Genomic and Secretomic Analyses Reveal Unique Features of the Lignocellulolytic Enzyme System of Penicillium decumbens

Abstract

Many Penicillium species could produce extracellular enzyme systems with good lignocellulose hydrolysis performance. However, these species and their enzyme systems are still poorly understood and explored due to the lacking of genetic information. Here, we present the genomic and secretomic analyses of Penicillium decumbens that has been used in industrial production of lignocellulolytic enzymes in China for more than fifteen years. Comparative genomics analysis with the phylogenetically most similar species Penicillium chrysogenum revealed that P. decumbens has evolved with more genes involved in plant cell wall degradation, but fewer genes in cellular metabolism and regulation. Compared with the widely used cellulase producer Trichoderma reesei, P. decumbens has a lignocellulolytic enzyme system with more diverse components, particularly for cellulose binding domain-containing proteins and hemicellulases. Further, proteomic analysis of secretomes revealed that P. decumbens produced significantly more lignocellulolytic enzymes in the medium with cellulose-wheat bran as the carbon source than with glucose. The results expand our knowledge on the genetic information of lignocellulolytic enzyme systems in Penicillium species, and will facilitate rational strain improvement for the production of highly efficient enzyme systems used in lignocellulose utilization from Penicillium species.

The genome sequence of the soft-rot fungus Penicillium purpurogenum reveals a high gene dosage for lignocellulolytic enzymes

“…Alignments were carried out using BLASTp version 2.2.29+ and were filtered for the first 10 hits with a cut-off e -value of 10 –5 as suggested in the literature (Clarke et al 2013; Liu et al 2013). BLASTp alignments against the non-redundant RefSeq protein database (22 January 2014) (Ye et al 2006; Pruitt et al 2012), UniProt (22 January 2014) (Consortium 2014) (including Swiss-Prot, fungal taxonomic division and uniref90) and KEGG (Release 69.0, 1 January 2014) (Kanehisa et al 2002) were performed to assign general protein function profiles.…”

“…However, several members of this genus have been reported as good producers of cellulases and xylanases. A strain of Penicillium decumbens (Liu et al 2013) has been used for industrial-scale cellulase production in China since 1996, and Gusakov and Sinitsyn (2012) have reviewed the production of cellulases by a set of Pencillium species, some of whose enzymes show superior performance to those of the better-known Trichoderma .…”

Genetic modification: a tool for enhancing cellulase secretion

“…Liu et al (2013b) sequenced and compared Penicillium decumbens (which was later identified as P. oxalicum) mutant JU-A10-T gene with the wild strain 112-2; transcriptomes and secretomes were also compared. P. oxalicum was selected for its strong cellulolytic ability in saprophytic condition.…”

Horizontal gene transfer and gene dosage drives adaptation to wood colonization in a tree pathogen

“…P. oxalicum is a saprophytic fungus commonly associated with wood decay and possesses improved lignocellulose degradation abilities (26). The striking conservation in synteny and gene sequence as well as the sporadic distribution of the full cluster in only two groups of the fungal phylogeny (Dothideomycetes and Eurotiales) raises the possibility that this cluster was acquired through horizontal gene transfer (HGT) (Fig.…”