title: Deciphering the signaling mechanisms of the plant cell wall degradation machinery in Aspergillus oryzae.
abstract: BACKGROUND
  The gene expression and secretion of fungal lignocellulolytic enzymes are tightly controlled at the transcription level using independent mechanisms to respond to distinct inducers from plant biomass. An advanced systems-level understanding of transcriptional regulatory networks is required to rationally engineer filamentous fungi for more efficient bioconversion of different types of biomass.
  
  
  RESULTS
  In this study we focused on ten chemically defined inducers to drive expression of cellulases, hemicellulases and accessory enzymes in the model filamentous fungus Aspergillus oryzae and shed light on the complex network of transcriptional activators required. The chemical diversity analysis of the inducers, based on 186 chemical descriptors calculated from the structure, resulted into three clusters, however, the global, metabolic and extracellular protein transcription of the A. oryzae genome were only partially explained by the chemical similarity of the enzyme inducers. Genes encoding enzymes that have attracted considerable interest such as cellobiose dehydrogenases and copper-dependent polysaccharide mono-oxygenases presented a substrate-specific induction. Several homology-model structures were derived using ab-initio multiple threading alignment in our effort to elucidate the interplay of transcription factors involved in regulating plant-deconstructing enzymes and metabolites. Systematic investigation of metabolite-protein interactions, using the 814 unique reactants involved in 2360 reactions in the genome scale metabolic network of A. oryzae, was performed through a two-step molecular docking against the binding pockets of the transcription factors AoXlnR and AoAmyR. A total of six metabolites viz., sulfite (H2SO3), sulfate (SLF), uroporphyrinogen III (UPGIII), ethanolamine phosphate (PETHM), D-glyceraldehyde 3-phosphate (T3P1) and taurine (TAUR) were found as strong binders, whereas the genes involved in the metabolic reactions that these metabolites appear were found to be significantly differentially expressed when comparing the inducers with glucose.
  
  
  CONCLUSIONS
  Based on our observations, we believe that specific binding of sulfite to the regulator of the cellulase gene expression, AoXlnR, may be the molecular basis for the connection of sulfur metabolism and cellulase gene expression in filamentous fungi. Further characterization and manipulation of the regulatory network components identified in this study, will enable rational engineering of industrial strains for improved production of the sophisticated set of enzymes necessary to break-down chemically divergent plant biomass.
authors.affiliation: The Norwegian Structural Biology Centre, Department of Chemistry, Faculty of Science and Technology, University of Tromsø, N-9037, Tromsø, Norway. d.b.r.k.g.udatha@ibv.uio.no.|Section for Genetics and Evolutionary Biology, Department of Biosciences, University of Oslo, Oslo, Norway. d.b.r.k.g.udatha@ibv.uio.no.
authors.forename: D B R K Gupta
authors.initials: DB
authors.lastname: Udatha
authors.affiliation: Biotechnology Laboratory, School of Chemical Engineering, National Technical University of Athens, 5 Iroon Polytechniou Str., Zografou Campus, Athens, 15780, Greece. vtopakas@chemeng.ntua.gr.
authors.forename: Evangelos
authors.initials: E
authors.lastname: Topakas
authors.affiliation: Department of Chemical and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden. margarita.salazar@chalmers.se.|Wallenberg Wood Science Center, Chalmers University of Technology, SE-412 96, Gothenburg, Sweden. margarita.salazar@chalmers.se.
authors.forename: Margarita
authors.initials: M
authors.lastname: Salazar
authors.affiliation: Department of Chemical and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden. lisbeth.olsson@chalmers.se.|Wallenberg Wood Science Center, Chalmers University of Technology, SE-412 96, Gothenburg, Sweden. lisbeth.olsson@chalmers.se.
authors.forename: Lisbeth
authors.initials: L
authors.lastname: Olsson
authors.affiliation: Department of Systems Biology, Technical University of Denmark, Søltofts plads 223, DK-2800, Lyngby, Denmark. mr@bio.dtu.dk.
authors.forename: Mikael R
authors.initials: MR
authors.lastname: Andersen
authors.affiliation: School of Biological Sciences, The University of Hong Kong, Kadoorie Biological Sciences Building, Hong Kong, China. gipa@hku.hk.
authors.forename: Gianni
authors.initials: G
authors.lastname: Panagiotou
mesh_terms: D001236:Aspergillus oryzae / Q000201:enzymology* / Q000235:genetics; D001665:Binding Sites; D044602:Cellulases / Q000235:genetics / Q000378:metabolism; D005656:Fungal Proteins / Q000235:genetics / Q000378:metabolism*; D020869:Gene Expression Profiling; D015966:Gene Expression Regulation, Fungal; D053263:Gene Regulatory Networks; D006026:Glycoside Hydrolases / Q000235:genetics / Q000378:metabolism; D053858:Metabolic Networks and Pathways / Q000235:genetics; D062105:Molecular Docking Simulation; D059828:Plant Cells / Q000382:microbiology; D013447:Sulfites / Q000737:chemistry / Q000378:metabolism; D014157:Transcription Factors / Q000378:metabolism; D014994:Xylose / Q000378:metabolism
chemical_list: D005656:Fungal Proteins; D013447:Sulfites; D014157:Transcription Factors; D014994:Xylose; D044602:Cellulases; D006026:Glycoside Hydrolases; C023305:hemicellulase