Genomic and secretomic analyses reveal unique features of the lignocellulolytic enzyme system of Penicillium decumbens.

Guodong Liu,Yinbo Qu,Zhihua Zhou,Shengyue Wang,Guo-Ping Zhao,Yuqi Qin,Liang Ma,Luying Xun,Huajun Zheng,Jie Li,Xiaomin Wei,Lei Zhang,Chengshu Wang,Gen Zou

doi:10.1371/journal.pone.0055185

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.

Highlights

Biorefinery of lignocellulosic biomass to liquid fuels and chemicals is considered to be an important alternative for sustainable development of the human economy and society [1,2]
6,186 proteins were assigned to Gene Ontology (GO) categories [27]
The determination of P. decumbens genome has expanded our understanding on the diversity of the composition of lignocellulolytic enzyme systems in fungi

Summary

Introduction

Biorefinery of lignocellulosic biomass to liquid fuels and chemicals is considered to be an important alternative for sustainable development of the human economy and society [1,2]. The high cost of lignocellulolytic enzymes (usually referred as lignocellulolytic enzyme systems [3]) is still a major barrier in the production of biofuels from lignocellulosic materials [4]. The fungus Trichoderma reesei is the major source of commercial lignocellulolytic enzyme systems [5]. Exhibiting high hydrolytic activity on pure cellulose, the enzyme system of T. reesei need to be supplemented with several kinds of exogenous enzymes to achieve effective degradation of natural complex lignocellulosic materials [6,7]. Many Penicillium species have been reported to produce native enzyme systems with better performance than that of T. reesei (reviewed in [8]). Systematic studies on these enzyme systems, and work on directed strain engineering are greatly limited, mainly due to the poor knowledge of their genetic backgrounds

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Results

Conclusion