Proteomic analysis reveals large amounts of decomposition enzymes and major metabolic pathways involved in algicidal process of Trametes versicolor F21a

Abstract

A recent algicidal mode indicates that fungal mycelia can wrap and eliminate almost all co-cultivated algal cells within a short time span. However, the underlying molecular mechanism is rarely understood. We applied proteomic analysis to investigate the algicidal process of Trametes versicolor F21a and identified 3,754 fungal proteins. Of these, 30 fungal enzymes with endo- or exoglycosidase activities such as β-1,3-glucanase, α-galactosidase, α-glucosidase, alginate lyase and chondroitin lyase were significantly up-regulated. These proteins belong to Glycoside Hydrolases, Auxiliary Activities, Carbohydrate Esterases and Polysaccharide Lyases, suggesting that these enzymes may degrade lipopolysaccharides, peptidoglycans and alginic acid of algal cells. Additionally, peptidase, exonuclease, manganese peroxidase and cytochrome c peroxidase, which decompose proteins and DNA or convert other small molecules of algal cells, could be other major decomposition enzymes. Gene Ontology and KEGG pathway enrichment analysis demonstrated that pyruvate metabolism and tricarboxylic acid cycle pathways play a critical role in response to adverse environment via increasing energy production to synthesize lytic enzymes or uptake molecules. Carbon metabolism, selenocompound metabolism, sulfur assimilation and metabolism, as well as several amino acid biosynthesis pathways could play vital roles in the synthesis of nutrients required by fungal mycelia.

The Algicidal Fungus Trametes versicolor F21a Eliminating Blue Algae via Genes Encoding Degradation Enzymes and Metabolic Pathways Revealed by Transcriptomic Analysis

“…Heparanase (EC 3.2.1.166) of the GH79 module can endohydrolyze (1 → 4)-β-D-glycosidic bonds of heparan sulfate chains in heparan sulfate proteoglycan from proteoglycan core proteins and degrade these into small oligosaccharides (Gong et al, 2003 ). Chondroitin ABC lyase (EC 4.2.2.1) of PL8 and alginate lyase (EC 4.2.2.3) of PL14 can both decompose peptidoglycan and alginate, which expression level was also significantly up-regulated and consistent with the previous proteomics study (Gao et al, 2017 ). Many peptidase and lipase genes were also significantly up-regulated during the algicidal process, which clearly indicates that the underlying algicidal mechanism is complicated, and suggests that many decomposition genes should participate in the process.…”

“…Lignocellulose genes are most important for degradation (Yin et al, 2012 ; Strasser et al, 2015 ). Here, we identified 70% lignocellulose genes of all CAZymes, which is more than those found in the previous proteomic analysis (Gao et al, 2017 ). Most of up-regulated lignocellulose-active enzymes previously detected via proteomic analysis were included in the gene list identified in this study (Supplementary Table 4 ).…”

“…Of these, about half of all DEGs were up-regulated (Supplementary Table 3 ). 207 up-regulated genes and 140 down-regulated genes were previously detected via proteomics (Gao et al, 2017 ). The number of DEGs detected via RNA-Seq was much higher than that detected by proteomic analysis.…”

“…The number of detected genes far exceeded that obtained via proteomic techniques, which was also observed in many other studies (Bai et al, 2015 ; Li et al, 2017 ). A previous proteomic study showed that pyruvate metabolism and tricarboxylic acid cycle pathways, carbon metabolism, selenocompound metabolism, sulfur assimilation and metabolism, and several amino acid biosynthesis pathways had been enriched (Gao et al, 2017 ). The pathways that were enriched in the present study included almost all enriched pathways obtained via proteomic analysis (Figure 2D ).…”

“…cells during the early stages (0 to 24 h), while β-glucosidase, protease, laccase, and manganese peroxidase could be involved in the late stages (24 to 60 h). In a recent study, our group detected 30 fungal enzymes with endo- or exo-glycosidase activities such as β-1,3-glucanase, α-galactosidase, α-glucosidase, alginate lyase, chondroitin lyase, peptidase, exonuclease, and manganese peroxidase, which should be involved in the algicidal process of fungus T. versicolor F21a (Gao et al, 2017 ). However, gene ontology (GO) terms or KEGG pathways related to degradation were not directly observed from the proteomic data, which might be due to the limitations of the currently available proteomics techniques.…”