Genome, transcriptome and proteome studies lead to interesting but perturbing questions. Several studies indicate that fungi could secrete up to 50 different CWDE in order to degrade cellulose, hemicellulose, pectin and, for some of them, lignin. Among these enzymes, some display the same EC number and/or belong to the same glycosyl hydrolase family (GH). Why fungi use up so much energy to secrete enzymes with quite similar activities? Is it true or apparent redundancy?

Several clues indicate that this is apparent redundancy. Most of the CWDE, still putative, wait for potent substrate specificities characterization. By analogy with the enzymes already characterized, it means that slightly different specificities are likely to be discovered and could be essential to complete plant cell wall degradation. Furthermore, quantitative studies performed on Fusarium hemicellulases demonstrate that on hop cell wall, the expression level of the 30 putative enzymes varies greatly from 1 (the less abundant) to 1500 (Hatsch et al., 2006). When another biomass is used for growth, the pattern of secreted enzymes is different, clearly indicating that there is no "general response" to the presence of plant material but specific responses to a given biomass. Taken together these studies mean that
the fungus exhibits a large flexibility in its response. Then it could be thought that the observed redundancy actually reflects the multitude of different structures of plant cell wall. Consequently, it is of primary importance that in silico studies should be carefully validated by enzymatic measurements. For example, an exponential increase of putative CAZY (Carbohydrate-Active enZYmes) described is observed, but unfortunately only a small proportion of them are biochemically characterized yet (Cantarel et al., 2009). Whereas entries in CAZY database increased exponentially from 1999 to 2007 (a 14-fold increase), less than 10% of them have been enzymatically characterized and less than 1% of the enzyme structures have been solved. This means that there is a real lack in enzyme knowledge regarding to the huge potential of new activities undiscovered yet. It should be noticed that the increasing difference between the number of putative enzymes and well characterized ones also lead to the possibility of mis-annotation and/or false identification. This phenomenon has been known for a long time by molecular biologists and correction of errors and inconsistencies in data bases became an authentic research area (Ghisalberti et al., 2010). In order to thoroughly characterize the enzyme activities and their capacity to degrade the complex structures found in plant cell wall, CWDE substrate specificity should be determined with both artificial and natural substrates. This absolute necessity drives us to perform the characterization of the enzyme cocktail produced by F. graminearum on hop cell wall. We used 29 different substrates, poly-or oligosaccharides, natural or artificial (Phalip et al., 2009). Enzyme activities were evaluated by assays of the products (monomers) or by their visualization by polysaccharide analysis using carbohydrate gel electrophoresis (PACE). The conclusion of this study is that the enzymes constituting this cocktail are no more putative but active on each layer of the plant cell wall. On the opposite, the enzyme cocktail produced on glucose displays very tiny activities, furthermore on a small number of substrates. The proof is then provided that to get a large diversity of cell wall degrading enzymes, it is very important to choose the right substrate for a given fungus to grow.