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24 p.-8 fig.-4 tab.-- Levasseur, Anthony et al., [Background] Saprophytic filamentous fungi are ubiquitous micro-organisms that play an essential role in photosynthetic carbon recycling. The wood-decayer Pycnoporus cinnabarinus is a model fungus for the study of plant cell wall decomposition and is used for a number of applications in green and white biotechnology., [Results] The 33.6 megabase genome of P. cinnabarinus was sequenced and assembled, and the 10,442 predicted genes were functionally annotated using a phylogenomic procedure. In-depth analyses were carried out for the numerous enzyme families involved in lignocellulosic biomass 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. P. cinnabarinus is thus fully equipped with the classical families involved in cellulose and hemicellulose degradation, whereas its pectinolytic repertoire appears relatively limited. In addition, P. cinnabarinus possesses a complete versatile enzymatic arsenal for lignin breakdown. We identified several genes encoding members of the three ligninolytic peroxidase types, namely lignin peroxidase, manganese peroxidase and versatile peroxidase. Comparative genome analyses were performed in fungi displaying different nutritional strategies (white-rot and brown-rot modes of decay). P. cinnabarinus presents a typical distribution of all the specific families found in the white-rot life style. Growth profiling of P. cinnabarinus was performed on 35 carbon sources including simple and complex substrates to study substrate utilization and preferences. P. cinnabarinus grew faster on crude plant substrates than on pure, mono- or polysaccharide substrates. 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 growth conditions, especially for lytic polysaccharide mono-oxygenases., [Conclusions] With its available genome sequence, P. cinnabarinus is now an outstanding model system for the study of the enzyme machinery involved in the degradation or transformation of lignocellulosic biomass., This work was funded by the Commission of the European Communities through the BIORENEW project (NMP2-CT-2006-026456 “White Biotechnology for added-value products from re newable plant polymers: Design of tailor-made biocatalysts and new industrial bioprocesses”) and the PEROXICATS project (KBBE-2010-4-265397 “Novel and more robust fungal peroxidases as industrial biocatalysts.”), and by the Spanish Ministerio de Economía y Competitividad (MINECO) through the HIPOP project (BIO2011-26694, “Screening and engineering of new high-redox-potential peroxidases”).

Document Type : Book Chapter; A number of microorganisms, bacteria and filamentous fungi, are able to degrade lignocellulosic components to various extents. However, only a few ones can degrade lignins, among which wood-rotting fungi. White-rot fungi, the most frequent ones, mineralize cell wall components (cellulose, hemicelluloses and lignins) and extensively degrade lignins, which results in a bleached aspect of decayed wood. Fungal lignin degradation involves secreted heme-peroxidases and laccases that use oxidants as electron acceptors (H2O2 and O-2). The three main heme-peroxidases are lignin peroxidases, manganese peroxidases and versatile peroxidases. Lignin and versatile peroxidases are able to oxidize non-phenolic lignin units. By contrast, manganese peroxidase needs diffusible Mn-chelated ions and mainly degrades lignin units with free phenolic groups. Other peroxidases have been recently found, such as dye peroxidases with potential applications in bioremediation and other industrial processes. Peroxidases need the cooperation of other oxidases such as glyoxal or aryl-alcohol oxidases to produce hydrogen peroxide. The recent availability of complete fungal genomes opens innovative opportunities to annotate lignocellulolytic gene families. Phylogenetic approaches are unique tools to comparatively analyse these data and predict or infer gene function. The increasing number of putative lignin-degrading enzymes emerging from genome analyses requires the development of high-throughput expression systems to meet the demands of industries. Several expression systems have been developed to produce more efficient recombinant 'ligninases' and auxiliary enzymes. Fungi and yeasts are useful hosts for the production of recombinant enzymes, but only a few ones are devoted to ligninase production. In this review, we give a survey of the main fungal and enzymatic actors of lignin degradation before discussing the phylogenetic inference strategy used to predict lignocellulolytic enzymes and reviewing the recombinant production of these enzymes in fungal hosts.