Genomics-guided approaches to enzyme discovery in disparate Galdieria species

Galdieria是一种红色的植物，在高酸性条件和高温下表现出巨大的生长能力。它显示了广泛的代谢库，几乎可以在任何碳源上蓬勃发展。Galdieria是一个代谢的主力。了解Galdieria在不同生长条件下的代谢能力评估了这种生物体的生物燃料，抗氧化剂和材料化学潜力。本申请旨在发现Galdieria酶，其在未处理的木质纤维素生物质的生物转化中起作用，用于液体燃料的生物能源生产。我们希望利用参考基因组来促进转录组学和蛋白质组学指导酶的发现。在第一阶段，将对诱导转录本进行基因组学检查，这是通过基因组学鉴定发现的Galdieria不同分支的许多不同碳水化合物培养基组成的结果。这些培养基来源包括可溶性碳水化合物和糖醇混合物以及复杂的不溶性残留物，如淀粉和小麦秸秆。这将产生数据集以揭示Galdieria中的新型木质纤维素降解酶，将对RNA进行定量，并与对照进行比较，以找到那些可以被注释为分解代谢酶的诱导表达的基因。注释的酶的列表将从比较测试中关联，以将转录组学与Galdieria基因组相关联。在第二阶段，我们将对加尔迪里亚的酶进行蛋白质组学研究。生长在复杂废物上的加尔迪氏菌菌株的组分将用于质谱分析。所得肽的鉴定指导进一步的注释。将这些鉴定的蛋白质与诱导的RNA进行比较。总的来说，从基因组到转录组再到分泌的蛋白质组，蛋白质的综合列表将被统一，这有助于这些酸和热稳定蛋白质的重组形式的酶学。

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.