ArticlePLoS computational biology2007
Metabolic reconstruction and modeling of nitrogen fixation in Rhizobium etli.
Article in PLoS computational biology, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 43 papers.
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Who cites it
43 citing papers in PubMed, 96 citations in OpenAlex.
- Synthetic Biology of Plants and Microbes for Agriculture, Environment, and Future Applications.Chemical reviews · 2026Review
- Diazotrophic growth of free-living Rhizobium etli: Community-like metabolic modeling of growing and non-growing nitrogen-fixing cells.PloS one · 2025Article
- Transcriptomic Response ofInternational journal of molecular sciences · 2024Article
- Quantitative principles of microbial metabolism shared across scales.Nature microbiology · 2024Review
- Crystal structures of the elusive Rhizobium etli L-asparaginase reveal a peculiar active site.Nature communications · 2021Article
- How Rhizobia Adapt to the Nodule Environment.Journal of bacteriology · 2021Article
- Reconstruction and analysis of a genome-scale metabolic model for Agrobacterium tumefaciens.Molecular plant pathology · 2021Article
- Review
- Genome-scale metabolic reconstruction of the symbiosis between a leguminous plant and a nitrogen-fixing bacterium.Nature communications · 2020Article
- Metabolic Analyses of Nitrogen Fixation in the Soybean Microsymbiont Sinorhizobium fredii Using Constraint-Based Modeling.mSystems · 2020Article
- MICOM: Metagenome-Scale Modeling To Infer Metabolic Interactions in the Gut Microbiota.mSystems · 2020Article
- The Impacts of Domestication and Agricultural Practices on Legume Nutrient Acquisition Through Symbiosis With Rhizobia and Arbuscular Mycorrhizal Fungi.Frontiers in genetics · 2020Review
- Quantitative models of nitrogen-fixing organisms.Computational and structural biotechnology journal · 2020Review
- Finding MEMo: minimum sets of elementary flux modes.Journal of mathematical biology · 2019Article
- Interaction and Regulation of Carbon, Nitrogen, and Phosphorus Metabolisms in Root Nodules of Legumes.Frontiers in plant science · 2018Review
- A Comprehensively Curated Genome-Scale Two-Cell Model for the Heterocystous Cyanobacterium Anabaena sp. PCC 7120.Plant physiology · 2017Article
- The Role of Soil Microorganisms in Plant Mineral Nutrition-Current Knowledge and Future Directions.Frontiers in plant science · 2017Review
- Understanding Plant Nitrogen Metabolism through Metabolomics and Computational Approaches.Plants (Basel, Switzerland) · 2016Review
- Metabolic modelling reveals the specialization of secondary replicons for niche adaptation in Sinorhizobium meliloti.Nature communications · 2016Article
- Host-Microbiome Interaction and Cancer: Potential Application in Precision Medicine.Frontiers in physiology · 2016Review
Corrections and comments
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Authors and funding
5 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Rhizobiaceas are bacteria that fix nitrogen during symbiosis with plants. This symbiotic relationship is crucial for the nitrogen cycle, and understanding symbiotic mechanisms is a scientific challenge with direct applications in agronomy and plant development. Rhizobium etli is a bacteria which provides legumes with ammonia (among other chemical compounds), thereby stimulating plant growth. A genome-scale approach, integrating the biochemical information available for R. etli, constitutes an important step toward understanding the symbiotic relationship and its possible improvement. In this work we present a genome-scale metabolic reconstruction (iOR363) for R. etli CFN42, which includes 387 metabolic and transport reactions across 26 metabolic pathways. This model was used to analyze the physiological capabilities of R. etli during stages of nitrogen fixation. To study the physiological capacities in silico, an objective function was formulated to simulate symbiotic nitrogen fixation. Flux balance analysis (FBA) was performed, and the predicted active metabolic pathways agreed qualitatively with experimental observations. In addition, predictions for the effects of gene deletions during nitrogen fixation in Rhizobia in silico also agreed with reported experimental data. Overall, we present some evidence supporting that FBA of the reconstructed metabolic network for R. etli provides results that are in agreement with physiological observations. Thus, as for other organisms, the reconstructed genome-scale metabolic network provides an important framework which allows us to compare model predictions with experimental measurements and eventually generate hypotheses on ways to improve nitrogen fixation.
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