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.
Highlights
The bioconversion of agricultural, forestry and industrial green wastes into renewable sources of energy with bio-based molecules is highly desirable
We examined transcriptomic and secretomic models of P. coccineus CIRM-BRFM 310 at two time points in response to three different types of lignocellulosic substrates representing gramineae, softwood and hardwood
Our observations were limited to two time points, the fungus seemed to execute an almost simultaneous recruitment of various enzymes targeting cellulose, hemicelluloses, lignin and pectin, rather than a step-by-step degradation of the plant polymers
Summary
The bioconversion of agricultural, forestry and industrial green wastes into renewable sources of energy with bio-based molecules is highly desirable. Innovations in ecologically-friendly technologies will lead to improvements in green chemistry and biorefinery, and contribute to the circular economy. Lignocellulose, the major component of plant biomass, is highly recalcitrant to enzymatic degradation because the cellulose forms crystalline structures and the lignin sets dense polyaromatic polymers. Great efforts have been made to convert lignocellulosic saccharides into biofuels, biogas, and bio-based chemicals [1,2]. Lignocellulose has enormous potential in the production of phenolics and aromatics-based products [3]. The problems are how to break down lignin unamenable to biochemical transformation and to degrade cellulose efficiently
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