Transcriptional analysis of Trichoderma reesei cultivated in the presence of different lignocellulose substrates

Trichoderma reesei is a soft rot Ascomycete fungus able to secrete enzymes extremely efficiently. Availability of the complete genome sequence of T. reesei has made it possible to utilise genome wide methods to study protein production by the fungus and to utilise the information obtained to develop new strains with better enzyme production qualities. In order to study the co-expression of enzyme genes, a complete list of CAZymes of T. reesei needed to be obtained. Novel CAZymes were searched from the genome by mapping T. reesei proteome with Blast search to the protein sequences of the CAZY database. New annotation was given to several genes in order to gain more information on the possible function of novel candidate genes and to specify the annotation of previously identified genes. A phylogenetic approach was used to reveal the functional diversification of T. reesei enzyme genes within CAZY families and between the gene duplicates. Expression of the hydrolytic system of T. reesei Rut-C30 was studied by cultivating the fungus in the presence of different lignocellulose substrates. Cultures were subjected to transcriptional profiling using oligonucleotide microarrays. Differentially expressed genes were identified and expression profiles of genes encoding lignocellulose degrading enzymes were compared to identify co-regulated groups of genes and genes needed for the degradation of specific substrates. Transcriptional profiling revealed a group of genes co-regulated on all of the substrates and genes which expression profiles were more diverse. Also some examples were found from co-regulation of enzyme genes according to genomic localization.