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The intertwined metabolism of Medicago truncatula and its nitrogen fixing symbiont Sinorhizobium meliloti elucidated by genome-scale metabolic models

https://doi.org/10.1101/067348
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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

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The Legume–Rhizobia Symbiosis
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Genome-Scale Metabolic Models: Reconstruction and Analysis
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Mechanisms of adaptation of plants to acid soils
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Reversible and irreversible inactivation of cellular nitrogenase upon oxygen stress in Azotobacter vinelandii growing in oxygen controlled continuous culture
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Inhibition of nitrate uptake by ammonia in a blue-green alga, Anabaena cylindrica
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Lipid extraction of tissues with a low-toxicity solvent
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Differential effects of ammonium and tungsten on nitrate and nitrite uptake and reduction by sunflower plants
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The mitochondrial proteome of the model legume Medicago truncatula
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Optimizing metabolic pathways by screening for feasible synthetic reactions
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Advances in flux balance analysis
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GC–MS based metabolite profiling implies three interdependent ways of ammonium assimilation in Medicago truncatula root nodules
inferredcites →https://doi.org/10.1016/j.mib.2010.03.003openalex-snapshot
The biomass objective function
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Systems-integration of plant metabolism: means, motive and opportunity
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Metabolic profiling and systematic identification of flavonoids and isoflavonoids in roots and cell suspension cultures of Medicago truncatula using HPLC–UV–ESI–MS and GC–MS
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Effect of salinity on root-nodule conductance to the oxygen diffusion in the Medicago truncatula–Sinorhizobium meliloti symbiosis
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Metabolic changes of rhizobia in legume nodules
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Metabolic profiling of saponins in Medicago sativa and Medicago truncatula using HPLC coupled to an electrospray ion-trap mass spectrometer
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Physiological and biochemical aspects of nitrogen fixation by bacteroids in soybean nodule cells
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Carbon and nitrogen metabolism in Rhizobium
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Molecular biology of jasmonic acid biosynthesis in plants
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Medicago truncatula — a model in the making!
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Accurate Assessment of Amino Acid Mass Isotopomer Distributions for Metabolic Flux Analysis
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Flavonoids from Barrel Medic ( Medicago truncatula ) Aerial Parts
inferredcites →https://doi.org/10.1021/np200218ropenalex-snapshot
Metabolite Profiling of Triterpene Saponins in Medicago truncatula Hairy Roots by Liquid Chromatography Fourier Transform Ion Cyclotron Resonance Mass Spectrometry
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In silico predictions of Escherichia coli metabolic capabilities are consistent with experimental data
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Ribosome and transcript copy numbers, polysome occupancy and enzyme dynamics in Arabidopsis
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A comprehensive genome‐scale reconstruction of Escherichia coli metabolism—2011
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A genome‐scale metabolic reconstruction for Escherichia coli K‐12 MG1655 that accounts for 1260 ORFs and thermodynamic information
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Amino-acid cycling drives nitrogen fixation in the legume–Rhizobium symbiosis
inferredcites →https://doi.org/10.1038/nature10625openalex-snapshot
The Medicago genome provides insight into the evolution of rhizobial symbioses
inferredcites →https://doi.org/10.1038/nbt.2870openalex-snapshot
Optimizing genome-scale network reconstructions
inferredcites →https://doi.org/10.1038/nprot.2006.59openalex-snapshot
