The integrative omics of white-rot fungus Pycnoporus coccineus reveals co-regulated CAZymes for orchestrated lignocellulose breakdown

Abstract

Innovative green technologies are of importance for converting plant wastes into renewable sources for materials, chemicals and energy. However, recycling agricultural and forestry wastes is a challenge. A solution may be found in the forest. Saprotrophic white-rot fungi are able to convert dead plants into consumable carbon sources. Specialized fungal enzymes can be utilized for breaking down hard plant biopolymers. Thus, understanding the enzymatic machineries of such fungi gives us hints for the efficient decomposition of plant materials. Using the saprotrophic white-rot fungus Pycnoporus coccineus as a fungal model, we examined the dynamics of transcriptomic and secretomic responses to different types of lignocellulosic substrates at two time points. Our integrative omics pipeline (SHIN+GO) enabled us to compress layers of biological information into simple heatmaps, allowing for visual inspection of the data. We identified co-regulated genes with corresponding co-secreted enzymes, and the biological roles were extrapolated with the enriched Carbohydrate-Active Enzyme (CAZymes) and functional annotations. We observed the fungal early responses for the degradation of lignocellulosic substrates including; 1) simultaneous expression of CAZy genes and secretion of the enzymes acting on diverse glycosidic bonds in cellulose, hemicelluloses and their side chains or lignin (i.e. hydrolases, esterases and oxido-reductases); 2) the key role of lytic polysaccharide monooxygenases (LPMO); 3) the early transcriptional regulation of lignin active peroxidases; 4) the induction of detoxification processes dealing with biomass-derived compounds; and 5) the frequent attachments of the carbohydrate binding module 1 (CBM1) to enzymes from the lignocellulose-responsive genes. Our omics combining methods and related biological findings may contribute to the knowledge of fungal systems biology and facilitate the optimization of fungal enzyme cocktails for various industrial applications.

An ectomycorrhizal fungus alters sensitivity to jasmonate, salicylate, gibberellin, and ethylene in host roots

“…To obtain a comprehensive view of the impact of hormone treatments on the poplar and L. bicolor transcriptomes, we constructed transcriptomic models using SHIN+GO (self-organizing map harboring informative nodes with gene ontology; Miyauchi et al, 2016Miyauchi et al, , 2017Miyauchi et al, , 2018. A self-organizing map was trained with the normalized read count of the selected replicates using Rsomoclu (Wittek et al, 2017).…”

Integrative visual omics of the white-rot fungus Polyporus brumalis exposes the biotechnological potential of its oxidative enzymes for delignifying raw plant biomass

“…S1). We constructed network maps for the fungal transcriptome and secretome using the visual multiomics pipeline SHIN+GO, which allowed us to overview the genome-wide transcriptomic and secretomic activities and pinpoint molecular events of interest (7). We made omics topographies ('Tatami maps') to; 1) visualize nodes containing genes with similar transcription patterns with the corresponding count of secreted proteins; 2) calculate the node-wise mean of the normalized transcript read counts in each condition; 3) identify gene clusters showing high transcription levels at specific time points and under specific conditions.…”

Dichomitus squalens partially tailors its molecular responses to the composition of solid wood

“…Other factors such as amount and composition of extractives from birch and aspen may play a role in the response of D. squalens, as well as the disruption of the native structure of wood by powdering it before use in submerged cultures. Physiological variability in one fungal strain with respect to a wood species and culturing condition further emphasizes the complexity to compare the results of the other white-rot species from diverse cultivation conditions (MacDonald et al, 2011;Vanden Wymelenberg et al, 2011;Couturier et al, 2015;Miyauchi et al, 2017). Of note however, in P. coccineus cultures on powdered wood agar, there was a subset of XC transcripts higher on hardwood (aspen) but no MCs transcripts high on softwood (pine) (Couturier et al, 2015).…”

“…Previously, in submerged cultures of D. squalens amended with aspen or spruce, no clear tailoring of both the transcriptome and exo‐proteome to the wood composition was detected (Rytioja et al ., ). In addition, in previous studies using submerged cultures with other white‐rot fungal species Phanerochaete chrysosporium (Vanden Wymelenberg et al ., ), Phanerochaete carnosa (MacDonald et al ., ) and Pycnoporus coccineus (Miyauchi et al ., ) no compositionally related response to both wood types was reported. In addition, P. coccineus also did not adjust its transcriptomes and proteomes to both powdered wood types in solid‐state cultures (Couturier et al ., ).…”