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.