Gas chromatography mass spectrometry–based metabolite profiling in plants
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Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0
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An integrative approach towards completing genome-scale metabolic networks
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Building and analysing genome-scale metabolic models
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Identification of alanine dehydrogenase and its role in mixed secretion of ammonium and alanine by pea bacteroids
inferredcites →https://doi.org/10.1046/j.1365-313x.2001.01150.xopenalex-snapshot
A plastid envelope location of Arabidopsis ent‐kaurene oxidase links the plastid and endoplasmic reticulum steps of the gibberellin biosynthesis pathway
inferredcites →https://doi.org/10.1049/ip-syb:20060010openalex-snapshot
ScrumPy: metabolic modelling with Python
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Reconstruction of Arabidopsis metabolic network models accounting for subcellular compartmentalization and tissue-specificity
inferredcites →https://doi.org/10.1073/pnas.95.20.12038openalex-snapshot
Alanine, not ammonia, is excreted from N 2 -fixing soybean nodule bacteroids
inferredcites →https://doi.org/10.1073/pnas.97.10.5528openalex-snapshot
The Escherichia coli MG1655 in silico metabolic genotype: Its definition, characteristics, and capabilities
inferredcites →https://doi.org/10.1093/bib/bbp043openalex-snapshot
Pathway Tools version 13.0: integrated software for pathway/genome informatics and systems biology
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Advances in network-based metabolic pathway analysis and gene expression data integration
inferredcites →https://doi.org/10.1093/bioinformatics/btm040openalex-snapshot
MedicCyc: a biochemical pathway database forMedicago truncatula
inferredcites →https://doi.org/10.1093/bioinformatics/btn425openalex-snapshot
Detection of stoichiometric inconsistencies in biomolecular models
inferredcites →https://doi.org/10.1093/jxb/erf106openalex-snapshot
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inferredcites →https://doi.org/10.1093/jxb/eri058openalex-snapshot
Metabolic profiling of Medicago truncatula cell cultures reveals the effects of biotic and abiotic elicitors on metabolism
inferredcites →https://doi.org/10.1093/jxb/erq014openalex-snapshot
The proteome map of spinach leaf peroxisomes indicates partial compartmentalization of phylloquinone (vitamin K1) biosynthesis in plant peroxisomes
inferredcites →https://doi.org/10.1093/mp/ssp108openalex-snapshot
Intracellular Metabolite Transporters in Plants
inferredcites →https://doi.org/10.1093/nar/29.1.159openalex-snapshot
The TIGR Gene Indices: analysis of gene transcript sequences in highly sampled eukaryotic species
inferredcites →https://doi.org/10.1093/nar/gkl863openalex-snapshot
SUBA: the Arabidopsis Subcellular Database
inferredcites →https://doi.org/10.1093/nar/gkp875openalex-snapshot
The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases
inferredcites →https://doi.org/10.1093/nar/gkr1090openalex-snapshot
The Arabidopsis Information Resource (TAIR): improved gene annotation and new tools
inferredcites →https://doi.org/10.1093/nar/gkv1164openalex-snapshot
The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases
inferredcites →https://doi.org/10.1093/nar/gkv294openalex-snapshot
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inferredcites →https://doi.org/10.1093/oxfordjournals.aob.a084919openalex-snapshot
The Cost of Maintenance Processes in Plant Cells
inferredcites →https://doi.org/10.1094/mpmi-2-273openalex-snapshot
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inferredcites →https://doi.org/10.1104/pp.010866openalex-snapshot
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inferredcites →https://doi.org/10.1104/pp.108.125195openalex-snapshot
Metabolic Network Fluxes in Heterotrophic Arabidopsis Cells: Stability of the Flux Distribution under Different Oxygenation Conditions
inferredcites →https://doi.org/10.1104/pp.109.141267openalex-snapshot
A Genome-Scale Metabolic Model of Arabidopsis and Some of Its Properties
inferredcites →https://doi.org/10.1104/pp.109.148817openalex-snapshot
AraGEM, a Genome-Scale Reconstruction of the Primary Metabolic Network in Arabidopsis
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A Genome-Scale Metabolic Model Accurately Predicts Fluxes in Central Carbon Metabolism under Stress Conditions
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Responses to Light Intensity in a Genome-Scale Model of Rice Metabolism
inferredcites →https://doi.org/10.1104/pp.59.4.741openalex-snapshot
