Lignocellulolytic carbohydrate-active enzyme-encoding gene clusters in novelTrichoderma atrovirideandTrichoderma harzianumstrains: A BAC-guided transcriptome analysis

Abstract

AbstractLignocellulosic biomass is a challenging substrate for enzymatic hydrolysis and therefore increases the process cost in biorefineries. In nature, filamentous fungi naturally degrade lignocellulose by using an arsenal of hydrolytic and oxidative enzymes, specifically, carbohydrate-active enzymes (CAZymes). These fungi, including those of the genusTrichoderma, produce and secrete an arsenal of CAZymes that act synergistically to efficiently degrade complex and recalcitrant substrates.Trichoderma atrovirideCBMAI-0020 andTrichoderma harzianumCBMAI-0179 are biocontrol strains against important phytopathogens and naturally degrade lignocellulosic substrates. We employed the bacterial artificial chromosome (BAC) methodology together with gene expression data under cellulose degradation conditions to identify novel degradative enzymes, explore their proximal context, and identify CAZyme gene clusters. Using this simple, time-saving, and cost-effective molecular tool, it was possible to identify genomic regions rich in CAZymes. We found important gene clusters related to lignocellulose degradation by inspecting the linear structure and expression data of CAZyme-rich regions. The results offered a genomic perspective of important regions related to carbohydrate metabolism, uncovering novel targets positively regulated in the degradation of lignocellulose and helping to elucidate differences in biomass degradation amongTrichodermaspecies.