Transcriptomics of white rot fungal decay of spruce wood and bioconversion of waste lignocellulose substrates by the Polyporales species Phlebia radiata

Mari Mäkinen 1 Jaana Kuuskeri 1 Hans Mattila 1 Netta Risulainen 1 Anna Hartikainen 1 Pia Laine 2 Olli-Pekka Smolander 2 Lars Paulin 2 Markku Varjosalo 2 Petri Auvinen 2 Taina Lundell 1
1Department of Microbiology, University of Helsinki, Helsinki, Finland
2Institute of Biotechnology, University of Helsinki, Helsinki, Finland

White rot Basidiomycota species secrete an array of carbohydrate-active enzymes and lignin-modifying oxidoreductases, in order to decompose wood lignocellulose polysaccharides and lignin. Phlebia radiata, the type species of the genus Phlebia, in phlebioid clade of the order Polyporales, is an ecologically important species able to decompose efficiently the main components of plant cell wall (1) and presenting high applicability in biotechnological processes, especially in production of ethanol from non-pretreated lignocellulose waste materials by a single-step process (2).

Genome sequencing of P. radiata resulted in construction of the mitochondrial genome (3) and in high-quality assembly and annotation of the nuclear genome. Transcriptomics by RNA-seq and proteomics analysis upon a six-week cultivation on Norway spruce wood confirmed the up-regulation of plant-cell wall degradation associated genes needed for white rot type of decay and production of the corresponding proteins upon fungal colonization of wood (4). Especially, the lignin-modifying class-II peroxidases together with glyoxal and alcohol oxidases were abundantly produced on wood indicating an initial oxidative attack against lignin units, while dynamic changes in quantities of LiP and MnP enzymes were detected, and several AA9 lytic polysaccharide monooxygenase encoding genes were highly up-regulated.

Expression of lignocellulose-decomposition associated genes and enzyme activities were studied while P. radiata was grown on lignocellulose waste materials and simultaneously producing ethanol under semi-aerobic conditions. RT-qPCR results supported the importance of specific genes coding for activities against cellulose, hemicellulose and lignin, also in conversion of the waste substrates. Indications on regulation of specific genes involved in glucose and xylose metabolism were obtained under fermentation conditions resulting in ethanol production from waste lignocelluloses, which will be discussed.

(1) Kuuskeri J (2015) BMC Microbiology 15:217

(2) Mattila H (2017) Bioresource Technology 225:254-261

(3) Salavirta H (2014) PLoS ONE 9(5):e97141

(4) Kuuskeri J (2016) Biotechnology for Biofuels 9:192