Changes in the Number, Viability, and Amino-acid-incorporating Activity of Rhizobium Bacteroids during Lupin Nodule Development
inferredcites →https://doi.org/10.1104/pp.64.1.1openalex-snapshot
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inferredcites →https://doi.org/10.1105/tpc.112.097188openalex-snapshot
Metabolism and Growth in Arabidopsis Depend on the Daytime Temperature but Are Temperature-Compensated against Cool Nights
inferredcites →https://doi.org/10.1111/j.1365-313x.2008.03519.xopenalex-snapshot
A gene expression atlas of the model legume Medicago truncatula
inferredcites →https://doi.org/10.1111/j.1469-8137.2004.01170.xopenalex-snapshot
Growth and maintenance respiration for individual plants in hierarchically structured canopies of Medicago sativa and Helianthus annuus: the contribution of current and old assimilates
inferredcites →https://doi.org/10.1111/j.1469-8137.2008.02502.xopenalex-snapshot
Multi‐site genetic modification of monolignol biosynthesis in alfalfa ( Medicago sativa ): effects on lignin composition in specific cell types
inferredcites →https://doi.org/10.1111/j.1744-7909.2010.00899.xopenalex-snapshot
Molecular Analysis of Legume Nodule Development and Autoregulation
inferredcites →https://doi.org/10.1111/tpj.12142openalex-snapshot
The metabolic flux phenotype of heterotrophic A rabidopsis cells reveals a complex response to changes in nitrogen supply
inferredcites →https://doi.org/10.1111/tpj.12252openalex-snapshot
A method for accounting for maintenance costs in flux balance analysis improves the prediction of plant cell metabolic phenotypes under stress conditions
inferredcites →https://doi.org/10.1126/science.1091811openalex-snapshot
A Previously Unknown Maltose Transporter Essential for Starch Degradation in Leaves
inferredcites →https://doi.org/10.1128/jb.187.15.5493-5495.2005openalex-snapshot
De Novo Alanine Synthesis by Bacteroids ofMesorhizobium lotiIs Not Required for Nitrogen Transfer in the Determinate Nodules ofLotus corniculatus
inferredcites →https://doi.org/10.1142/9781848163003_0008openalex-snapshot
COMPARING FLUX BALANCE ANALYSIS TO NETWORK EXPANSION: PRODUCIBILITY, SUSTAINABILITY AND THE SCOPE OF COMPOUNDS
inferredcites →https://doi.org/10.1146/annurev-arplant-050312-120235openalex-snapshot
Transport and Metabolism in Legume-Rhizobia Symbioses
inferredcites →https://doi.org/10.1146/annurev.arplant.48.1.493openalex-snapshot
METABOLITE TRANSPORT ACROSS SYMBIOTIC MEMBRANES OF LEGUME NODULES
inferredcites →https://doi.org/10.1146/annurev.arplant.55.031903.141616openalex-snapshot
BIOSYNTHESIS AND ACCUMULATION OF STEROLS
inferredcites →https://doi.org/10.1146/annurev.cb.07.110191.001203openalex-snapshot
Development of the Legume Root Nodule
inferredcites →https://doi.org/10.1146/annurev.cellbio.7.1.191openalex-snapshot
Development Of The Legume Root Nodule
inferredcites →https://doi.org/10.1186/gb-2010-11-4-r43openalex-snapshot
Flux balance analysis accounting for metabolite dilution
inferredcites →https://doi.org/10.1371/journal.pcbi.1003424openalex-snapshot
Fast Reconstruction of Compact Context-Specific Metabolic Network Models
inferredcites →https://doi.org/10.1371/journal.pone.0013933openalex-snapshot
Role of Symbiotic Auxotrophy in the Rhizobium-Legume Symbioses
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Zea mays iRS1563: A Comprehensive Genome-Scale Metabolic Reconstruction of Maize Metabolism
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Understanding Regulation of Metabolism through Feasibility Analysis
inferredcites →https://doi.org/10.2135/cropsci2002.0524openalex-snapshot
Alfalfa Stem Tissues
inferredcites →https://doi.org/10.2135/cropsci2002.5240openalex-snapshot
Alfalfa Stem Tissues: Cell Wall Deposition, Composition, and Degradability
inferredcites →https://doi.org/10.2136/sssaj2005.0419openalex-snapshot
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Untersuchungen über die Stickstoffnahrung der Gramineen und Leguminosen

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.1002/9781119409144.ch03openalex-snapshot
Medicago truncatula as an ecological, evolutionary, and forage legume model: new directions forward
inferred← citeshttps://doi.org/10.1038/s41598-020-57861-7openalex-snapshot
Magnetic Resonance Microscopy at Cellular Resolution and Localised Spectroscopy of Medicago truncatula at 22.3 Tesla
inferred← citeshttps://doi.org/10.1139/cjm-2018-0377openalex-snapshot
Multidisciplinary approaches for studying rhizobium–legume symbioses
inferred← citeshttps://doi.org/10.18174/512982openalex-snapshot
Higher, better, faster!? : Ultra-high field magnetic resonance imaging and spatially resolved spectroscopy
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