Validation of metabolic models, extrapolated from the reference sugar catabolism genetic network of Aspergillus niger by using an orthology-based approach, of evolutionarily diverse fungi
EMSL Project ID
50379
Abstract
Sugar conversion through central carbon catabolism in filamentous fungi is a complex process that involves many pathways, some with shared and/or redundant components. During growth on plant biomass, multiple 5- and 6-carbon monomeric sugars become simultaneously available to the fungus. Whether fungi convert these sugars simultaneously or sequentially is not known. Additionally, our knowledge on the conservation of the catabolic pathways and the order in which sugars are converted across the fungal kingdom is limited. Using the high quality manually curated genome sequence of Aspergillus niger NRRL3 and a large transcriptomic dataset on individual monomeric sugars, we have curated a genetic network for sugar catabolism (paper in preparation) from the metabolic model generated for this strain. We are currently validating this model by deleting all genes identified to be involved in the pathways and verifying the phenotypes of the deletion strains. This metabolic model has the potential of being a reference for other fungi, but to which extent the knowledge can be extrapolated is not known.
In this project, we aim to test the potential and limits of extrapolating the A. niger catabolic model to other fungi. The fungi we have chosen for testing range from very close (Aspergillus nidulans -- other species of the same genus), to less close (Penicillium subrubescens -- sister genus in the order of Eurotiales), to more distant (Trichoderma reesei -- member of a different ascomycete class, Sordariomycetes), to very distant (Phanerochaete -- member of a different phylum, Basidiomycota) fungi. This will allow us to test the accuracy of the model at different taxonomic distances.
Using the catabolic model of A .niger as a reference, orthologs will be identified to construct the initial catabolic models for the four test fungi. We propose to culture the four fungi independently on ten monomeric sugars and two crude biomass substrates. Transcriptomes, proteomes, and metabolomes under the different culture conditions will be analyzed. The results obtained will be used to validate the catabolic models of the four fungi. Should the catabolic machineries of the test fungi differ from that of A. niger, the omics results will help to identify the components in the alternate and/or diverged pathways to refine their catabolic models. The results from the proposed research would generate the genetic networks of sugar catabolic models for four evolutionarily diverse fungi for future studies and applications development.
Knowledge on sugar catabolism is not only relevant in understanding the roles and abilities of these fungi in natural habitats, but can also be exploited to construct synthetic pathways for the production of valued and/or bioinspired chemicals and materials.
Project Details
Project type
FICUS Research
Start Date
2018-10-01
End Date
2021-03-31
Status
Closed
Released Data Link
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