scholarly journals Transcriptomic Responses of the Softwood-Degrading White-Rot Fungus Phanerochaete carnosa during Growth on Coniferous and Deciduous Wood

2011 ◽  
Vol 77 (10) ◽  
pp. 3211-3218 ◽  
Author(s):  
Jacqueline MacDonald ◽  
Matt Doering ◽  
Thomas Canam ◽  
Yunchen Gong ◽  
David S. Guttman ◽  
...  
Keyword(s):  
Nutrient Medium ◽  
Sugar Maple ◽  
Glycosyl Hydrolase ◽  
Transcript Abundance ◽  
White Rot ◽  
White Rot Fungus ◽  
P450 Monooxygenase ◽  
Content Type ◽  
Phanerochaete Carnosa ◽  
Genes Encoding

ABSTRACTTo identify enzymes that could be developed to reduce the recalcitrance of softwood resources, the transcriptomes of the softwood-degrading white-rot fungusPhanerochaete carnosawere evaluated after growth on lodgepole pine, white spruce, balsam fir, and sugar maple and compared to the transcriptome ofP. carnosaafter growth on liquid nutrient medium. One hundred fifty-two million paired-end reads were obtained, and 63% of these reads were mapped to 10,257 gene models fromP. carnosa.Five-hundred thirty-three of these genes had transcripts that were at least four times more abundant during growth on at least one wood medium than on nutrient medium. The 30 transcripts that were on average over 100 times more abundant during growth on wood than on nutrient medium included 6 manganese peroxidases, 5 cellulases, 2 hemicellulases, a lignin peroxidase, glyoxal oxidase, and a P450 monooxygenase. Notably, among the genes encoding putative cellulases, one encoding a glycosyl hydrolase family 61 protein had the highest relative transcript abundance during growth on wood. Overall, transcripts predicted to encode lignin-degrading activities were more abundant than those predicted to encode carbohydrate-active enzymes. Transcripts predicted to encode three MnPs represented the most highly abundant transcripts in wood-grown cultivations compared to nutrient medium cultivations. Gene set enrichment analyses did not distinguish transcriptomes resulting from softwood and hardwood cultivations, suggesting that similar sets of enzyme activities are elicited byP. carnosagrown on different wood substrates, albeit to different expression levels.

scholarly journals Time-Dependent Profiles of Transcripts Encoding Lignocellulose-Modifying Enzymes of the White Rot Fungus Phanerochaete carnosa Grown on Multiple Wood Substrates

2011 ◽  
Vol 78 (5) ◽  
pp. 1596-1600 ◽  
Author(s):  
Jacqueline MacDonald ◽  
Emma R. Master
Keyword(s):  
Wood Species ◽  
Chitin Synthase ◽  
Time Dependent ◽  
White Rot ◽  
White Rot Fungus ◽  
Internal Reference ◽  
Sequential Decay ◽  
Content Type ◽  
Transcript Quantification ◽  
Phanerochaete Carnosa

ABSTRACTThe abundances of nine transcripts predicted to encode lignocellulose-modifying enzymes were measured over the course ofPhanerochaete carnosacultivation on four wood species. Profiles were consistent with sequential decay; transcripts encoding lignin-degrading peroxidases featured a significant substrate-dependent response. The chitin synthase gene was identified as the optimal internal reference gene for transcript quantification.

scholarly journals Glucose-Mediated Repression of Plant Biomass Utilization in the White-Rot Fungus Dichomitus squalens

2019 ◽  
Vol 85 (23) ◽  
Author(s):  
Paul Daly ◽  
Mao Peng ◽  
Marcos Di Falco ◽  
Anna Lipzen ◽  
Mei Wang ◽  
...  
Keyword(s):  
Catabolite Repression ◽  
Carbon Catabolite Repression ◽  
Plant Biomass ◽  
Carbon Sources ◽  
White Rot Fungi ◽  
White Rot ◽  
White Rot Fungus ◽  
Content Type ◽  
Dichomitus Squalens ◽  
Genes Encoding

