The genome of the white-rot fungus Pycnoporus cinnabarinus: a basidiomycete model with a versatile arsenal for lignocellulosic biomass breakdown. Trametes cinnabarina BRFM137

The wood-decayer Pycnoporus cinnabarinus is a model fungus for the study of plant cell wall deconstruction, and is used for a number of biotechnological applications in green and white chemistry. The 33.6 megabase genome of P. cinnabarinus was sequenced and assembled, and the predicted 10,442 genes were functionally annotated using a phylogenomic procedure. In-depth analyses were carried out for the numerous enzyme families involved in the lignocellulose breakdown, for protein secretion and glycosylation pathways, and for mating type. The P. cinnabarinus genome sequence revealed a consistent repertoire of genes shared with wood-decaying basidiomycetes. Thus P. cinnabarinus is fully equipped with the classical families involved in cellulose and hemicellulose degradation, while its pectinolytic repertoire seems to be limited. In addition, P. cinnabarinus possesses a complete, versatile enzymatic arsenal for lignin deconstruction. We evidenced several genes encoding members of the three ligninolytic peroxidase types, namely lignin peroxidase, manganese peroxidase and versatile peroxidase (AA2). Comparative genome analyses were performed in fungi belonging to different nutritional modes (white-rot and brown-rot). P. cinnabarinus presents a typical distribution of all the specific families found in the white-rot mode of wood decay. The growth profiling of P. cinnabarinus was performed on 35 carbon sources including simple and complex substrates to study substrate utilization and preferences. The growth of P. cinnabarinus was faster on crude plant substrates than on pure, mono- or polysaccharide subtrates. Finally, proteomic analyses were conducted from liquid and solid-state fermentation to analyze the composition of the secretomes corresponding to growth on different substrates. The distribution of lignocellulolytic enzymes in the secretomes was strongly dependent on the growth conditions, especially for lytic polysaccharide mono-oxygenases. The sequencing of the P. cinnabarinus genome makes this organism an outstanding model system for the study of the enzyme machinery involved in the degradation or transformation of lignocellulose.