title: AlgaGEM--a genome-scale metabolic reconstruction of algae based on the Chlamydomonas reinhardtii genome.
abstract: BACKGROUND
  Microalgae have the potential to deliver biofuels without the associated competition for land resources. In order to realise the rates and titres necessary for commercial production, however, system-level metabolic engineering will be required. Genome scale metabolic reconstructions have revolutionized microbial metabolic engineering and are used routinely for in silico analysis and design. While genome scale metabolic reconstructions have been developed for many prokaryotes and model eukaryotes, the application to less well characterized eukaryotes such as algae is challenging not at least due to a lack of compartmentalization data.
  
  
  RESULTS
  We have developed a genome-scale metabolic network model (named AlgaGEM) covering the metabolism for a compartmentalized algae cell based on the Chlamydomonas reinhardtii genome. AlgaGEM is a comprehensive literature-based genome scale metabolic reconstruction that accounts for the functions of 866 unique ORFs, 1862 metabolites, 2249 gene-enzyme-reaction-association entries, and 1725 unique reactions. The reconstruction was compartmentalized into the cytoplasm, mitochondrion, plastid and microbody using available data for algae complemented with compartmentalisation data for Arabidopsis thaliana. AlgaGEM describes a functional primary metabolism of Chlamydomonas and significantly predicts distinct algal behaviours such as the catabolism or secretion rather than recycling of phosphoglycolate in photorespiration. AlgaGEM was validated through the simulation of growth and algae metabolic functions inferred from literature. Using efficient resource utilisation as the optimality criterion, AlgaGEM predicted observed metabolic effects under autotrophic, heterotrophic and mixotrophic conditions. AlgaGEM predicts increased hydrogen production when cyclic electron flow is disrupted as seen in a high producing mutant derived from mutational studies. The model also predicted the physiological pathway for H2 production and identified new targets to further improve H2 yield.
  
  
  CONCLUSIONS
  AlgaGEM is a viable and comprehensive framework for in silico functional analysis and can be used to derive new, non-trivial hypotheses for exploring this metabolically versatile organism. Flux balance analysis can be used to identify bottlenecks and new targets to metabolically engineer microalgae for production of biofuels.
authors.affiliation: Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane Qld 4072 Australia. c.gomesdeoliveira@uq.edu.au
authors.forename: Cristiana Gomes de Oliveira
authors.initials: CG
authors.lastname: Dal'Molin
authors.forename: Lake-Ee
authors.initials: LE
authors.lastname: Quek
authors.forename: Robin W
authors.initials: RW
authors.lastname: Palfreyman
authors.forename: Lars K
authors.initials: LK
authors.lastname: Nielsen
mesh_terms: D017360:Arabidopsis / Q000235:genetics; D056804:Biofuels; D016825:Chlamydomonas reinhardtii / Q000235:genetics* / Q000378:metabolism; D016208:Databases, Factual; D016678:Genome; D006859:Hydrogen / Q000378:metabolism; D053858:Metabolic Networks and Pathways / Q000235:genetics; D008957:Models, Genetic
chemical_list: D056804:Biofuels; D006859:Hydrogen