The first genome-level transcriptome of the wood-degrading fungus Phanerochaete chrysosporium grown on red oak

Abstract

As part of an effort to determine all the gene products involved in wood degradation, we have performed massively parallel pyrosequencing on an expression library from the white rot fungus Phanerochaete chrysosporium grown in shallow stationary cultures with red oak as the carbon source. Approximately 48,000 high quality sequence tags (246 bp average length) were generated. 53% of the sequence tags aligned to 4,262 P. chrysosporium gene models, and an additional 18.5% of the tags reliably aligned to the P. chrysosporium genome providing evidence for 961 putative novel fragmented gene models. Due to their role in lignocellulose degradation, the secreted proteins were focused upon. Our results show that the four enzymes required for cellulose degradation: endocellulase, exocellulase CBHI, exocellulase CBHII, and beta-glucosidase are all produced. For hemicellulose degradation, not all known enzymes were produced, but endoxylanases, acetyl xylan esterases and mannosidases were detected. For lignin degradation, the role of peroxidases has been questioned; however, our results show that lignin peroxidase is highly expressed along with the H(2)O(2) generating enzyme, alcohol oxidase. The transcriptome snapshot reveals that H(2)O(2) generation and utilization are central in wood degradation. Our results also reveal new transcripts that encode extracellular proteins with no known function.

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

“…For example, previous transcriptome sequencing of P. carnosa suggested a principal role for manganese peroxidase (MnP) activity in lignin degradation (9). Moreover, the abundance of transcripts encoding lignindegrading activity were much higher than those encoding carbohydrate-active enzymes, which is consistent with the selective lignin decay elicited by P. carnosa grown on softwood (10) but opposite to previous transcriptomic analyses of Phanerochaete chrysosporium grown on hardwood (12,20). However, the transcriptome study of P. carnosa analyzed a single time point, and it is known that enzyme and transcript expression in white-rot fungi growing on lignocellulosic substrates can vary over time (2,16,18).…”

Transcriptomic Responses of Phanerochaete chrysosporium to Oak Acetonic Extracts: Focus on a New Glutathione Transferase

“…The induction of genes coding for enzymes involved in the extracellular degradation of aromatic compounds suggests putative extracellular oxidation of the tannin-derived molecules. Indeed, genes coding for a chloroperoxidase and a benzoquinone reductase and five genes coding for some class II peroxidases (lignin and manganese peroxidases) are induced by oak extracts (38). The cDNAs highly expressed in that study on wood material also are globally upregulated in our study.…”

“…Genes coding for carbohydrate active enzymes (CAZymes) also have been found differentially expressed under our conditions (Table 3). Again, some of the genes induced by oak extracts are highly expressed in wood (38). This is the case for some cellobiohydrolases (ProtID 127029, 129072, and 133052), endoglucanases (ProtID 129325, 41563, and 31049), ␤-glucosidase (ProtID 8072), endoxylanase (ProtID 133788, 138715, and 138345), and acetyl xylan esterase (ProtID 130517) ( Table 3; also see Table S1 in the supplemental material) (38).…”

“…Again, some of the genes induced by oak extracts are highly expressed in wood (38). This is the case for some cellobiohydrolases (ProtID 127029, 129072, and 133052), endoglucanases (ProtID 129325, 41563, and 31049), ␤-glucosidase (ProtID 8072), endoxylanase (ProtID 133788, 138715, and 138345), and acetyl xylan esterase (ProtID 130517) ( Table 3; also see Table S1 in the supplemental material) (38). Inversely, we show a downregulation leading to very low expression of genes coding for alcohol oxidase (ProtID 126879), cellobiohydrolase (ProtID 137372), endoglucanase (ProtID 6458 and 8466), and endomannanase (ProtID 140501), while from 72 to 377 tags have been reported for these genes in the culture with oak.…”

Cellotriose and Cellotetraose as Inducers of the Genes Encoding Cellobiohydrolases in the Basidiomycete Phanerochaete chrysosporium

“…Identification and analysis of the effects of the compounds contained in these peaks will be necessary to understand the modes of expression control of the genes. Recently, transcriptome and secretome analyses of P. chrysosporium have revealed a complex pattern of production of wood-degrading enzymes (33,34,53,55), but detailed investigation of the regulatory mechanisms involved remains to be undertaken. The results presented here indicate that cellotriose and cellotetraose are candidates for natural inducers generated by cellulose hydrolysis, whereas cellobiose was not effective.…”