title: Direct target network of the Neurospora crassa plant cell wall deconstruction regulators CLR-1, CLR-2, and XLR-1.
abstract: Fungal deconstruction of the plant cell requires a complex orchestration of a wide array of intracellular and extracellular enzymes. In Neurospora crassa, CLR-1, CLR-2, and XLR-1 have been identified as key transcription factors regulating plant cell wall degradation in response to soluble sugars. The XLR-1 regulon was defined using a constitutively active mutant allele, resulting in hemicellulase gene expression and secretion under noninducing conditions. To define genes directly regulated by CLR-1, CLR-2, and XLR-1, we performed chromatin immunoprecipitation and next-generation sequencing (ChIPseq) on epitope-tagged constructs of these three transcription factors. When N. crassa is exposed to plant cell wall material, CLR-1, CLR-2, and XLR-1 individually bind to the promoters of the most strongly induced genes in their respective regulons. These include promoters of genes encoding cellulases for CLR-1 and CLR-2 (CLR-1/CLR-2) and promoters of genes encoding hemicellulases for XLR-1. CLR-1 bound to its regulon under noninducing conditions; however, this binding alone did not translate into gene expression and enzyme secretion. Motif analysis of the bound genes revealed conserved DNA binding motifs, with the CLR-2 motif matching that of its closest paralog in Saccharomyces cerevisiae, Gal4p. Coimmunoprecipitation studies showed that CLR-1 and CLR-2 act in a homocomplex but not as a CLR-1/CLR-2 heterocomplex.
  
  
  OBJECTIVE
  Understanding fungal regulation of complex plant cell wall deconstruction pathways in response to multiple environmental signals via interconnected transcriptional circuits provides insight into fungus/plant interactions and eukaryotic nutrient sensing. Coordinated optimization of these regulatory networks is likely required for optimal microbial enzyme production.
authors.affiliation: Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, California, USA Energy Biosciences Institute, University of California, Berkeley, Berkeley, California, USA Chan Soon-Shiong Institute of Molecular Medicine, Windber, Pennsylvania, USA.
authors.forename: James P
authors.initials: JP
authors.lastname: Craig
authors.affiliation: Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, California, USA Energy Biosciences Institute, University of California, Berkeley, Berkeley, California, USA Buck Institute for Research on Aging, Novato, California, USA.
authors.forename: Samuel T
authors.initials: ST
authors.lastname: Coradetti
authors.affiliation: Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, California, USA Energy Biosciences Institute, University of California, Berkeley, Berkeley, California, USA Dupont Industrial Biosciences, Palo Alto, California, USA.
authors.forename: Trevor L
authors.initials: TL
authors.lastname: Starr
authors.affiliation: Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, California, USA Energy Biosciences Institute, University of California, Berkeley, Berkeley, California, USA Lglass@berkeley.edu.
authors.forename: N Louise
authors.initials: NL
authors.lastname: Glass
mesh_terms: D020816:Amino Acid Motifs; D001665:Binding Sites; D002241:Carbohydrates / Q000032:analysis; D044602:Cellulases / Q000235:genetics; D047369:Chromatin Immunoprecipitation; D003600:Cytosol / Q000737:chemistry; D016054:DNA, Protozoan / Q000378:metabolism; D004268:DNA-Binding Proteins / Q000737:chemistry / Q000378:metabolism*; D005786:Gene Expression Regulation; D053263:Gene Regulatory Networks; D009492:Neurospora crassa / Q000235:genetics*; D059828:Plant Cells; D011401:Promoter Regions, Genetic; D011485:Protein Binding; D015800:Protozoan Proteins / Q000737:chemistry / Q000378:metabolism*; D018085:Regulon; D012441:Saccharomyces cerevisiae; D017422:Sequence Analysis, DNA
chemical_list: D002241:Carbohydrates; D016054:DNA, Protozoan; D004268:DNA-Binding Proteins; D015800:Protozoan Proteins; D044602:Cellulases