|
Status |
Public on Sep 01, 2015 |
Title |
Identification of direct target genes of the Neurospora crassa essential plant biomass deconstruction transcription factors CLR-1, CLR-2 and XLR-1 (RNA-Seq) |
Organism |
Neurospora crassa |
Experiment type |
Expression profiling by high throughput sequencing
|
Summary |
abstract: The plant cell wall is composed of many complex polymers, and its deconstruction requires an equally complex orchestration of a wide array of enzymes. In Neurospora crassa, clr-1, clr-2 and xlr-1 have been identified as the key transcription factors involved in cell wall breakdown. In order to define their regulons, we performed ChIPseq upon these three transcription factors. CLR-1, CLR-2 and XLR-1 each bind to the most highly and differentially expressed gene populations, which include the cellulases for the CLRs and the hemicellulases for XLR-1. CLR-1 also bound to its regulon under non-inducing conditions; however, this did not translate into gene expression. Motif analysis of the bound genes revealed conserved DNA binding motifs, with the CLR-2 motif matching that of its closest yeast homolog, GAL4. Co-immunoprecipitation studies were able to show that CLR-1 and CLR-2 act as homodimers. Finally, we report on a conserved XLR-1 point mutation that is sufficient to drive hemicellulase expression under non-inducing conditions. Understanding how these transcription factors work in concert to break down plant biomass can inform decisions on how to best engineer future fungal strains for decreased enzyme costs.
|
|
|
Overall design |
RNAseq and ChIPseq was performed upon knockout mutants and wild type strains growing on various carbon sources to determin the role of the transcription factors CLR-1, CLR-2, and XLR-1 in plant cell wall degradation
|
|
|
Contributor(s) |
Craig J, Coradetti S, Starr T, Glass NL |
Citation(s) |
26463163 |
|
Submission date |
May 04, 2015 |
Last update date |
May 15, 2019 |
Contact name |
James Craig |
E-mail(s) |
jimcraig134@gmail.com
|
Organization name |
UC Berkeley
|
Department |
Plant & Microbial Biology
|
Lab |
N. Louise Glass
|
Street address |
341A Koshland Hall
|
City |
Berkeley |
State/province |
CA |
ZIP/Postal code |
94720 |
Country |
USA |
|
|
Platforms (1) |
GPL16164 |
Illumina HiSeq 2000 (Neurospora crassa) |
|
Samples (11)
|
|
This SubSeries is part of SuperSeries: |
GSE68517 |
Identification of direct target genes of the Neurospora crassa essential plant biomass deconstruction transcription factors CLR-1, CLR-2 and XLR-1 |
|
Relations |
BioProject |
PRJNA282963 |
SRA |
SRP057989 |