ArticlePlant physiology2014
Assessing the metabolic impact of nitrogen availability using a compartmentalized maize leaf genome-scale model.
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Article in Plant physiology, 2014. 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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52citing papers in PubMed
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Who cites it
52 citing papers in PubMed.
- Synthetic Biology of Plants and Microbes for Agriculture, Environment, and Future Applications.Chemical reviews · 2026Review
- Fermi calculations enable quick downselection of target genes and process optimization in photosynthetic systems.Plant physiology · 2025Review
- Metabolic modeling identifies determinants of thermal growth responses in Arabidopsis thaliana.The New phytologist · 2025Article
- Nitrogen deficiency identifies carbon metabolism pathways and root adaptation in maize.Physiology and molecular biology of plants : an international journal of functional plant biology · 2025Article
- Flux-sum coupling analysis of metabolic network models.PLoS computational biology · 2025Article
- A data-integrative modeling approach accurately characterizes the effects of mutations on Arabidopsis lipid metabolism.Plant physiology · 2025Article
- A Guide to Metabolic Network Modeling for Plant Biology.Plants (Basel, Switzerland) · 2025Review
- Multiscale Mathematical Modeling in Systems Biology: A Framework to Boost Plant Synthetic Biology.Plants (Basel, Switzerland) · 2025Review
- Identification of metabolic and protein markers representative of the impact of mild nitrogen deficit on agronomic performance of maize hybrids.Metabolomics : Official journal of the Metabolomic Society · 2024Article
- A diel multi-tissue genome-scale metabolic model of Vitis vinifera.PLoS computational biology · 2024Article
- A multi-organ maize metabolic model connects temperature stress with energy production and reducing power generation.iScience · 2023Article
- Toward mechanistic modeling and rational engineering of plant respiration.Plant physiology · 2023Article
- Metabolic modelling revealed source-sink interactions between four segments ofJournal of biosciences · 2023Article
- Elucidating the impact ofFrontiers in plant science · 2023Article
- Genome-scale metabolic network models: from first-generation to next-generation.Applied microbiology and biotechnology · 2022Review
- Systems-level analysis of the plasticity of the maize metabolic network reveals novel hypotheses in the nitrogen-use efficiency of maize roots.Journal of experimental botany · 2022Article
- Elucidation of Triacylglycerol Overproduction in the CFrontiers in plant science · 2022Article
- Exploring synergies between plant metabolic modelling and machine learning.Computational and structural biotechnology journal · 2022Review
- Impacts of environmental conditions, and allelic variation of cytosolic glutamine synthetase on maize hybrid kernel production.Communications biology · 2021Article
- The utility of metabolomics as a tool to inform maize biology.Plant communications · 2021Review
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Authors and funding
12 authors.
Margaret SimonsDepartments of Chemical Engineering (M.S., R.S., C.D.M.) and Bioinformatics and Genomics, Huck Institutes of the Life Sciences (A.K.), Pennsylvania State University, University Park, Pennsylvania 16802;Institut Jean-Pierre Bourgin, Institut National de la Recherche Agronomique, Centre de Versailles-Grignon, Unité Mixte de Recherche 1318 Institut National de la Recherche Agronomique-Agro-ParisTech, Equipe de Recherce Labellisée, Centre National de la Recherche Scientifique 3559, F-78026 Versailles cedex, France (N.A., L.G., G.C., M.M., Z.L., G.M., B.H.); andLancaster Environment Centre, Lancaster University, Lancaster LA1 4YQ, United Kingdom (P.J.L.).
Rajib SahaDepartments of Chemical Engineering (M.S., R.S., C.D.M.) and Bioinformatics and Genomics, Huck Institutes of the Life Sciences (A.K.), Pennsylvania State University, University Park, Pennsylvania 16802;Institut Jean-Pierre Bourgin, Institut National de la Recherche Agronomique, Centre de Versailles-Grignon, Unité Mixte de Recherche 1318 Institut National de la Recherche Agronomique-Agro-ParisTech, Equipe de Recherce Labellisée, Centre National de la Recherche Scientifique 3559, F-78026 Versailles cedex, France (N.A., L.G., G.C., M.M., Z.L., G.M., B.H.); andLancaster Environment Centre, Lancaster University, Lancaster LA1 4YQ, United Kingdom (P.J.L.).
