Genomics-guided approaches to enzyme discovery in disparate Galdieria species

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Galdieria is a red alga that displays enormous capacity to thrive at highly acidic conditions and elevated temperatures. Itdisplays broad metabolic repertoires allowing vigorous growth on virtually any carbon source. Galdieria is a metabolicworkhorse. Understanding the metabolic capacity of Galdieria under differing growth conditions assesses the biofuel,antioxidant and materials-chemistry potential for this organism. This application is to discover Galdieria enzymes thatwork in the bioconversion of untreated lignocellulosic biomass for bioenergy production of liquid fuels. We wish to usethe reference genome to facilitate transcriptomics and proteomics to guide enzyme discovery.In phase 1 a genomics examination will be performed of induced transcripts as a result of numerous, differingcarbohydrate-media compositions of differing clades of Galdieria discovered through phylogenomic identification. Thesegrowth-media sources include soluble carbohydrate and sugar-alcohol mixtures and complex insoluble residues suchas starch and wheat straw. This generates data sets to reveal novel lignocellulosic degradation enzymes in Galdieria.The RNAs would be quantified and comparisons to the control would be performed to find those genes induced inexpression that can be annotated as catabolic enzymes. The list of annotated enzymes would be correlated fromcompared tests to associate the transcriptomics compared to the Galdieria genome. Together a list of genes would becomplied for future exploration of encoded activity.In phase 2 a proteomics survey would be performed of enzymes from Galdieria. Fractions of Galdieria strains grown oncomplex wastes would be applied to mass spectroscopy. The identification of resultant peptides guides furtherannotation. These proteins identified will be compared to the induced RNAs. In total a comprehensive list of proteins willbe unified from the genome to the transcriptome to the excreted proteome and this serves enzymology of recombinantforms of such acid and heat stable proteins.