title: A transcriptomic analysis of Neurospora crassa using five major crop residues and the novel role of the sporulation regulator rca-1 in lignocellulase production.
abstract: BACKGROUND
  Crop residue is an abundant, low-cost plant biomass material available worldwide for use in the microbial production of enzymes, biofuels, and valuable chemicals. However, the diverse chemical composition and complex structure of crop residues are more challenging for efficient degradation by microbes than are homogeneous polysaccharides. In this study, the transcriptional responses of Neurospora crassa to various plant straws were analyzed using RNA-Seq, and novel beneficial factors for biomass-induced enzyme production were evaluated.
  
  
  RESULTS
  Comparative transcriptional profiling of N. crassa grown on five major crop straws of China (barley, corn, rice, soybean, and wheat straws) revealed a highly overlapping group of 430 genes, the biomass commonly induced core set (BICS). A large proportion of induced carbohydrate-active enzyme (CAZy) genes (82 out of 113) were also conserved across the five plant straws. Excluding 178 genes within the BICS that were also upregulated under no-carbon conditions, the remaining 252 genes were defined as the biomass regulon (BR). Interestingly, 88 genes were only induced by plant biomass and not by three individual polysaccharides (Avicel, xylan, and pectin); these were denoted as the biomass unique set (BUS). Deletion of one BUS gene, the transcriptional regulator rca-1, significantly improved lignocellulase production using plant biomass as the sole carbon source, possibly functioning via de-repression of the regulator clr-2. Thus, this result suggests that rca-1 is a potential engineering target for biorefineries, especially for plant biomass direct microbial conversion processes.
  
  
  CONCLUSIONS
  Transcriptional profiling revealed a large core response to different sources of plant biomass in N. crassa. The sporulation regulator rca-1 was identified as beneficial for biomass-based enzyme production.
authors.affiliation: Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 China ; University of Chinese Academy of Sciences, Beijing, 100049 China.
authors.forename: Bang
authors.initials: B
authors.lastname: Wang
authors.affiliation: Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 China ; University of Chinese Academy of Sciences, Beijing, 100049 China.
authors.forename: Pengli
authors.initials: P
authors.lastname: Cai
authors.affiliation: Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 China.
authors.forename: Wenliang
authors.initials: W
authors.lastname: Sun
authors.affiliation: Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 China ; University of Chinese Academy of Sciences, Beijing, 100049 China.
authors.forename: Jingen
authors.initials: J
authors.lastname: Li
authors.affiliation: Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 China.
authors.forename: Chaoguang
authors.initials: C
authors.lastname: Tian
authors.affiliation: Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 China.
authors.forename: Yanhe
authors.initials: Y
authors.lastname: Ma
keywords: Biomass regulon; Crop residues; Neurospora crassa; Transcriptional profiling; rca-1