<p>We performed a comparative analysis of the expression levels of proteins secreted by Phanerochaete chrysosporium cultured with either untreated or ammonia-treated lignocellulosic biomass. In the culture with ammonia-treated biomass, the relative production of a xylanase belonging to the glycoside hydrolase (GH) family 11 increased significantly, while that of acetyl xylan esterases, belonging to carbohydrate esterase family 1, decreased. During the enzymatic saccharificaion of the ammonia-treated biomass, the addition of a xylanase (belonging to GH family 11) to the culture with non-treated birch wood meal significantly increased saccharification yield. These results indicated that P. chrysosporium produced enzymes related to degradation of the de-acetylated xylan-containing biomass. Therefore, enzymes with potential applications in biofuel production, such as xylanase belonging to GH family 11, could be selected from the sequenced genome of P. chrysosporium. Importantly, utilization of these data to assist in the selection of enzyme cocktails for effective degradation of lignocellulosic biomass might contribute to the development and production of biofuels.</p>