The white-rot fungus Phanerochaete chrysosporium: conditions for the production of lignin-degrading enzymes

Gene expression analysis of Phanerochaete chrysosporium during the transition time from primary growth to secondary metabolism

In order to identify the secondary metabolism-related genes of Phanerochaete chrysosporium growing under pure O2 and nitrogen-limited conditions, 2322 ESTs fragments originated from two suppression-subtractive libraries were analyzed using the cDNA microarray technique. Ten significantly upregulated and 22 significantly downregulated genes were identified in the 72 h cultured mycelia RNA samples (secondary metabolism). According to qPCR, 16 out of the 32 genes were expressed differently in secondary metabolism. Transcripts of secondary metabolism up-regulation genes exhibited homologies to aryl-alcohol dehydrogenase (SShl554), ABC transporter gene (SSH624), chitinase (SSH963), heat shock protein (SSH1193), catalase (SSH317), cytochrome P450 (SSH331), glucosamine-6-phosphate isomerase (SSH611), and alkyl hydroperoxide reductase (SSH362) genes. Ninety-three genes could be classified by Eukaryotic Orthologous Groups (KOG). Among the genes assigned a function, gene expression patterns were different in both secondary metabolism and primary metabolism. In the group of "Cellular Processes and Signaling," most of the genes were from the primary metabolism library. On the other hand, genes from the secondary metabolism library were found mainly in the "Information Storage" and "Processing and Poorly Characterized" groups. Based on the KOG functional assignments, six genes belong to the ubiquitin system, and all of them were from primary metabolism phase. The presence of the H2O2-relevant genes suggested that parts of the genes expressed in 72 h might be involved in the ligninolytic process during secondary metabolism of P. chrysosporium.

Physiological regulation of laccase and manganese peroxidase production by white-rot Basidiomycetes

This review integrates recent literature and our own data on the physiology of laccase and manganese peroxidase synthesis, focusing on the common characteristics and unique properties of individual fungi as well as on several approaches providing enhanced enzyme secretion. Firstly, the enzyme yield is species-dependent and strain-dependent and selection of new organisms with tremendous synthesis of these enzymes is possible. For example, in screening program the laccase activity of tested basidiomycetes varied from 0.5Uml(-1) to 75Uml(-1). Secondly, the carbon source and lignocellulosic substrate play a crucial role in enzyme production. Thus, laccase activity of Pseudotrametes gibbosa varied from 0.3Uml(-1) (Avicel) to 13.7Uml(-1) (lactose), while the substitution of wheat bran with walnut pericarp increased Cerrena unicolor manganese peroxidase yield from 0.7Uml(-1) to 8.3Uml(-1). Thirdly, aromatic compounds regulate the ligninolytic enzyme synthesis although their effect is very specific depending on fungi physiological peculiarities. 2,4,6-trinitrotoluene (TNT) supplemented to the medium at appropriate concentration significantly accelerated C. unicolor laccase production and 4-fold increased laccase specific activity. Fourthly, co-cultivation of appropriate fungi shows considerable promise as a strategy to highly enhance the enzyme production. For example, pairing of C. unicolor and Phellinus robustus 2-fold increased the total laccase yield.

Role of P450 monooxygenases in the degradation of the endocrine-disrupting chemical nonylphenol by the white rot fungus Phanerochaete chrysosporium

The white rot fungus Phanerochaete chrysosporium extensively degraded the endocrine disruptor chemical nonylphenol (NP; 100% of 100 ppm) in both nutrient-limited cultures and nutrient-sufficient cultures. The P450 enzyme inhibitor piperonyl butoxide caused significant inhibition (approximately 75%) of the degradation activity in nutrient-rich malt extract (ME) cultures but no inhibition in defined low-nitrogen (LN) cultures, indicating an essential role of P450 monooxygenase(s) in NP degradation under nutrient-rich conditions. A genome-wide analysis using our custom-designed P450 microarray revealed significant induction of multiple P450 monooxygenase genes by NP: 18 genes were induced (2- to 195-fold) under nutrient-rich conditions, 17 genes were induced (2- to 6-fold) in LN cultures, and 3 were induced under both nutrient-rich and LN conditions. The P450 genes Pff 311b (corresponding to protein identification number [ID] 5852) and Pff 4a (protein ID 5001) showed extraordinarily high levels of induction (195- and 167-fold, respectively) in ME cultures. The P450 oxidoreductase (POR), glutathione S-transferase (gst), and cellulose metabolism genes were also induced in ME cultures. In contrast, certain metabolic genes, such as five of the peroxidase genes, showed partial downregulation by NP. This study provides the first evidence for the involvement of P450 enzymes in NP degradation by a white rot fungus and the first genome-wide identification of specific P450 genes responsive to an environmentally significant toxicant.

Transcriptome and secretome analyses of Phanerochaete chrysosporium reveal complex patterns of gene expression

The wood decay basidiomycete Phanerochaete chrysosporium was grown under standard ligninolytic or cellulolytic conditions and subjected to whole-genome expression microarray analysis and liquid chromatography-tandem mass spectrometry of extracellular proteins. A total of 545 genes were flagged on the basis of significant changes in transcript accumulation and/or peptide sequences of the secreted proteins. Under nitrogen or carbon limitation, lignin and manganese peroxidase expression increased relative to nutrient replete medium. Various extracellular oxidases were also secreted in these media, supporting a physiological connection based on peroxide generation. Numerous genes presumed to be involved in mobilizing and recycling nitrogen were expressed under nitrogen limitation, and among these were several secreted glutamic acid proteases not previously observed. In medium containing microcrystalline cellulose as the sole carbon source, numerous genes encoding carbohydrate-active enzymes were upregulated. Among these were six members of the glycoside hydrolase family 61, as well as several polysaccharide lyases and carbohydrate esterases. Presenting a daunting challenge for future research, more than 190 upregulated genes are predicted to encode proteins of unknown function. Of these hypothetical proteins, approximately one-third featured predicted secretion signals, and 54 encoded proteins detected in extracellular filtrates. Our results affirm the importance of certain oxidative enzymes and, underscoring the complexity of lignocellulose degradation, also support an important role for many new proteins of unknown function.