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.

Fig 1. Overview of the genome-wide integrative omics profiling of Pycnoporus coccineus CIRM-BRFM 310 at two time points.

The SHIN+GO platform; 1) integrated the fungal transcriptome from RNA-seq data and the secretome from liquid chromatography mass spectrometry; and 2) assisted the biological interpretation of the outputs of the omics models with functional gene annotations.

Fig 2. Genome-wide integrative omics models of P. coccineus in response to the substrates at day 3 and 7.

Transcriptomic topography: Mean transcription levels per node for each cultivation condition. Secretomic topography: The total count of secreted proteins per node indicates secretion hotspots. (A): Magnified version of the topographies. The node identification is labeled (i.e. 1 to 456). (B): Transcriptomic and secretomic topographies from the four substrates. An animated version of transcriptomic topographies is available (S1 File).

Fig 3. Transcriptomic changes of the lignocellulosic substrate-specific nodes from day 3 to day 7.

The specific transcription patterns for the lignocellulosic substrates were extracted from Fig 2. The highlighted nodes met either of two criteria; 1) > 11.7 log2 read counts; or 2) > 2 log2 fold changes on aspen (Asp), pine (Pin), and wheat straw (Whs) in comparison with maltose at each time point.

Fig 4. Transcription intensity of CAZyme coding genes in nodes 7, 8, 14, and 15 at day 3 and day 7.

The X and Y axes represent the values of transcription induction factor (TIF). TIF values > 200 are labeled at each time point. TIF were estimated by squaring log2 fold change values of the transcript read counts on lignocellulosic substrates compared to the control condition with maltose. Detailed information is provided (S2 Table).