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Series GSE60986 Query DataSets for GSE60986
Status Public on Jan 21, 2015
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
Organism Neurospora crassa OR74A
Experiment type Expression profiling by high throughput sequencing
Summary 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 up-regulated 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.
 
Overall design Conidia of Neurospora crass wild type were inoculated at 10^6 conidia/mL into 100 mL 1×Vogel’s salts with 2% (w/w) ground crop straws, barley straw, corn straw, rice straw, soybean straw and wheat straw respectively for 30 h or 2% sucrose for 16 h. Then, mycelia were harvested through filtration and immediately frozen in liquid nitrogen.Total RNA from frozen sample was isolated with TRIzol reagent (Invitrogen) and further treated with DNase I (RNeasy Mini Kit, QIAGEN). The qualified RNA was prepared with standard protocol from Shenzhen BGI (China) and sequenced on the Illumina HiSeqTM 2000 platform.
 
Contributor(s) Wang B, Tian C
Citation(s) 25691917
Submission date Sep 02, 2014
Last update date May 15, 2019
Contact name Bang Wang
E-mail(s) b.wangair@gmail.com
Phone +86-22-84861948
Organization name Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences
Lab Key Laboratory of Systems Microbial Biotechnology
Street address 32 Xi Qi Dao, Tianjin Airport Economic Area
City Tianjin
ZIP/Postal code 300308
Country China
 
Platforms (1)
GPL15146 Illumina HiSeq 2000 (Neurospora crassa OR74A)
Samples (6)
GSM1495254 BarleyStraw_30h
GSM1495255 CornStraw_30h
GSM1495256 RiceStraw_30h
Relations
BioProject PRJNA260043
SRA SRP045980

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE60986_RAW.tar 710.0 Kb (http)(custom) TAR (of TXT)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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