Comparative Transcriptome and Secretome Analysis of Wood Decay Fungi Postia placenta and Phanerochaete chrysosporium

Abstract

Cellulose degradation by brown rot fungi, such as Postia placenta, is poorly understood relative to the phylogenetically related white rot basidiomycete, Phanerochaete chrysosporium. To elucidate the number, structure, and regulation of genes involved in lignocellulosic cell wall attack, secretome and transcriptome analyses were performed on both wood decay fungi cultured for 5 days in media containing ball-milled aspen or glucose as the sole carbon source. Using liquid chromatography-tandem mass spectrometry (LC-MS/MS), a total of 67 and 79 proteins were identified in the extracellular fluids of P. placenta and P. chrysosporium cultures, respectively. Viewed together with transcript profiles, P. chrysosporium employs an array of extracellular glycosyl hydrolases to simultaneously attack cellulose and hemicelluloses. In contrast, under these same conditions, P. placenta secretes an array of hemicellulases but few potential cellulases. The two species display distinct expression patterns for oxidoreductase-encoding genes. In P. placenta, these patterns are consistent with an extracellular Fenton system and include the upregulation of genes involved in iron acquisition, in the synthesis of low-molecular-weight quinones, and possibly in redox cycling reactions.

Comparative genomics of Ceriporiopsis subvermispora and Phanerochaete chrysosporium provide insight into selective ligninolysis

“…See Gene Expression Omnibus accession no. GSE14736 (33) for P. chrysosporium data. Both gene families are expanded in C. subvermispora relative to P. chrysosporium.…”

Localizing gene regulation reveals a staggered wood decay mechanism for the brown rot fungus Postia placenta

“…S2). This brief window of differential gene regulation has been missed in earlier studies of brown rot that used homogenized whole-wood specimens, likely because that approach inevitably mixes hyphae acting asynchronously at different stages of biodegradation (7,9,21,26,29).…”

“…2). Those differentially expressed CAZys that are likely involved in lignocellulose saccharification and have been predicted as secreted enzymes (50 total, 82% of them GHs) are listed in Table S2, including well-characterized endoglucanases Cel5A 115648/108962, Cel5B 103675/117690, and Cel12A 121191/112658, a xylanase (Xyn10A-1 113670/90657), and a mannanase (Man5A 57321/ 121831), as shown by previous work with P. placenta (9,26,29). Consistent with an increase in polysaccharide hydrolysis, sugar transporters, sugar-metabolic enzymes, and aldo keto reductases were also up-regulated during later decay stages (Dataset S3).…”

“…There is evidence that fungal methoxyhydroquinones with a role in reducing Fe 3+ to initiate Fenton chemistry are mostly secreted at the outset of brown rot, and then decrease as decay progresses (7,16,24,25). There is also evidence of inducible expression and secretion of enzymes among brown rot fungi (9,26), once characterized as having constitutive cellulase production (27). However, it has so far not been possible to determine whether the oxidative and GH systems are temporally separated by these fungi on wood.…”

Bioprocess Evaluation of Water Soaking-Based Microbiological Biodegradation with Exposure of Cellulosic Microfibers Relevant to Bioconversion Efficiency

“…2 and Table 2), the connective modules of both carbohydrateactive enzymes (CAZys; especially cellulose-binding region) and the ligninolytic degraders, ureidoglycolate hydrolase as a glyoxalate generator, as the hydrolysable triggers, were responsible for the optimized metabolic conversion of pre-processed RS into a fermentable carbon chain and ethanol. Remarkably, the expression level of CAZys, namely β-glucosidase, CDH, and hemicellulolytic xylanase, which are target factors for the practical downstream index, and peroxidative enzymes, including copper amine oxidase, in WSMB had a very low rate (fold <2) of intracellular activities in the context of cellulolytic mechanism, unlike previously identified microbial biosystems [26,33,34]. This difference is likely due to the platform being optimized for extracting cellulosic microfibers, which is based on the ligninolytic cascade via target optimization, especially by MnP.…”