ABSTRACT The extent of carbon catabolite repression (CCR) at a global level is unknown in wood-rotting fungi, which are critical to the carbon cycle and are a source of biotechnological enzymes. CCR occurs in the presence of sufficient concentrations of easily metabolizable carbon sources (e.g., glucose) and involves downregulation of the expression of genes encoding enzymes involved in the breakdown of complex carbon sources. We investigated this phenomenon in the white-rot fungus Dichomitus squalens using transcriptomics and exoproteomics. In D. squalens cultures, approximately 7% of genes were repressed in the presence of glucose compared to Avicel or xylan alone. The glucose-repressed genes included the essential components for utilization of plant biomass—carbohydrate-active enzyme (CAZyme) and carbon catabolic genes. The majority of polysaccharide-degrading CAZyme genes were repressed and included activities toward all major carbohydrate polymers present in plant cell walls, while repression of ligninolytic genes also occurred. The transcriptome-level repression of the CAZyme genes observed on the Avicel cultures was strongly supported by exoproteomics. Protease-encoding genes were generally not glucose repressed, indicating their likely dominant role in scavenging for nitrogen rather than carbon. The extent of CCR is surprising, given that D. squalens rarely experiences high free sugar concentrations in its woody environment, and it indicates that biotechnological use of D. squalens for modification of plant biomass would benefit from derepressed or constitutively CAZyme-expressing strains. IMPORTANCE White-rot fungi are critical to the carbon cycle because they can mineralize all wood components using enzymes that also have biotechnological potential. The occurrence of carbon catabolite repression (CCR) in white-rot fungi is poorly understood. Previously, CCR in wood-rotting fungi has only been demonstrated for a small number of genes. We demonstrated widespread glucose-mediated CCR of plant biomass utilization in the white-rot fungus Dichomitus squalens. This indicates that the CCR mechanism has been largely retained even though wood-rotting fungi rarely experience commonly considered CCR conditions in their woody environment. The general lack of repression of genes encoding proteases along with the reduction in secreted CAZymes during CCR suggested that the retention of CCR may be connected with the need to conserve nitrogen use during growth on nitrogen-scarce wood. The widespread repression indicates that derepressed strains could be beneficial for enzyme production.

scholarly journals Expression of the Laccase Gene from a White Rot Fungus in Pichia pastoris Can Enhance the Resistance of This Yeast to H2O2-Mediated Oxidative Stress by Stimulating the Glutathione-Based Antioxidative System

2012 ◽  
Vol 78 (16) ◽  
pp. 5845-5854 ◽  
Author(s):  
Yang Yang ◽  
Fangfang Fan ◽  
Rui Zhuo ◽  
Fuying Ma ◽  
Yangmin Gong ◽  
...  
Keyword(s):  
Oxidative Stress ◽  
Gene Expression ◽  
Pichia Pastoris ◽  
Oxidative Damage ◽  
White Rot ◽  
Antioxidative System ◽  
White Rot Fungus ◽  
Laccase Gene ◽  
Content Type ◽  
Glutamylcysteine Synthetase

ABSTRACTLaccase is a copper-containing polyphenol oxidase that has great potential in industrial and biotechnological applications. Previous research has suggested that fungal laccase may be involved in the defense against oxidative stress, but there is little direct evidence supporting this hypothesis, and the mechanism by which laccase protects cells from oxidative stress also remains unclear. Here, we report that the expression of the laccase gene from white rot fungus inPichia pastoriscan significantly enhance the resistance of yeast to H2O2-mediated oxidative stress. The expression of laccase in yeast was found to confer a strong ability to scavenge intracellular H2O2and to protect cells from lipid oxidative damage. The mechanism by which laccase gene expression increases resistance to oxidative stress was then investigated further. We found that laccase gene expression inPichia pastoriscould increase the level of glutathione-based antioxidative activity, including the intracellular glutathione levels and the enzymatic activity of glutathione peroxidase, glutathione reductase, and γ-glutamylcysteine synthetase. The transcription of the laccase gene inPichia pastoriswas found to be enhanced by the oxidative stress caused by exogenous H2O2. The stimulation of laccase gene expression in response to exogenous H2O2stress further contributed to the transcriptional induction of the genes involved in the glutathione-dependent antioxidative system, includingPpYAP1,PpGPX1,PpPMP20,PpGLR1, andPpGSH1. Taken together, these results suggest that the expression of the laccase gene inPichia pastoriscan enhance the resistance of yeast to H2O2-mediated oxidative stress by stimulating the glutathione-based antioxidative system to protect the cell from oxidative damage.

