Transcriptome Comparison of Secondary Metabolite Biosynthesis Genes Expressed in Cultured and Lichenized Conditions of Cladonia rangiferina

Abstract

Lichen secondary metabolites are natural products of high medicinal and industrial value, which are produced by the fungal symbiont (mycobiont) of lichens in response to environmental changes. It has been shown that the cultured mycobiont is capable of secondary metabolite production, specifically polyketides, and polyketide production is affected by the presence or absence of the algal or cyanobacterial symbiont (photobiont). Identification of polyketide synthases encoding genes is, in turn, key for understanding the regulation of secondary metabolite synthesis. Using a previously established method of resynthesis for Cladonia rangiferina as well as the sequenced and assembled genome of that species, we compared transcriptomes of C. rangiferina cultured alone and resynthesized with the photobiont (Asterochloris glomerata) to reveal transcriptionally active genes in secondary metabolic gene clusters, as well some of the neighbouring genes, induced by the presence of the photobiont and events of lichenization. The results identify potential candidates for PKS genes in C. rangiferina, identify potential neighbouring genes in the PKS cluster, and offer insights into further research. The study provides preliminary insights into the activity of several identified biosynthetic gene clusters (BGC) as well as interactions of genes within those clusters.

How to build a lichen: from metabolite release to symbiotic interplay

“…Polyketide production by axenically cultured mycobionts differs from that of resynthesizing myco‐ and photobiont co‐cultures (Sveshnikova & Piercey‐Normore, 2021) and does not necessarily correspond to the set of polyketides found in lichen thalli collected in nature. In addition, specific conditions of temperature, light and water availability, and growth media with added sugars or sugar alcohols appear to be required for the production of specific secondary metabolites (Stocker‐Wörgötter, 2002; Elshobary et al ., 2016).…”

“…On the contrary, certain polyketides such as atranorin, usnic acid, and anthraquinones produced by the mycobiont can act as 'sunscreen' pigments in the upper cortex, regulating the amount of incident light received by the photobiont (Solhaug et al, 2003;Beckett et al, 2021). Polyketide production by axenically cultured mycobionts differs from that of resynthesizing myco-and photobiont co-cultures (Sveshnikova & Piercey-Normore, 2021) and does not necessarily correspond to the set of polyketides found in lichen thalli collected in nature. In addition, specific conditions of temperature, light and water availability, and growth media with added sugars or sugar alcohols appear to be required for the production of specific secondary metabolites (Stocker-W€ org€ otter, 2002;Elshobary et al, 2016).…”

“…These results, together with the finding that between 11 and 28% of mycobiont and photobiont genes are already upregulated during the ‘pre‐contact’ and the ‘contact stage’, supported the ‘signalling hypothesis’ based on chemical signalling between symbionts before physical contact (Joneson et al ., 2011 ). We now know that lichenization is accompanied by regulation of gene expression in each partner involved, and this will induce downstream proteomic and metabolomic re‐arrangements (Trembley et al ., 2002 ; Joneson et al ., 2011 ; Armaleo et al ., 2019 ; Kono et al ., 2020 ; Sveshnikova & Piercey‐Normore, 2021 ). For example, genes encoding signal transduction components are already upregulated in the contact stage in both, mycobiont and photobiont, as elegantly demonstrated for the model lichen, Cladonia grayi , and its Asterochloris glomerata photobiont: specifically, genes encoding extracellular hydrolases and membrane transport proteins are upregulated in both prospective symbionts, and ammonium and ribitol transporters in the fungus only (Armaleo et al ., 2019 ).…”

“…The mere existence of the lichen microbiota implies that lichen‐associated bacteria have adapted tolerance of lichen compounds. Interestingly, certain gene clusters encoding secondary metabolite synthases are downregulated in Cladonia rangiferina co‐cultured with its compatible photobiont, suggesting that potential allelopathic effects towards the photobiont can be avoided in the early stages of lichenization (Sveshnikova & Piercey‐Normore, 2021 ). Which compounds precisely are affected is not yet clear and considering the large number of gene clusters for biosynthetic pathways present in lichens genomes, linking all biosynthetic genes with products will be a tall order.…”