Deciphering lignocellulose deconstruction by the white rot fungus Irpex lacteus based on genomic and transcriptomic analyses

Abstract

BackgroundIrpex lacteus is one of the most potent white rot fungi for biological pretreatment of lignocellulose for second biofuel production. To elucidate the underlying molecular mechanism involved in lignocellulose deconstruction, genomic and transcriptomic analyses were carried out for I. lacteus CD2 grown in submerged fermentation using ball-milled corn stover as the carbon source.ResultsIrpex lacteus CD2 efficiently decomposed 74.9% lignin, 86.3% cellulose, and 83.5% hemicellulose in corn stover within 9 days. Manganese peroxidases were rapidly induced, followed by accumulation of cellulase and hemicellulase. Genomic analysis revealed that I. lacteus CD2 possessed a complete set of lignocellulose-degrading enzyme system composed mainly of class II peroxidases, dye-decolorizing peroxidases, auxiliary enzymes, and 182 glycoside hydrolases. Comparative transcriptomic analysis substantiated the notion of a selection mode of degradation. These analyses also suggested that free radicals, derived either from MnP-organic acid interplay or from Fenton reaction involving Fe2+ and H2O2, could play an important role in lignocellulose degradation.ConclusionsThe selective strategy employed by I. lacteus CD2, in combination with low extracellular glycosidases cleaving plant cell wall polysaccharides into fermentable sugars, may account for high pretreatment efficiency of I. lacteus. Our study also hints the importance of free radicals for future designing of novel, robust lignocellulose-degrading enzyme cocktails.Electronic supplementary materialThe online version of this article (10.1186/s13068-018-1060-9) contains supplementary material, which is available to authorized users.

Biochemical features of dye‐decolorizing peroxidases: Current impact on lignin degradation

“…Substrates tested include a variety of aromatic compounds classified as dyes [50,[53][54][55][56], beta-carotene [57], and aromatic sulfides [48]; some of which are poorly metabolized by other heme peroxidases. Numerous studies have shown that DyPs play a key role in the degradation of lignin [54,55,[58][59][60][61][62][63][64][65]. Their catalytic properties make them very interesting because the bacterial enzymes can be easily engineered, heterologously expressed in E. coli and purified [65] avoiding the issues of using a eukaryotic hosts.…”

Transcriptomic analysis ofLentinus squarrosulusprovide insights into its biodegradation ability

“…Production and expression of these enzymes is regulated chiefly by the environmental conditions and substrate of growth [4].Having stated the complexity of lignocellulose degradation, relatively little is known about this metabolic process and the subsequent polysaccharide degradation. Hence in this arena, transcriptomic analysis of the lignicolous fungi grown on different substrates was attempted by researchers worldwide to gain more insight into the degradation process [5][6][7][8][9]. Nevertheless, these studies have so far focused on fairly small group of specieswherein the expression of fungal genes in response to lignocellulosic biomass as substrate was reported.…”

“…With the genomic data of white-rot fungal species accumulating, characterization of the biomass degrading enzymes for functional exploitation has increased. Transcriptomic studies have also revealed the expression of an array of catabolic enzymes differentially based on the lignocellulosic substrate[4,5,6,9,41]. Accordingly in our study, we studied the transcriptome of L.squarrosulus, a white-rot belonging to Polyporaceae family grown in simple culture medium with azo dye Reactive Black 5 (RB5) added for ligninolytic enzyme induction.…”

Dye-decolorizing peroxidases in Irpex lacteus combining the catalytic properties of heme peroxidases and laccase play important roles in ligninolytic system

“…Irpex lacteus is a white rot fungus with a significant potential for various biotechnological applications such as bioremediation of organopollutants in water and soil environments and biopretreatment of lignocellulose [ 12 , 13 ]. Its biotechnological applications were attributed to the extracellular ligninolytic enzymes, including MnP, LiP, laccase-like, and DyP [ 14 – 18 ]. Our preliminary work demonstrated I. lacteus CD2 could degrade all kinds of lignocellulose and dyes [ 13 – 15 ].…”

“…Our preliminary work demonstrated I. lacteus CD2 could degrade all kinds of lignocellulose and dyes [ 13 – 15 ]. Genome analysis reveals that I. lacteus CD2 has seven mnp genes, two lip genes, and four dyp genes, without lac gene [ 14 ]. Compared with MnP, the main ligninolytic enzyme of I. lacteus , DyP is scarcely known for catalytic properties and substrate specificities, especially in lignin degradation.…”