GSE68516
Identification of direct target genes of the Neurospora crassa essential plant biomass deconstruction transcription factors CLR-1, CLR-2 and XLR-1 (ChIP-Seq)
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 upon knockout mutants and sild type 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