Nardjis AmiourDepartments of Chemical Engineering (M.S., R.S., C.D.M.) and Bioinformatics and Genomics, Huck Institutes of the Life Sciences (A.K.), Pennsylvania State University, University Park, Pennsylvania 16802;Institut Jean-Pierre Bourgin, Institut National de la Recherche Agronomique, Centre de Versailles-Grignon, Unité Mixte de Recherche 1318 Institut National de la Recherche Agronomique-Agro-ParisTech, Equipe de Recherce Labellisée, Centre National de la Recherche Scientifique 3559, F-78026 Versailles cedex, France (N.A., L.G., G.C., M.M., Z.L., G.M., B.H.); andLancaster Environment Centre, Lancaster University, Lancaster LA1 4YQ, United Kingdom (P.J.L.).
Akhil KumarDepartments of Chemical Engineering (M.S., R.S., C.D.M.) and Bioinformatics and Genomics, Huck Institutes of the Life Sciences (A.K.), Pennsylvania State University, University Park, Pennsylvania 16802;Institut Jean-Pierre Bourgin, Institut National de la Recherche Agronomique, Centre de Versailles-Grignon, Unité Mixte de Recherche 1318 Institut National de la Recherche Agronomique-Agro-ParisTech, Equipe de Recherce Labellisée, Centre National de la Recherche Scientifique 3559, F-78026 Versailles cedex, France (N.A., L.G., G.C., M.M., Z.L., G.M., B.H.); andLancaster Environment Centre, Lancaster University, Lancaster LA1 4YQ, United Kingdom (P.J.L.).
Lenaïg GuillardDepartments of Chemical Engineering (M.S., R.S., C.D.M.) and Bioinformatics and Genomics, Huck Institutes of the Life Sciences (A.K.), Pennsylvania State University, University Park, Pennsylvania 16802;Institut Jean-Pierre Bourgin, Institut National de la Recherche Agronomique, Centre de Versailles-Grignon, Unité Mixte de Recherche 1318 Institut National de la Recherche Agronomique-Agro-ParisTech, Equipe de Recherce Labellisée, Centre National de la Recherche Scientifique 3559, F-78026 Versailles cedex, France (N.A., L.G., G.C., M.M., Z.L., G.M., B.H.); andLancaster Environment Centre, Lancaster University, Lancaster LA1 4YQ, United Kingdom (P.J.L.).
Gilles ClémentDepartments of Chemical Engineering (M.S., R.S., C.D.M.) and Bioinformatics and Genomics, Huck Institutes of the Life Sciences (A.K.), Pennsylvania State University, University Park, Pennsylvania 16802;Institut Jean-Pierre Bourgin, Institut National de la Recherche Agronomique, Centre de Versailles-Grignon, Unité Mixte de Recherche 1318 Institut National de la Recherche Agronomique-Agro-ParisTech, Equipe de Recherce Labellisée, Centre National de la Recherche Scientifique 3559, F-78026 Versailles cedex, France (N.A., L.G., G.C., M.M., Z.L., G.M., B.H.); andLancaster Environment Centre, Lancaster University, Lancaster LA1 4YQ, United Kingdom (P.J.L.).
Martine MiquelDepartments of Chemical Engineering (M.S., R.S., C.D.M.) and Bioinformatics and Genomics, Huck Institutes of the Life Sciences (A.K.), Pennsylvania State University, University Park, Pennsylvania 16802;Institut Jean-Pierre Bourgin, Institut National de la Recherche Agronomique, Centre de Versailles-Grignon, Unité Mixte de Recherche 1318 Institut National de la Recherche Agronomique-Agro-ParisTech, Equipe de Recherce Labellisée, Centre National de la Recherche Scientifique 3559, F-78026 Versailles cedex, France (N.A., L.G., G.C., M.M., Z.L., G.M., B.H.); andLancaster Environment Centre, Lancaster University, Lancaster LA1 4YQ, United Kingdom (P.J.L.).
Zhenni LiDepartments of Chemical Engineering (M.S., R.S., C.D.M.) and Bioinformatics and Genomics, Huck Institutes of the Life Sciences (A.K.), Pennsylvania State University, University Park, Pennsylvania 16802;Institut Jean-Pierre Bourgin, Institut National de la Recherche Agronomique, Centre de Versailles-Grignon, Unité Mixte de Recherche 1318 Institut National de la Recherche Agronomique-Agro-ParisTech, Equipe de Recherce Labellisée, Centre National de la Recherche Scientifique 3559, F-78026 Versailles cedex, France (N.A., L.G., G.C., M.M., Z.L., G.M., B.H.); andLancaster Environment Centre, Lancaster University, Lancaster LA1 4YQ, United Kingdom (P.J.L.).
