Systems biology-guided understanding of white-rot fungi for biotechnological applications: A review

Abstract

Plant-derived biomass is the most abundant biogenic carbon source on Earth. Despite this, only a small clade of organisms known as white-rot fungi (WRF) can efficiently break down both the polysaccharide and lignin components of plant cell walls. This unique ability imparts a key role for WRF in global carbon cycling and highlights their potential utilization in diverse biotechnological applications. To date, research on WRF has primarily focused on their extracellular 'digestive enzymes' whereas knowledge of their intracellular metabolism remains underexplored. Systems biology is a powerful approach to elucidate biological processes in numerous organisms, including WRF. Thus, here we review systems biology methods applied to WRF to date, highlight observations related to their intracellular metabolism, and conduct comparative extracellular proteomic analyses to establish further correlations between WRF species, enzymes, and cultivation conditions. Lastly, we discuss biotechnological opportunities of WRF as well as challenges and future research directions.

Keywords: Mycology; biotechnology.

Graphical abstract

Figure 1

White-rot fungi (WRF) distribution in the fungal kingdom and examples of a WRF growing in different environments and experimental conditions (A) Simplified diagram of the fungal kingdom with branches that include WRF with the number of published genomes in parentheses at the time of writing (the species are detailed in Table S1). (B) Fruiting bodies of Trametes versicolor (commonly known as turkey tail) growing on woody biomass. (C–E) Mycelia of T. versicolor growing (C) on a yeast extract-peptone-dextrose (YPD) agar plate, (D) in YPD broth under submerged-state and agitation cultivation conditions, and (E) on milled poplar in solid-state cultivation conditions (defined as cultivations in the absence of free water).

Figure 2

Cumulative number of WRF genomes published over time and transcriptomic, proteomic, and metabolomic studies of WRF conducted on lignocellulose or lignocellulosic-derived substrates The references used to generate these graphs are shown in Tables S1 and S2.

Figure 3

Summary of proposed intracellular catabolic pathways during lignocellulose degradation in WRF Extracellular cellulose-, hemicellulose-, and lignin-degrading enzymes break down biopolymers from lignocellulose into low molecular weight products (e.g., glucose, xylose, aromatic compounds) which are subsequently funneled to the tricarboxylic acid and glyoxylate shunt pathways. Solid arrows represent enzymatic reactions and faded arrows represent transport in or out of organelles. Key proteins and enzymes highlighted in this review are shown in dark gray ovals. Metabolic compound abbreviations: 3PG, 3-phosphoglycerate; 6PGL, 6-phosphogluconolactone; AcP, acetyl phosphate; DHAP, dihydroxyacetone phosphate; EtOH, ethanol; FBP, fructose 1,6-bisphosphate; G3P, glyceraldehyde 3-phosphate; G6P, glucose-6-phosphate; GLOX, glyoxal oxidase; X5P, xylulose-5-phosphate; Gly3P, glycerol-3-phosphate. Enzyme and protein abbreviations: ABC, ATP-binding cassette efflux transporters; HMT, heavy metal translocation protein; ICL, isocitrate lyase; MD, malate dehydrogenase; MFS, major facilitator superfamily; MS, malate synthase; OXA, oxaloacetase; OXO, oxalate oxidase; TFs, transcription factors. Figure created with BioRender.com.

Figure 4

Prevalence of detected CAZymes families in WRF secretomes from cultivations in different substrates The presence of CAZyme families was examined in 92 secretomic datasets from 19 WRF. Colors in each cell indicate the prevalence of a CAZyme family detected in secretomes for each substrate type. Color keys in the leftmost column indicate substrate specificity of CAZyme families, which has been retrieved from a recent publication (Miyauchi et al., 2020b). Values in parentheses on the top indicate the number of examined datasets for each substrate type and ‘All’ includes the datasets containing all the substrates. Euclidean distance method was used for clustering. A full list of secreted CAZyme families in each dataset can be found in Table S4. Detailed information about the examined datasets can be found in Table S3.

Figure 5

Number of detected and undetected CAZymes in WRF secretomes based on predicted CAZymes in the reference genomes To have a reasonable coverage of secreted proteins for these analyses, we selected fungal species that have at least three corresponding datasets, with each dataset containing at least 50 detected proteins. This results in 80 secretomic datasets from 11 WRF. CAZyme counts were based on substrate specificity of CAZyme families: cellulose, hemicellulose, pectin, lignin, and all substrates. Numbers on bar plots indicate the proportion of detected CAZymes compared to total predicted genes. Values in parentheses on the X-axis indicate numbers of examined datasets for each species. The full list of enzyme counts for each CAZyme family can be found in Tables S3 and S4. Abbreviations: Cersu1, Ceriporiopsis (Gelatoporia) subvermispora; Dicsq1, Dichomitus squalens; Phchr2, Phanerochaete chrysosporium; Phlgi1, Phlebiopsis gigantea; Phlrad1, Phlebia radiata; Pleery1, Pleurotus eryngii; PleosPC15_2, Pleurotus ostreatus PC15; PleosPC9_1, Pleurotus ostreatus PC9; Pycci1, Pycnoporus cinnabarinus; Pycco1, Pycnoporus coccineus; Trave1, Trametes versicolor.

Figure 6

Biotechnological applications of WRF WRF offer a variety of biotechnological opportunities. The metabolic capabilities of WRF to degrade lignocellulose and xenobiotic compounds can be utilized for the treatment of plant derived biomass and plastics, bioremediation and production of bioenergy (bioconversion to fuels, chemicals, or materials precursors) or natural products. The fruiting bodies or fungal mycelia can be processed into food or biomaterials. Figure created with BioRender.com.