ArticleFrontiers in bioengineering and biotechnology2014
Microalgal Metabolic Network Model Refinement through High-Throughput Functional Metabolic Profiling.
Article in Frontiers in bioengineering and biotechnology, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
- Dissolved Organic Carbon Regulates Bacterial Ingestion by Tetraselmis sp.Microbial ecology · 2026Article
- The difference in light intensities during culture affects the production of health-beneficial metabolites in a diatom used in producing aquaculture feed.Scientific reports · 2026Article
- Charting the state of GEMs in microalgae: progress, challenges, and innovations.Frontiers in plant science · 2025Review
- Genetic evidence for algal auxin production iniScience · 2024Article
- Review
- Unraveling the Antimicrobial Effectiveness ofMicroorganisms · 2022Article
- Data Management and Modeling in Plant Biology.Frontiers in plant science · 2021Review
- Bioengineering of Microalgae: Recent Advances, Perspectives, and Regulatory Challenges for Industrial Application.Frontiers in bioengineering and biotechnology · 2020Review
- Advances in metabolic modeling of oleaginous microalgae.Biotechnology for biofuels · 2018Review
- Reconstruction of the microalga Nannochloropsis salina genome-scale metabolic model with applications to lipid production.BMC systems biology · 2017Article
- The genome and phenome of the green algaeLife · 2017Article
- Algal Cell Factories: Approaches, Applications, and Potentials.Marine drugs · 2016Review
- Genome-Scale Metabolic Model for the Green Alga Chlorella vulgaris UTEX 395 Accurately Predicts Phenotypes under Autotrophic, Heterotrophic, and Mixotrophic Growth Conditions.Plant physiology · 2016Article
- Whole-Genome Resequencing Reveals Extensive Natural Variation in the Model Green Alga Chlamydomonas reinhardtii.The Plant cell · 2015Article
- Editorial: Current Challenges in Modeling Cellular Metabolism.Frontiers in bioengineering and biotechnology · 2015Article
- Carbon Source Flexibility in Chlamydomonas reinhardtii: Impact of Glycolate on Mixotrophic Growth.Physiologia plantarumArticle
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Metabolic modeling provides the means to define metabolic processes at a systems level; however, genome-scale metabolic models often remain incomplete in their description of metabolic networks and may include reactions that are experimentally unverified. This shortcoming is exacerbated in reconstructed models of newly isolated algal species, as there may be little to no biochemical evidence available for the metabolism of such isolates. The phenotype microarray (PM) technology (Biolog, Hayward, CA, USA) provides an efficient, high-throughput method to functionally define cellular metabolic activities in response to a large array of entry metabolites. The platform can experimentally verify many of the unverified reactions in a network model as well as identify missing or new reactions in the reconstructed metabolic model. The PM technology has been used for metabolic phenotyping of non-photosynthetic bacteria and fungi, but it has not been reported for the phenotyping of microalgae. Here, we introduce the use of PM assays in a systematic way to the study of microalgae, applying it specifically to the green microalgal model species Chlamydomonas reinhardtii. The results obtained in this study validate a number of existing annotated metabolic reactions and identify a number of novel and unexpected metabolites. The obtained information was used to expand and refine the existing COBRA-based C. reinhardtii metabolic network model iRC1080. Over 254 reactions were added to the network, and the effects of these additions on flux distribution within the network are described. The novel reactions include the support of metabolism by a number of d-amino acids, l-dipeptides, and l-tripeptides as nitrogen sources, as well as support of cellular respiration by cysteamine-S-phosphate as a phosphorus source. The protocol developed here can be used as a foundation to functionally profile other microalgae such as known microalgae mutants and novel isolates.
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