scholarly journals Interdependence of Primary Metabolism and Xenobiotic Mitigation Characterizes the Proteome of Bjerkandera adusta during Wood Decomposition

2017 ◽  
Vol 84 (2) ◽  
Author(s):  
S. C. Moody ◽  
E. Dudley ◽  
J. Hiscox ◽  
L. Boddy ◽  
D. C. Eastwood
Keyword(s):  
Incubation Temperature ◽  
Protein Profile ◽  
Nutrient Acquisition ◽  
Protein Domain ◽  
White Rot ◽  
White Rot Fungus ◽  
Primary Metabolism ◽  
Bjerkandera Adusta ◽  
Content Type ◽  
Key Features

ABSTRACTThe aim of the current work was to identify key features of the fungal proteome involved in the active decay of beechwood blocks by the white rot fungusBjerkandera adustaat 20°C and 24°C. A combination of protein and domain analyses ensured a high level of annotation, which revealed that while the variation in the proteins identified was high between replicates, there was a considerable degree of functional conservation between the two temperatures. Further analysis revealed differences in the pathways and processes employed by the fungus at the different temperatures, particularly in relation to nutrient acquisition and xenobiotic mitigation. Key features showing temperature-dependent variation in mechanisms for both lignocellulose decomposition and sugar utilization were found, alongside differences in the enzymes involved in mitigation against damage caused by toxic phenolic compounds and oxidative stress.IMPORTANCEThis work was conducted using the wood decay fungusB. adusta, grown on solid wood blocks to closely mimic the natural environment, and gives greater insight into the proteome of an important environmental fungus during active decay. We show that a change in incubation temperature from 20°C to 24°C altered the protein profile. Proteomic studies in the field of white-rotting basidiomycetes have thus far been hampered by poor annotation of protein databases, with a large proportion of proteins simply with unknown function. This study was enhanced by extensive protein domain analysis, enabling a higher level of functional assignment and greater understanding of the proteome composition. This work revealed a strong interdependence of the primary process of nutrient acquisition and specialized metabolic processes for the detoxification of plant extractives and the phenolic breakdown products of lignocellulose.

scholarly journals Induction of Genes Encoding Plant Cell Wall-Degrading Carbohydrate-Active Enzymes by Lignocellulose-Derived Monosaccharides and Cellobiose in the White-Rot FungusDichomitus squalens

2018 ◽  
Vol 84 (11) ◽  
Author(s):  
Sara Casado López ◽  
Mao Peng ◽  
Tedros Yonatan Issak ◽  
Paul Daly ◽  
Ronald P. de Vries ◽  
...  
Keyword(s):  
Cell Wall ◽  
Plant Cell ◽  
Plant Cell Wall ◽  
Plant Biomass ◽  
Expression Patterns ◽  
Fine Tuning ◽  
White Rot ◽  
White Rot Fungus ◽  
Content Type ◽  
Dichomitus Squalens

ABSTRACTFungi can decompose plant biomass into small oligo- and monosaccharides to be used as carbon sources. Some of these small molecules may induce metabolic pathways and the production of extracellular enzymes targeted for degradation of plant cell wall polymers. Despite extensive studies in ascomycete fungi, little is known about the nature of inducers for the lignocellulolytic systems of basidiomycetes. In this study, we analyzed six sugars known to induce the expression of lignocellulolytic genes in ascomycetes for their role as inducers in the basidiomycete white-rot fungusDichomitus squalensusing a transcriptomic approach. This identified cellobiose andl-rhamnose as the main inducers of cellulolytic and pectinolytic genes, respectively, ofD. squalens. Our results also identified differences in gene expression patterns between dikaryotic and monokaryotic strains ofD. squalenscultivated on plant biomass-derived monosaccharides and the disaccharide cellobiose. This suggests that despite conservation of the induction between these two genetic forms ofD. squalens, the fine-tuning in the gene regulation of lignocellulose conversion is differently organized in these strains.IMPORTANCEWood-decomposing basidiomycete fungi have a major role in the global carbon cycle and are promising candidates for lignocellulosic biorefinery applications. However, information on which components trigger enzyme production is currently lacking, which is crucial for the efficient use of these fungi in biotechnology. In this study, transcriptomes of the white-rot fungusDichomitus squalensfrom plant biomass-derived monosaccharide and cellobiose cultures were studied to identify compounds that induce the expression of genes involved in plant biomass degradation.

