Biomass Depolymerization projects
Genome-Scale Network Modeling of Neurospora crassa
This project incorporates computational modeling into the ongoing EBI efforts to study and engineer Neurospora crassa. It focuses on building genome-scale models of metabolism and associated transcriptional regulation, in order to help rationally engineer filamentous fungus for enhanced enzyme secretion for industrial use, particularly for conversion of lignocellulosics into biofuels.
Using their transcriptional regulatory network (TRN) inference algorithm, Price’s group inferred regulatory relationships for cellulase digestion enzymes. Two of the regulatory relationships inferred were experimentally confirmed. Using only the organism’s genome and databases of known reactions, they applied their automated metabolic reconstruction method (GEMMAKER) to the N. crassa genome. Preliminary results show that 545 annotated reactions are incorporated into the model and can carry flux.
Price’s group has focused primarily on building the genome-scale metabolic network and have a draft network built, but not yet a computable model. They have generated the first biomass function for N. crassa describing all the major cellular building blocks as needed to simulate growth. They also have worked on an automated metabolic reconstruction package to help complete the metabolic network to form the first computable model of genome-scale metabolism in N. crassa. Price’s team is working to modify its Probabilistic Regulation of Metabolism (PROM) modeling approach for integrated regulatory-metabolic networks to use the RNAseq data compiled by Glass.