Abstract
BackgroundThe genome of Pleurotus ostreatus, an important edible mushroom and a model ligninolytic organism of interest in lignocellulose biorefineries due to its ability to delignify agricultural wastes, was sequenced with the purpose of identifying and characterizing the enzymes responsible for lignin degradation.ResultsHeterologous expression of the class II peroxidase genes, followed by kinetic studies, enabled their functional classification. The resulting inventory revealed the absence of lignin peroxidases (LiPs) and the presence of three versatile peroxidases (VPs) and six manganese peroxidases (MnPs), the crystal structures of two of them (VP1 and MnP4) were solved at 1.0 to 1.1 Å showing significant structural differences. Gene expansion supports the importance of both peroxidase types in the white-rot lifestyle of this fungus. Using a lignin model dimer and synthetic lignin, we showed that VP is able to degrade lignin. Moreover, the dual Mn-mediated and Mn-independent activity of P. ostreatus MnPs justifies their inclusion in a new peroxidase subfamily. The availability of the whole POD repertoire enabled investigation, at a biochemical level, of the existence of duplicated genes. Differences between isoenzymes are not limited to their kinetic constants. Surprising differences in their activity T50 and residual activity at both acidic and alkaline pH were observed. Directed mutagenesis and spectroscopic/structural information were combined to explain the catalytic and stability properties of the most interesting isoenzymes, and their evolutionary history was analyzed in the context of over 200 basidiomycete peroxidase sequences.ConclusionsThe analysis of the P. ostreatus genome shows a lignin-degrading system where the role generally played by LiP has been assumed by VP. Moreover, it enabled the first characterization of the complete set of peroxidase isoenzymes in a basidiomycete, revealing strong differences in stability properties and providing enzymes of biotechnological interest.
Highlights
The genome of Pleurotus ostreatus, an important edible mushroom and a model ligninolytic organism of interest in lignocellulose biorefineries due to its ability to delignify agricultural wastes, was sequenced with the purpose of identifying and characterizing the enzymes responsible for lignin degradation
Peroxidase genes in the genome of P. ostreatus Seventeen putative peroxidase genes were identified in the genomes of each of the two P. ostreatus monokaryons (PC9 and PC15) sequenced at Joint Genome Institute (JGI)
One of them is substituted by one aspartate/glutamate in the superfamily of dye-decolorizing peroxidases (DyPs), while one cysteine and one glutamate occupy their positions in the heme-thiolate peroxidase (HTP) superfamily [19,20]
Summary
The genome of Pleurotus ostreatus, an important edible mushroom and a model ligninolytic organism of interest in lignocellulose biorefineries due to its ability to delignify agricultural wastes, was sequenced with the purpose of identifying and characterizing the enzymes responsible for lignin degradation. From an ecophysiological point of view, Pleurotus species belong to the group of fungi causing a so-called white rot of wood and other lignocellulosic materials, due to their ability to degrade the recalcitrant lignin polymer that protects polysaccharides in vascular plants [4] Among these fungi, Pleurotus species are of particular biotechnological interest because they degrade lignin selectively (that is, with limited attack on cellulose) when growing on cereal straw and related materials [5]. From 2004, when the first basidiomycete genome (from the model white-rot fungus Phanerochaete chrysosporium) was sequenced at the Joint Genome Institute (JGI; Walnut Creek, CA, USA) [12], the US Department of Energy (DOE) has funded genome sequencing of ascomycetes and basidiomycetes that are potentially applicable in lignocellulose biorefineries The latter fungi include the brown-rot basidiomycetes Rhodonia placenta (synonym: Postia placenta) and Serpula lacrymans (which are able to use wood cellulose without the prior removal of lignin) [13,14] and the selective degrader of wood lignin Gelatoporia subvermispora (synonym: Ceriporiopsis subvermispora) [15], among others. Over 30 fungal genomes were comparatively analyzed to obtain an overview of the enzymatic machinery involved in the two main types of wood decay (white rot and brown rot), and to establish the evolutionary history of ligninolytic peroxidases belonging to class II of the superfamily of non-animal (plant-fungal-prokaryotic) heme peroxidases (hereinafter PODs) [16]
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a call
