In vitro resynthesis of lichenization reveals the genetic background of symbiosis-specific fungal-algal interaction in Usnea hakonensis

Abstract

Background Symbiosis is central to ecosystems and has been an important driving force of the diversity of life. Close and long-term interactions are known to develop cooperative molecular mechanisms between the symbiotic partners and have often given them new functions as symbiotic entities. In lichen symbiosis, mutualistic relationships between lichen-forming fungi and algae and/or cyanobacteria produce unique features that make lichens adaptive to a wide range of environments. Although the morphological, physiological, and ecological uniqueness of lichens has been described for more than a century, the genetic mechanisms underlying this symbiosis are still poorly known. Results This study investigated the fungal-algal interaction specific to the lichen symbiosis using Usnea hakonensis as a model system. The whole genome of U. hakonensis, the fungal partner, was sequenced by using a culture isolated from a natural lichen thallus. Isolated cultures of the fungal and the algal partners were co-cultured in vitro for 3 months, and thalli were successfully resynthesized as visible protrusions. Transcriptomes of resynthesized and natural thalli (symbiotic states) were compared to that of isolated cultures (non-symbiotic state). Sets of fungal and algal genes up-regulated in both symbiotic states were identified as symbiosis-related genes. Conclusion From predicted functions of these genes, we identified genetic association with two key features fundamental to the symbiotic lifestyle in lichens. The first is establishment of a fungal symbiotic interface: (a) modification of cell walls at fungal-algal contact sites; and (b) production of a hydrophobic layer that ensheaths fungal and algal cells;. The second is symbiosis-specific nutrient flow: (a) the algal supply of photosynthetic product to the fungus; and (b) the fungal supply of phosphorous and nitrogen compounds to the alga. Since both features are widespread among lichens, our result may indicate important facets of the genetic basis of the lichen symbiosis.

Large differences in carbohydrate degradation and transport potential in the genomes of lichen fungal symbionts

“…Transcriptomic studies of isolates, co-cultures and natural lichens could provide evidence of this. However, the one study to date to report CAZyme differential expression (35) only detected upregulation of multifunctional GHs that could also be involved in fungal cell wall modification (GH2 and GH12), but none of the core lecanoromycete cellulases or hemicellulases we report here. Most common algal symbionts are thought to contain cellulose in their cell walls but no pectin (36); it is unclear if any lichen algal symbiont possesses pectin in its cell walls.…”

Predicted Input of Uncultured Fungal Symbionts to a Lichen Symbiosis from Metagenome-Assembled Genomes

“…The lecanoromycete MAG was the only one to code for a putative secreted glucanase or xyloglucanase from the GH12 family ( fig. 5 A and B ), which might target cellulose and is known to be upregulated in lecanoromycete-alga coculturing experiments ( Kono et al 2020 ), and a secreted β-mannanase or β-1,4-glucanase from the GH45 family. Some secreted auxiliary activity CAZymes (AA) belonged to families likewise involved in digesting plant polymers through oxidative processes: AA3 (active on cellobiose and lignin) in all three secretomes and AA9 (active on cellulose) in the lecanoromycete secretome.…”

Towards a Systems Biology Approach to Understanding the Lichen Symbiosis: Opportunities and Challenges of Implementing Network Modelling

“…The literature on lichen metabolism has been largely focused on understanding the exchange of key nutrients between symbionts ( Lines et al, 1989 ; Kono et al, 2020 ; ten Veldhuis et al, 2020 ) and identifying lichen secondary metabolites and their biosynthetic pathways (i.e., metabolite profiling) ( Fahselt, 1994 ; Aubert et al, 2007 ; Elix and Stocker-Worgotter, 2008 ; Mittermeier et al, 2015 ; Bertrand et al, 2018b ; Brakni et al, 2018 ; Calcott et al, 2018 ; Kuhn et al, 2019 ; Goga et al, 2020 ; Figure 4 ). In the 1960s, observations of carbohydrate storage and translocation between the symbionts of Peltigera polydactyla ( Smith and Drew, 1965 ; Drew and Smith, 1967a , b ) together with a series of similar studies on other lichens ( Smith et al, 1969 ) established the foundations for studying the metabolic interplay in lichens.…”

“…Because mycobionts grow relatively slowly, the application of classical experimental microbiology techniques and co-culture/resynthesis experiments to the understanding of the development and functioning of the lichen symbiosis has lagged. Despite some recent studies focusing on early stages of lichenisation ( Joneson et al, 2011 ; Armaleo et al, 2019 ; Kono et al, 2020 ), the molecular basis of fungal-algal interactions during lichenisation remains mostly uncharacterised, and processes involved in signalling and metabolic interplays between the symbionts are poorly understood. Contemporary systems biology approaches may facilitate tackling long-standing questions about the lichen symbiosis.…”