Genomic and Proteomic Analyses Provide Insights into the Potential of Filamentous Fungi for Biomass Degradation
- Pp. 45-56 (12)Jean Marie Francois and Olivier Guais
Fungi are metabolically versatile organisms in Nature, existing either as free-living species, in association with other species, e.g. lichens, mycorrhiza, or as pathogens in animals and plants. They are characterized by their notable ability to degrade a wide variety of complex polysaccharides and recalcitrant waste organic materials. Their attractiveness in Biotechnology comes from the remarkable capacity to secrete a wide spectrum of enzymes that are used in food and for biomass degradation, as well as to produce a variety of secondary metabolites ranging from human therapeutics (e.g. antibacterial and antifungal agents) to specialty chemicals such as polyketides and organic acids. This minireview is mainly focused on filamentous fungi as a mycofactory for enzyme production dedicated for plant biomass (lignocellulose, hemicelluloses) degradation. As several filamentous fungi relevant to this industrial application have been recently sequenced, we will first provide an overview on the main fungal genome sequences, pointing out that 7 to 12 % of the gene content of these genomes codes for secreted proteins, collectively termed as the ‘secretome’, among which a significant proportion encodes putative ‘Carbohydrate-Active enzymes’. In the second part, we will review how the exoproteome, which represents the set of secreted proteins in the medium, has been initially characterized, and then show that a combination of computational, transcriptomic and proteomics methods is the most effective approach to reveal the reliability of predicted secretomes. At this stage, two major observations can be made. Firstly, the exoproteome of a fungus is strongly tied to its culture conditions and/or nutrient source. Secondly, and more interestingly, a catalog of genes encoding putative Carbohydrate Active enzymes greater than ever expected has been revealed from genome sequencing. Moreover, transcriptome analyses of filamentous fungi cultivated under cellulolytic/hemicellulolytic conditions have shed light on an impressive collection of upregulated genes encoding putative secreted proteins with yet uncharacterized function. Altogether, these new findings show that there is still a long way to go for a comprehensive understanding of the fungal secretome, which is the basis for a rational development of optimized strains in white biotechnology.