In order to appreciate if the information provided by genome analysis is pertinent, transcriptome studies should also be performed. Our purpose is not to describe the regulation of CWDE in fungi, but it is essential to determinate efficiency of CWDE transcription depending on growth conditions. The goal is of course to optimize conditions leading to high transcription of the required enzymes. This regulation is rather complex, variable and well described in reviews (as an example see Aro et al., 2005). However, global characteristics leading to transcription of hydrolases genes are interesting to point out, since they could be a rational strategy basis for ethanol production. First, and for a long time, CWDE genes were considered generally as being repressed by glucose (catabolic repression) and by other released monosaccharides upon polysaccharide hydrolysis (de Vries & Visser, 2001). On the opposite, CWDE are massively expressed when fungi are grown in presence of polysaccharides and plant material (de Vries & Visser, 2001; Foreman et al., 2003 ; Aro et al., 2005). However, the view of a strict co-regulation of all CWDE is wrong. Induction of a given hydrolase goes on as a function of the polysaccharide in contact with the fungus. An interesting illustration is found in the pea pathogen Nectria hematococca. Two pectate lyases were found to be involved in pathology (Rogers et al., 2000). The first one was induced by pectin and repressed in planta, whereas the other was induced in planta but repressed by pectin. This means that CWDE transcription could be individual and precise. In Fusarium graminearum, well known as pathogen of cereals, we performed microarray experiments to test the expression on the whole genome on glucose, cellulose, xylan and hop cell wall (Carapito et al., 2008). Methods and essential findings are summarized in Fig. 3.

First, some genes were actually found to be over-expressed on polysaccharides comparatively to their expression on glucose (Fig. 3.). Their number varies depending on carbon source. CWDE represent also a variable part of overexpressed genes. It is particularly interesting to note that the largest proportion of CWDE was observed when the fungus was grown on plant cell wall (19% of overexpressed genes) i. e. the most diverse substrate. It denotes a strong re-orientation of the metabolism towards cell wall degradation since CWDE correspond to approximately 0.5% of the genome only. Furthermore, cellulases, hemicellulases and pectinases encoding genes are quite equally represented as overexpressed ones when the fungus is grown on plant cell wall, whereas mostly cellulases were shown to be overexpressed on cellulose and mostly hemicellulases were overexpressed on xylan. This data suggest that there is no global response to the presence of plant cell wall, but that the different polysaccharides sent specific signals which are recognized by the fungus and induce various responses.