Mode of coniferous wood decay by the white rot fungus Phanerochaete carnosa as elucidated by FTIR and ToF-SIMS

2012 ◽  
Vol 94 (5) ◽  
pp. 1303-1311 ◽  
Author(s):  
Sonam Mahajan ◽  
Dragica Jeremic ◽  
Robyn E. Goacher ◽  
Emma R. Master
Keyword(s):  
Wood Decay ◽  
White Rot ◽  
White Rot Fungus ◽  
Tof Sims ◽  
Phanerochaete Carnosa ◽  
Coniferous Wood

scholarly journals Heterologous Production and Characterization of Two Glyoxal Oxidases from Pycnoporus cinnabarinus

2016 ◽  
Vol 82 (16) ◽  
pp. 4867-4875 ◽  
Author(s):  
Marianne Daou ◽  
François Piumi ◽  
Daniel Cullen ◽  
Eric Record ◽  
Craig B. Faulds
Keyword(s):  
Substrate Specificity ◽  
Metal Ion ◽  
Inorganic Compounds ◽  
Glyoxylic Acid ◽  
Catalytic Efficiency ◽  
White Rot ◽  
White Rot Fungus ◽  
Pycnoporus Cinnabarinus ◽  
Content Type ◽  
Glyoxal Oxidase

ABSTRACTThe genome of the white rot fungusPycnoporus cinnabarinusincludes a large number of genes encoding enzymes implicated in lignin degradation. Among these, three genes are predicted to encode glyoxal oxidase, an enzyme previously isolated fromPhanerochaete chrysosporium. The glyoxal oxidase ofP. chrysosporiumis physiologically coupled to lignin-oxidizing peroxidases via generation of extracellular H2O2and utilizes an array of aldehydes and α-hydroxycarbonyls as the substrates. Two of the predicted glyoxal oxidases ofP. cinnabarinus, GLOX1 (PciGLOX1) and GLOX2 (PciGLOX2), were heterologously produced inAspergillus nigerstrain D15#26 (pyrGnegative) and purified using immobilized metal ion affinity chromatography, yielding 59 and 5 mg of protein forPciGLOX1 andPciGLOX2, respectively. Both proteins were approximately 60 kDa in size and N-glycosylated. The optimum temperature for the activity of these enzymes was 50°C, and the optimum pH was 6. The enzymes retained most of their activity after incubation at 50°C for 4 h. The highest relative activity and the highest catalytic efficiency of both enzymes occurred with glyoxylic acid as the substrate. The twoP. cinnabarinusenzymes generally exhibited similar substrate preferences, butPciGLOX2 showed a broader substrate specificity and was significantly more active on 3-phenylpropionaldehyde.IMPORTANCEThis study addresses the poorly understood role of how fungal peroxidases obtain anin situsupply of hydrogen peroxide to enable them to oxidize a variety of organic and inorganic compounds. This cooperative activity is intrinsic in the living organism to control the amount of toxic H2O2in its environment, thus providing a feed-on-demand scenario, and can be used biotechnologically to supply a cheap source of peroxide for the peroxidase reaction. The secretion of multiple glyoxal oxidases by filamentous fungi as part of a lignocellulolytic mechanism suggests a controlled system, especially as these enzymes utilize fungal metabolites as the substrates. Two glyoxal oxidases have been isolated and characterized to date, and the differentiation of the substrate specificity of the two enzymes produced byPycnoporus cinnabarinusillustrates the alternative mechanisms existing in a single fungus, together with the utilization of these enzymes to prepare platform chemicals for industry.

scholarly journals Role of P450 Monooxygenases in the Degradation of the Endocrine-Disrupting Chemical Nonylphenol by the White Rot Fungus Phanerochaete chrysosporium

2009 ◽  
Vol 75 (17) ◽  
pp. 5570-5580 ◽  
Author(s):  
Venkataramanan Subramanian ◽  
Jagjit S. Yadav
Keyword(s):  
Phanerochaete Chrysosporium ◽  
Protein Identification ◽  
Enzyme Inhibitor ◽  
White Rot ◽  
White Rot Fungus ◽  
Malt Extract ◽  
P450 Monooxygenase ◽  
Genome Wide ◽  
A Genome

ABSTRACT 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 (∼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.

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