Development of Highly Efficient, Low-Cost Lignocellulolytic Enzyme Systems in a Penicillium: From Strain Screening to Systems Biology

Abstract

Some Penicillium species have been reported to produce enzyme systems with good performances in lignocellulose degradation. Penicillium oxalicum (formerly classified as P. decumbens) strains, which produce more balanced native lignocellulolytic enzyme systems than Trichoderma reesei, have been studied for more than 30 years. The original P. oxalicum isolate 114 was obtained from decayed straw-covered soil in 1979 and has been improved through a series of mutagenesis and screening over the years. The whole genome sequence of the P. oxalicum was finished in 2009. Comparative and functional genomics studies between P. oxalicum mutant JU-A10-T and wild-type strain 114-2 were performed to decipher how strain improvement has significantly improved the production of the lignocellulolytic enzyme system. Further, the transcriptomes and secretomes of the P. oxalicum were determined. The applications of genomic, transcriptomic, and proteomic analysis methods make it possible in evaluation of the native enzyme system, discovery of novel auxiliary proteins, understanding of regulatory mechanisms by key transcription factors, and exploration of the cellular network controlling lignocellulolytic enzyme synthesis. A single-gene disruptant library for 470 transcription factors was constructed, and several activators and repressors were identified to play essential roles in regulating lignocellulolytic enzyme production. Redesigning the regulatory pathway substantially improves lignocellulolytic enzyme production up to the industrial level by combinational manipulation of three key genes to amplify the induction along with derepression. By combining systems biology tools, engineered fungal strains are expected to produce high levels of optimized lignocellulolytic enzyme systems.