ArticlePloS one2016
Genome-Scale Model Reveals Metabolic Basis of Biomass Partitioning in a Model Diatom.
Article in PloS one, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 52 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
52 citing papers in PubMed, 120 citations in OpenAlex.
- Article
- Predictive Algal Systems Biology: Integrating Omics, Genome-Scale Metabolic Models, and Machine Learning.Bioengineering (Basel, Switzerland) · 2026Review
- Review
- Diatom triacylglycerol metabolism: from carbon fixation to lipid droplet degradation.Biological reviews of the Cambridge Philosophical Society · 2025Review
- Unveiling organ-specific metabolism ofProceedings of the National Academy of Sciences of the United States of America · 2025Article
- Charting the state of GEMs in microalgae: progress, challenges, and innovations.Frontiers in plant science · 2025Review
- Complementary environmental analysis and functional characterization of lower glycolysis-gluconeogenesis in the diatom plastid.The Plant cell · 2024Article
- Mixotrophic growth of a ubiquitous marine diatom.Science advances · 2024Article
- Crosstalk between photosynthesis and respiration in microbes.Journal of biosciences · 2024Article
- Identification of gene function based on models capturing natural variability of Arabidopsis thaliana lipid metabolism.Nature communications · 2023Article
- The Special and General Mechanism of Cyanobacterial Harmful Algal Blooms.Microorganisms · 2023Review
- Toward mechanistic modeling and rational engineering of plant respiration.Plant physiology · 2023Article
- Comparison of twoFrontiers in plant science · 2023Article
- Integration of physiologically relevant photosynthetic energy flows into whole genome models of light-driven metabolism.The Plant journal : for cell and molecular biology · 2022Article
- Proteomic analysis of metabolic pathways supports chloroplast-mitochondria cross-talk in a Cu-limited diatom.Plant direct · 2022Article
- Recent Progress on Systems and Synthetic Biology of Diatoms for Improving Algal Productivity.Frontiers in bioengineering and biotechnology · 2022Review
- Review
- Path to improving the life cycle and quality of genome-scale models of metabolism.Cell systems · 2021Review
- Phylogenomic fingerprinting of tempo and functions of horizontal gene transfer within ochrophytes.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- Boosting Biomass Quantity and Quality by Improved Mixotrophic Culture of the DiatomFrontiers in plant science · 2021Article
Corrections and comments
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Authors and funding
10 authors at 4 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Diatoms are eukaryotic microalgae that contain genes from various sources, including bacteria and the secondary endosymbiotic host. Due to this unique combination of genes, diatoms are taxonomically and functionally distinct from other algae and vascular plants and confer novel metabolic capabilities. Based on the genome annotation, we performed a genome-scale metabolic network reconstruction for the marine diatom Phaeodactylum tricornutum. Due to their endosymbiotic origin, diatoms possess a complex chloroplast structure which complicates the prediction of subcellular protein localization. Based on previous work we implemented a pipeline that exploits a series of bioinformatics tools to predict protein localization. The manually curated reconstructed metabolic network iLB1027_lipid accounts for 1,027 genes associated with 4,456 reactions and 2,172 metabolites distributed across six compartments. To constrain the genome-scale model, we determined the organism specific biomass composition in terms of lipids, carbohydrates, and proteins using Fourier transform infrared spectrometry. Our simulations indicate the presence of a yet unknown glutamine-ornithine shunt that could be used to transfer reducing equivalents generated by photosynthesis to the mitochondria. The model reflects the known biochemical composition of P. tricornutum in defined culture conditions and enables metabolic engineering strategies to improve the use of P. tricornutum for biotechnological applications.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.