BioModelsapplication/xmlhttps://www.ebi.ac.uk/biomodels/model/download/MODEL1804130001?filename=iBP722.xmlprimaryOK200SóniaNon-curatedL2V1https://www.ebi.ac.uk/biomodels/MODEL180413000129843739falseBioModelsSBMLModelsPereira2018 Genome scale metabolic model for Actinobacillus succinogenes 130Z2018MODEL1804130001Non KineticPereira B, Miguel J, Vilaça P, Soares S, Rocha I, Carneiro S, Carneiro SPereira B29843739,
Actinobacillus succinogenes is a promising bacterial catalyst for the bioproduction of succinic acid from low-cost raw materials. In this work, a genome-scale metabolic model was reconstructed and used to assess the metabolic capabilities of this microorganism under producing conditions.The model, iBP722, was reconstructed based on the functional reannotation of the complete genome sequence of A. succinogenes 130Z and manual inspection of metabolic pathways, covering 1072 enzymatic reactions associated with 722 metabolic genes that involve 713 metabolites. The highly curated model was effective in capturing the growth of A. succinogenes on various carbon sources, as well as the SA production under various growth conditions with fair agreement between experimental and predicted data. Calculated flux distributions under different conditions show that a number of metabolic pathways are affected by the activity of some metabolic enzymes at key nodes in metabolism, including the transport mechanism of carbon sources and the ability to fix carbon dioxide.The established genome-scale metabolic model can be used for model-driven strain design and medium alteration to improve succinic acid yields.. 1, 12.
SilicoLife Lda, Rua do Canastreiro 15, 4715-387, Braga, Portugal.
CEB - Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal.
Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB-NOVA), Oeiras, Portugal.
SilicoLife Lda, Rua do Canastreiro 15, 4715-387, Braga, Portugal. scarneiro@silicolife.com.scarneiro@silicolife.comSilicoLife<h4>Background</h4>Actinobacillus succinogenes is a promising bacterial catalyst for the bioproduction of succinic acid from low-cost raw materials. In this work, a genome-scale metabolic model was reconstructed and used to assess the metabolic capabilities of this microorganism under producing conditions.<h4>Results</h4>The model, iBP722, was reconstructed based on the functional reannotation of the complete genome sequence of A. succinogenes 130Z and manual inspection of metabolic pathways, covering 1072 enzymatic reactions associated with 722 metabolic genes that involve 713 metabolites. The highly curated model was effective in capturing the growth of A. succinogenes on various carbon sources, as well as the SA production under various growth conditions with fair agreement between experimental and predicted data. Calculated flux distributions under different conditions show that a number of metabolic pathways are affected by the activity of some metabolic enzymes at key nodes in metabolism, including the transport mechanism of carbon sources and the ability to fix carbon dioxide.<h4>Conclusions</h4>The established genome-scale metabolic model can be used for model-driven strain design and medium alteration to improve succinic acid yields.Reconstruction of a genome-scale metabolic model for Actinobacillus succinogenes 130Z.Pereira Bruno B, Miguel Joana J, Vilaça Paulo P, Soares Simão S, Rocha Isabel I, Carneiro Sónia Sscale (sensu Metazoa), scale tissue, scales, peltate hair., scale, Genomes, plant peltate hairbiochemical pathways, Metabolic Networks, Networks, Ammonium, Bru, scale tissue, Metabolic Process, Materials, Carbon dioxide, Raw, Activity, Biocatalysts, Processes, peltate hair, postnatal development, number, Metabolic Concepts, secondary metabolites, Gene, growth and development, carbon, Network, Metabolic Processes, AKL3L1, dIKK-gamma, solute:solute exchange, Anhydride, primary metabolites, Succinate, Carbon-12, Carbonic, Metabolism, DmIKK-gamma, 1, Concepts, Dioxide, Low, Del(8)44H, dmIKKgamma, Metabolism Concept, IKK[[gamma]], Phenomenon, Metabolism Phenomena, IKKg, Ammonium., Ammonium Succinate, KEY, Key, Svc, C, catalyseur, E290, me75, CO2, Genetic, enzymes, Genomes, 2 Ethanedicarboxylic