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

Abstract

Efficient lignin depolymerization is unique to the wood decay basidiomycetes, collectively referred to as white rot fungi. Phanerochaete chrysosporium simultaneously degrades lignin and cellulose, whereas the closely related species, Ceriporiopsis subvermispora, also depolymerizes lignin but may do so with relatively little cellulose degradation. To investigate the basis for selective ligninolysis, we conducted comparative genome analysis of C. subvermispora and P. chrysosporium. Genes encoding manganese peroxidase numbered 13 and five in C. subvermispora and P. chrysosporium, respectively. In addition, the C. subvermispora genome contains at least seven genes predicted to encode laccases, whereas the P. chrysosporium genome contains none. We also observed expansion of the number of C. subvermispora desaturase-encoding genes putatively involved in lipid metabolism. Microarray-based transcriptome analysis showed substantial up-regulation of several desaturase and MnP genes in wood-containing medium. MS identified MnP proteins in C. subvermispora culture filtrates, but none in P. chrysosporium cultures. These results support the importance of MnP and a lignin degradation mechanism whereby cleavage of the dominant nonphenolic structures is mediated by lipid peroxidation products. Two C. subvermispora genes were predicted to encode peroxidases structurally similar to P. chrysosporium lignin peroxidase and, following heterologous expression in Escherichia coli, the enzymes were shown to oxidize high redox potential substrates, but not Mn(2+). Apart from oxidative lignin degradation, we also examined cellulolytic and hemicellulolytic systems in both fungi. In summary, the C. subvermispora genetic inventory and expression patterns exhibit increased oxidoreductase potential and diminished cellulolytic capability relative to P. chrysosporium.

Fig. 1.

Phylogenetic analysis of selected peroxidases from C. subvermispora and P. chrysosporium. The analysis was performed in RAxML Blackbox under the model GTRGAMMA, using the substitution matrix WAG with 100 rapid bootstrap replicates. The ascomycete sequences of class II peroxidases were used to root the tree (http://phylobench.vital-it.ch/raxml-bb/) (32). Ball-milled aspen versus glucose transcript ratios (BMA/Glu) are indicated, and complete data are available under Gene Expression Omnibus accession nos. GSE1473 and GSE34636 for P. chrysosporium and C. subvermispora, respectively.

Fig. 2.

Phylogenetic analysis of all MCO oxidases from C. subvermispora, P. chrysosporium, and the related polypore P. placenta. Analysis was performed by using RAxML with the WAG substitution matrix, γ-distributed rates among sites, a proportion of invariant sites and empirical amino acid frequencies (i.e., m = PROTGAMMAIWAGF). Shown is the maximum-likelihood tree found by using 1,000 heuristic searches, with bootstrap support shown for nodes with values greater than 50%. As in Fig. 1, transcript level ratios are adjacent to protein identification numbers. Complete P. placenta microarray data are available under Gene Expression Omnibus accession no. GSE12540 (33).

Fig. 3.

Distribution of GHs in P. placenta (inner ring), C. subvermispora (middle ring), and P. chrysosporium (outer ring). Families absent from at least one species are underlined. Detailed listings of gene numbers within these and other species appear in Dataset S1, and expression patterns (transcript and protein) are presented in SI Appendix, Table S1.