title: Genome-wide analysis of the endoplasmic reticulum stress response during lignocellulase production in Neurospora crassa.
abstract: BACKGROUND
  Lignocellulolytic fungal cells suffer endoplasmic reticulum (ER) stress during lignocellulase synthesis; however, an understanding of this integrated process on a genome-wide scale remains poor. Here, we undertook a systematic investigation of this process in Neurospora crassa (N. crassa) using transcriptomic analysis coupled with genetic screens.
  
  
  RESULTS
  A set of 766 genes was identified as the ER stress response targets (ESRTs) in N. crassa under cellulose utilization conditions. Among these, the expression of 223 and 186 genes showed dependence on IRE-1 and HAC-1, respectively. A total of 527 available mutants for ESRT genes were screened, 249 of which exhibited ER stress susceptibility, including 100 genes with unknown function. Disruption of ire-1 or hac-1 in N. crassa did not affect transcriptional induction of lignocellulase genes by cellulose but severely affected secretion of the corresponding enzymes. A global investigation of transcription factors (TFs) discovered three novel regulators (RES-1, RES-2, RRG-2) involved in lignocellulase secretion. Production of lignocellulases in Δres-1 increased by more than 30% in comparison to wild type (WT), while secretion decreased by nearly 30% in strains Δres-2 and Δrrg-2. Transcriptional profiling of the three TF mutants suggests they are deeply involved in lignocellulase secretion and ER stress response.
  
  
  CONCLUSIONS
  Here, we determined the transcriptional scope of the ER stress response during lignocellulase synthesis in the model cellulolytic fungus N. crassa. Through genome-wide mutant screening and analysis, dozens of novel genes were discovered to be involved in the process. The findings of this work will be useful for strain improvement to facilitate lignocellulase and biomass-based chemical production.
authors.affiliation: Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Xiqi Dao32, Tianjin Airport Economic Area, Tianjin 300308 China ; University of Chinese Academy of Sciences, Yuquan Road, Beijing, 100049 China.
authors.forename: Feiyu
authors.initials: F
authors.lastname: Fan
authors.affiliation: Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Xiqi Dao32, Tianjin Airport Economic Area, Tianjin 300308 China ; University of Chinese Academy of Sciences, Yuquan Road, Beijing, 100049 China.
authors.forename: Guoli
authors.initials: G
authors.lastname: Ma
authors.affiliation: Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Xiqi Dao32, Tianjin Airport Economic Area, Tianjin 300308 China ; University of Chinese Academy of Sciences, Yuquan Road, 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, Xiqi Dao32, Tianjin Airport Economic Area, Tianjin 300308 China.
authors.forename: Qian
authors.initials: Q
authors.lastname: Liu
authors.affiliation: Holzforschung München, TUM School of Life Sciences Weihenstephan, Technische Universität München, Hans-Carl-von-Carlowitz-Platz 2, Freising, Germany.
authors.forename: Johan Philipp
authors.initials: JP
authors.lastname: Benz
authors.affiliation: Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Xiqi Dao32, Tianjin Airport Economic Area, 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, Xiqi Dao32, Tianjin Airport Economic Area, Tianjin 300308 China.
authors.forename: Yanhe
authors.initials: Y
authors.lastname: Ma
keywords: ER stress; Lignocellulase secretion; RESS; RNA-seq; Transcription factor; UPR