Algae Genome-Scale Reconstruction, Modelling and Applications
Driven by revolutionary advances in high-throughput omics technologies, genome-scale metabolic reconstructions are a common denominator in systems biology and are available for a wide range of organisms. The constraint modelling formulation approach derived from the metabolic reconstructions have been successfully used to a number of applications including: metabolic engineering, biofuel research, genome functional annotation, omics data integration and in particular global pathway analysis. Recent advances have been made on plant and algae genome-scale metabolic reconstruction. In this book chapter we present the genome-scale reconstructions based on Chlamydomonas reinhardtii along with modelling formulation. We also give a few examples of the use of genome-scale models to algae biotechnological applications.
KeywordsGenome-scale reconstruction Algae metagbolism Systems biology Modelling Chlamydomonas reinhardtii
- Chang RL, Ghamsari L, Manichaikul A, Hom EF, Balaji S, Fu W, Shen Y, Hao T, Palsson B, Salehi-Ashtiani K, Papin JA (2011) Metabolic network reconstruction of Chlamydomonas offers insight into light-driven algal metabolism. Mol Syst Biol 7:518. doi: 10.1038/msb.2011.52 CrossRefPubMedPubMedCentralGoogle Scholar
- Escobar R, Garcia-Dominguez S, Guiraum A, Montes O, Galvan F, de La Rosa FF (2000) A flow injection chemiluminescence method using Cr(III) as a catalyst for determining hydrogen peroxide. Application to H2O2 determination in cultures of microalgae. Luminescence 15:131–135CrossRefPubMedGoogle Scholar
- Mendoza E (2007) What we can learn from a genome scale model of unicellular metabolism? Amino Acids 33(3):XXVGoogle Scholar
- Schellenberger J, Que R, Fleming RMT, Thiele I, Orth JD, Feist AM, Zielinski DC, Bordbar A, Lewis NE, Rahmanian S, Kang J, Hyduke DR, Palsson BO (2011) Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0. Nat Protoc 6:1290–1307CrossRefPubMedPubMedCentralGoogle Scholar