmental triggers (Collemare and Seidl, 2019).
Besides impacting their expression, the subtelomeric localization of secondary BGC is believed to affect evolution and horizontal gene transfer as these regions usually are highly prone to recombination. While gene duplication had a prominent role in the evolution and subsequent diversification of secondary metabolic genes, several BGC seem to have originated from the horizontal transfer of genes from bacteria to fungi. The clustering of secondary metabolism genes then further facilitates their intra-kingdom horizontal transfer between different fungal species and contributes to metabolic diversity (Osbourn, 2010).
The metabolic potential of a given fungus can be explored directly from its genome sequence by screening for backbone genes and gene clusters using bioinformatics approaches. Among the different groups of fungi, filamentous ascomycetes are especially rich in secondary metabolism BGC. In these organisms, which typically harbor dozens of these clusters, a significant portion of their genome is devoted to secondary metabolite biosynthesis and its regulation. However, many gene clusters for secondary metabolism pathways are unexpressed and hence no product is present under standard laboratory culture conditions, as these do not mimic the required physiological triggers the producing fungus encounters in its natural habitat. The activation of these unexpressed BGC is a promising avenue to further exploit fungi as a source of bioactive natural products, including novel drug leads. Hitherto successful approaches tackled cluster composition and regulation by using genetic engineering, chromatin structure modification by using epigenetic modifiers, as well as simulation of the natural habitat by using co-cultivation and synthetic microbial communities (Keller, 2019).
References:
Martin, J.-F., Garcia-Estrada, C., Zeilinger, S., 2014. Biosynthesis and Molecular Genetics of Fungal Secondary Metabolites. New York: Springer, doi:10.1007/978-1-4939-1191-2.
Zeilinger, S., Martin, J.-F., Garcia-Estrada, C., 2015. Biosynthesis and molecular genetics of fungal secondary metabolites. vol. 2. New York: Springer, doi:10.1007/978-1-4939-2531-5.
Collemare, J., Seidl, M.F., 2019. Chromatin-dependent regulation of secondary metabolite biosynthesis in fungi: Is the picture complete? FEMS Microbiology. Rev. 43, 591–607.
Osbourn, A., 2010. Secondary metabolic gene clusters: Evolutionary toolkits for chemical innovation. Trends Genet. 26, 449–457.
Keller, N.P., 2019. Fungal secondary metabolism: Regulation, function and drug discovery. Nat. Rev. Microbiol. 17, 167–180.