Gregory MouilleDepartments of Chemical Engineering (M.S., R.S., C.D.M.) and Bioinformatics and Genomics, Huck Institutes of the Life Sciences (A.K.), Pennsylvania State University, University Park, Pennsylvania 16802;Institut Jean-Pierre Bourgin, Institut National de la Recherche Agronomique, Centre de Versailles-Grignon, Unité Mixte de Recherche 1318 Institut National de la Recherche Agronomique-Agro-ParisTech, Equipe de Recherce Labellisée, Centre National de la Recherche Scientifique 3559, F-78026 Versailles cedex, France (N.A., L.G., G.C., M.M., Z.L., G.M., B.H.); andLancaster Environment Centre, Lancaster University, Lancaster LA1 4YQ, United Kingdom (P.J.L.).
Peter J LeaDepartments of Chemical Engineering (M.S., R.S., C.D.M.) and Bioinformatics and Genomics, Huck Institutes of the Life Sciences (A.K.), Pennsylvania State University, University Park, Pennsylvania 16802;Institut Jean-Pierre Bourgin, Institut National de la Recherche Agronomique, Centre de Versailles-Grignon, Unité Mixte de Recherche 1318 Institut National de la Recherche Agronomique-Agro-ParisTech, Equipe de Recherce Labellisée, Centre National de la Recherche Scientifique 3559, F-78026 Versailles cedex, France (N.A., L.G., G.C., M.M., Z.L., G.M., B.H.); andLancaster Environment Centre, Lancaster University, Lancaster LA1 4YQ, United Kingdom (P.J.L.).
Bertrand HirelDepartments of Chemical Engineering (M.S., R.S., C.D.M.) and Bioinformatics and Genomics, Huck Institutes of the Life Sciences (A.K.), Pennsylvania State University, University Park, Pennsylvania 16802;Institut Jean-Pierre Bourgin, Institut National de la Recherche Agronomique, Centre de Versailles-Grignon, Unité Mixte de Recherche 1318 Institut National de la Recherche Agronomique-Agro-ParisTech, Equipe de Recherce Labellisée, Centre National de la Recherche Scientifique 3559, F-78026 Versailles cedex, France (N.A., L.G., G.C., M.M., Z.L., G.M., B.H.); andLancaster Environment Centre, Lancaster University, Lancaster LA1 4YQ, United Kingdom (P.J.L.).
Costas D MaranasDepartments of Chemical Engineering (M.S., R.S., C.D.M.) and Bioinformatics and Genomics, Huck Institutes of the Life Sciences (A.K.), Pennsylvania State University, University Park, Pennsylvania 16802;Institut Jean-Pierre Bourgin, Institut National de la Recherche Agronomique, Centre de Versailles-Grignon, Unité Mixte de Recherche 1318 Institut National de la Recherche Agronomique-Agro-ParisTech, Equipe de Recherce Labellisée, Centre National de la Recherche Scientifique 3559, F-78026 Versailles cedex, France (N.A., L.G., G.C., M.M., Z.L., G.M., B.H.); andLancaster Environment Centre, Lancaster University, Lancaster LA1 4YQ, United Kingdom (P.J.L.) costas@psu.edu.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Maize (Zea mays) is an important C4 plant due to its widespread use as a cereal and energy crop. A second-generation genome-scale metabolic model for the maize leaf was created to capture C4 carbon fixation and investigate nitrogen (N) assimilation by modeling the interactions between the bundle sheath and mesophyll cells. The model contains gene-protein-reaction relationships, elemental and charge-balanced reactions, and incorporates experimental evidence pertaining to the biomass composition, compartmentalization, and flux constraints. Condition-specific biomass descriptions were introduced that account for amino acids, fatty acids, soluble sugars, proteins, chlorophyll, lignocellulose, and nucleic acids as experimentally measured biomass constituents. Compartmentalization of the model is based on proteomic/transcriptomic data and literature evidence. With the incorporation of information from the MetaCrop and MaizeCyc databases, this updated model spans 5,824 genes, 8,525 reactions, and 9,153 metabolites, an increase of approximately 4 times the size of the earlier iRS1563 model. Transcriptomic and proteomic data have also been used to introduce regulatory constraints in the model to simulate an N-limited condition and mutants deficient in glutamine synthetase, gln1-3 and gln1-4. Model-predicted results achieved 90% accuracy when comparing the wild type grown under an N-complete condition with the wild type grown under an N-deficient condition.
Indexed as
Models, BiologicalBiological AvailabilityBiomassGene Expression ProfilingGenome, PlantMetabolomeMutationNitrogenPlant LeavesProteomeZea maysNitrogenProteome
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