Abstract
BackgroundThe 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.ResultsIn 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.ConclusionsBased 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.Electronic supplementary materialThe online version of this article (doi:10.1186/s12918-015-0224-5) contains supplementary material, which is available to authorized users.
Highlights
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
Summary of transcription analysis datasets To obtain a global view of the A. oryzae transcriptome activated for plant biomass conversion, mRNA from mycelium after a 2 h-induction on 10 different carbohydrate active enzyme inducers was subjected to custom-designed NimbleGen microarray analysis
Xylopentaose was used in the report by Gilad et al, where integration of transcriptome and proteome data was applied to develop a mechanistic model of the substrate utilization [14]
Summary
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. The three major polymers in the plant cell wall build a complex network structure, which largely contributes to its recalcitrant nature. From standard combustion to complex bioconversion processes, have been applied to access the energy stored in the plant cell wall polymers and the clear objective now is to make this process cost competitive in today’s markets [4]. The plant cell wall and its metabolism are currently poorly understood due to its complex structure and biological recalcitrance, which is largely responsible for the high cost of lignocelluloses conversion [5]
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