Acid, Butanedioic Acid, dioxidocarbon, catabolism, AK6, plant peltate hair, 4-Butanedioic Acid, Pathways, Metabolic Concept, metabolic process resulting in cell growth, W, number of, D17Mit170, ecotype, T1, Katalysator, Kohlenstoff, R-744, Enzyme, IKK, Carbon, has or lacks parts of type, scale (sensu Metazoa), biotransformation, catalizador, associated, Catabolism, Potassium, data, Pathway, cou, degradation, Process, metabolism resulting in cell growth, carbonic anhydride, [CO2], enzyme activity, extra or missing physical or functional parts, Metabolic Network, Potassium Succinate, Tl3, Tl2, Cistrons, carbone, results, predicted, Concept, Metabolic Phenomena, E-290, strain, carbono, mereological quality, development, Vitreous, IKKgamma, Metabolism Concepts, DmIKKgamma, Lr, single-organism transport, dIKK, Kenny, Phenomena, sequence, Genetic Materials, secretion, cultivar, catalyst, materials, E 290, background, scales, metabolism, Metabolic Pathways, Genetic Material, Metabolic Phenomenon, multicellular organism metabolic process, 4 Butanedioic Acid, Col4a-1, methanedione, scale, biodegradation, Carbonic Anhydride, Metabolic, growth pattern, Dmikkgamma, non-developmental growth, 6C, postnatal growth, IKK-gamma, metabolite, AK3L1, CG16910, primary structure of sequence macromolecule, introduction, Carbon 12, carbon dioxide, Vitreous Carbon, single-organism metabolic process, DmelCG16910, Material, AKL3L, metabolites, carbonium, cardinality, Biocatalyst, Bra, Metabolic Pathway, small molecule transport, Cistron, FIX, 2-Ethanedicarboxylic Acid, growth, General activity, CARBON DIOXIDE, Anabolismbiochemical pathways, Metabolic Process, Materials, Carbon dioxide, Activity, experimental, Biocatalysts, Processes, postnatal development, number, Metabolic Concepts, Gene, growth and development, carbon, Metabolic Processes, AKL3L1, solute:solute exchange, Anhydride, CARBON DIOXIDE., Carbon-12, Carbonic, Metabolism, Concepts, Dioxide, Metabolism Concept, Phenomenon, Metabolism Phenomena, C, E290, methods, CO2, Genetic, enzymes, Genomes, dioxidocarbon, catabolism, AK6, experimental section, Metabolic Concept, metabolic process resulting in cell growth, number of, Kohlenstoff, R-744, Enzyme, Carbon, has or lacks parts of type, biotransformation, associated, Catabolism, data, degradation, Process, metabolism resulting in cell growth, carbonic anhydride, [CO2], enzyme activity, extra or missing physical or functional parts, Cistrons, carbone, predicted, Concept, Metabolic Phenomena, E-290, carbono, mereological quality, development, Vitreous, Metabolism Concepts, single-organism transport, Phenomena, sequence, Genetic Materials, secretion, E 290, metabolism, Genetic Material, Metabolic Phenomenon, multicellular organism metabolic process, methanedione, biodegradation, Carbonic Anhydride, growth pattern, Metabolic, non-developmental growth, 6C, postnatal growth, AK3L1, primary structure of sequence macromolecule, Carbon 12, experimental procedures, carbon dioxide, Vitreous Carbon, single-organism metabolic process, Material, AKL3L, carbonium, cardinality, Biocatalyst, small molecule transport, Cistron, FIX, growth, General activity, Anabolismscale (sensu Metazoa), scale tissue, scales, peltate hair., scale, Genomes, plant peltate hairfalsePereira2018 - Genome-scale metabolic model for Actinobacillus succinogenes 130Z
The model, iBP722, was reconstructed based on the functional reannotation of the complete genome sequence of A. succinogenes 130Z and manual inspection of metabolic pathways, covering 1072 enzymatic reactions associated with 722 metabolic genes that involve 713 metabolites. The highly curated model was effective in capturing the growth of A. succinogenes on various carbon sources, as well as the SA production under various growth conditions with fair agreement between experimental and predicted data. Calculated flux distributions under different conditions show that a number of metabolic pathways are affected by the activity of some metabolic enzymes at key nodes in metabolism, including the transport mechanism of carbon sources and the ability to fix carbon dioxide.
2019-05-162019-05-162018-04-13MODEL180413000129843739