title: Metabolic network reconstruction of Chlamydomonas offers insight into light-driven algal metabolism.
abstract: Metabolic network reconstruction encompasses existing knowledge about an organism's metabolism and genome annotation, providing a platform for omics data analysis and phenotype prediction. The model alga Chlamydomonas reinhardtii is employed to study diverse biological processes from photosynthesis to phototaxis. Recent heightened interest in this species results from an international movement to develop algal biofuels. Integrating biological and optical data, we reconstructed a genome-scale metabolic network for this alga and devised a novel light-modeling approach that enables quantitative growth prediction for a given light source, resolving wavelength and photon flux. We experimentally verified transcripts accounted for in the network and physiologically validated model function through simulation and generation of new experimental growth data, providing high confidence in network contents and predictive applications. The network offers insight into algal metabolism and potential for genetic engineering and efficient light source design, a pioneering resource for studying light-driven metabolism and quantitative systems biology.
authors.affiliation: Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA.
authors.forename: Roger L
authors.initials: RL
authors.lastname: Chang
authors.forename: Lila
authors.initials: L
authors.lastname: Ghamsari
authors.forename: Ani
authors.initials: A
authors.lastname: Manichaikul
authors.forename: Erik F Y
authors.initials: EF
authors.lastname: Hom
authors.forename: Santhanam
authors.initials: S
authors.lastname: Balaji
authors.forename: Weiqi
authors.initials: W
authors.lastname: Fu
authors.forename: Yun
authors.initials: Y
authors.lastname: Shen
authors.forename: Tong
authors.initials: T
authors.lastname: Hao
authors.forename: Bernhard Ø
authors.initials: BØ
authors.lastname: Palsson
authors.forename: Kourosh
authors.initials: K
authors.lastname: Salehi-Ashtiani
authors.forename: Jason A
authors.initials: JA
authors.lastname: Papin
mesh_terms: D016825:Chlamydomonas reinhardtii / Q000235:genetics* / Q000254:growth & development / Q000378:metabolism*; D003198:Computer Simulation; D030541:Databases, Genetic; D005818:Genetic Engineering; D050356:Lipid Metabolism; D053858:Metabolic Networks and Pathways / Q000235:genetics*; D008954:Models, Biological; D010641:Phenotype; D058433:Photobioreactors; D010788:Photosynthesis / Q000235:genetics; D020133:Reverse Transcriptase Polymerase Chain Reaction; D017423:Sequence Analysis, RNA; D049490:Systems Biology / Q000379:methods