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https://www.ebi.ac.uk/biomodels/model/download/MODEL2204150001?filename=miniFROG%20Report_kulyashov2020.xlsxhttps://www.ebi.ac.uk/biomodels/model/download/MODEL2204150001?filename=Kulyashov2020_SBMLL3V1fbcV2-GSM+model_Geobacillus+icigianus.xmlhttps://www.ebi.ac.uk/biomodels/model/download/MODEL2204150001?filename=FROG.omexhttps://www.ebi.ac.uk/biomodels/model/download/MODEL2204150001?filename=MemoteReport.htmlprimaryOK200Ilya R AkberdinNon-curatedconstraint-based modelL3V1FROGhttps://www.ebi.ac.uk/biomodels/MODEL220415000132635563falseBioModelsModelsSBMLKulyashov2020 Genome Scale Metabolic Model for Geobacillus icigianus2020MODEL2204150001Mikhail KulyashovMikhail Kulyashov, Sergey E Peltek, Ilya R Akberdin32635563, The thermophilic strain of the genus Geobacillus, Geobacillus icigianus is a promising bacterial chassis for a wide range of biotechnological applications. In this study, we explored the metabolic potential of Geobacillus icigianus for the production of 2,3-butanediol (2,3-BTD), one of the cost-effective commodity chemicals. Here we present a genome-scale metabolic model iMK1321 for Geobacillus icigianus constructed using an auto-generating pipeline with consequent thorough manual curation. The model contains 1321 genes and includes 1676 reactions and 1589 metabolites, representing the most-complete and publicly available model of the genus Geobacillus. The developed model provides new insights into thermophilic bacterial metabolism and highlights new strategies for biotechnological applications of the strain. Our analysis suggests that Geobacillus icigianus has a potential for 2,3-butanediol production from a variety of utilized carbon sources, including glycerine, a common byproduct of biofuel production. We identified a set of solutions for enhancing 2,3-BTD production, including cultivation under anaerobic or microaerophilic conditions and decreasing the TCA flux to succinate via reducing citrate synthase activity. Both in silico predicted metabolic alternatives have been previously experimentally verified for closely related strains including the genus Bacillus.. 7, 8. Biosoft.ru, 630058 Novosibirsk, Russia.akberdinir@gmail.comBiosoft.ru, 630058 Novosibirsk, Russia.Department of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia.Department of Molecular Biotechnology, Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia.The thermophilic strain of the genus Geobacillus, Geobacillus icigianus is a promising bacterial chassis for a wide range of biotechnological applications. In this study, we explored the metabolic potential of Geobacillus icigianus for the production of 2,3-butanediol (2,3-BTD), one of the cost-effective commodity chemicals. Here we present a genome-scale metabolic model iMK1321 for Geobacillus icigianus constructed using an auto-generating pipeline with consequent thorough manual curation. The model contains 1321 genes and includes 1676 reactions and 1589 metabolites, representing the most-complete and publicly available model of the genus Geobacillus. The developed model provides new insights into thermophilic bacterial metabolism and highlights new strategies for biotechnological applications of the strain. Our analysis suggests that Geobacillus icigianus has a potential for 2,3-butanediol production from a variety of utilized carbon sources, including glycerine, a common byproduct of biofuel production. We identified a set of solutions for enhancing 2,3-BTD production, including cultivation under anaerobic or microaerophilic conditions and decreasing the TCA flux to succinate via reducing citrate synthase activity. Both in silico predicted metabolic alternatives have been previously experimentally verified for closely related strains including the genus Bacillus.A Genome-Scale Metabolic Model of 2,3-Butanediol Production by Thermophilic Bacteria Geobacillus icigianus.Kulyashov Mikhail M, Peltek Sergey E SE, Akberdin Ilya R IRBacteria Woese et al. 2024, Bacteria (ex Cavalier-Smith 1987), scale tissue, bacteria, Prokaryota., Eubacteria, Bacteria <bacteria>, scale, Genomes, Prokaryotae, prokaryote, plant peltate hair, peltate hair, prokaryotes, fungi, Procaryotae, Bacteriobiota, whole genome, scales, eubacteria, Monerascale tissue, whole genome, scales, peltate hair., scale, Genomes, plant peltate hairbiochemical pathways, Ammonium, scale tissue, IPP2A2, Metabolic Process, Materials, (pro-R)-carboxymethyl-forming], determination, Processes, CoA-acetylating activity, peltate hair, Metabolic Concepts, Bacillus rRNA group 1., secondary metabolites, Gene, carbon, broad, Metabolic Processes, PHAPII, 5730420M11Rik, Bacillus <firmicutes>, Glycerine, primary metabolites, glycyl alcohol, Succinate, Propanetriol, Carbon-12, Metabolism, Trihydroxypropane, Concepts, 1, 2, CG3599, BTD, (R)-citric synthase activity, Metabolism Concept, Phenomenon, Sprains, Metabolism Phenomena, Re-citrate-synthase activity, Ammonium Succinate, succinate anion, citrate oxaloacetate-lyase ((pro-3S)-CH2COO-rightacetyl-CoA), 3-Propanetriol, study, succinates, C, SET, Oelsuess, Genetic, Genomes, (pro-S)-carboxymethyl forming], TAF-I, 2 Ethanedicarboxylic Acid, Butanedioic Acid, catabolism, plant peltate hair, Glycerin, ipp2a2, 4-Butanedioic Acid, Bacillus bacterium, citrate oxaloacetate-lyase, Metabolic Concept, 2pp2a, metabolic process resulting in cell growth, ecotype, CG10574, Solution, citrate synthase activity, DmelCG4299, IGAAD, set, Kohlenstoff, glycerolum, 2PP2A, citrate oxaloacetate-lyase [(pro-3S)-CH2COOrightacetyl-CoA], DmelCG10574, taf-ibeta, citrate synthetase activity, Carbon, dSET, dSet, biotransformation, Strains, Catabolism, citric synthase activity, Potassium, citrate oxaloacetate-lyase ((pro-3R)-CH(2)COO(-)->acetyl-CoA) activity, citrate condensing enzyme activity, Glyceritol, phapii, DmelCG3599, wide/broad, degradation, Process, succinic acid anion, citrate oxaloacetate-lyase ((pro-3R)-CH2COO-rightacetyl-CoA), Glyzerin, metabolism resulting in cell growth, (R)-citrate synthase activity, Sprain, igaad, StF-IT-1, Bacillus <walking sticks>, Bacillus, Potassium Succinate, oxalacetic transacetase activity, Cistrons, carbone, predicted, group, citric-condensing enzyme activity, strain, Concept, Metabolic Phenomena, carbono, Vitreous, Metabolism Concepts, I-2PP2A, chemical analysis, glycerol, Dm I-2, Strain, Phenomena, I2PP2A, Genetic Materials, secretion, cultivar, butanedioic acid, scales, metabolism, Genetic Material, Metabolic Phenomenon, 3-Trihydroxypropane, multicellular organism metabolic process, Gro, 4 Butanedioic Acid, HLA-DR-associated protein II, scale, biodegradation, Metabolic, glycerine, ensemble, DI-2, acetyl-CoA:oxaloacetate C-acetyltransferase [thioester-hydrolysing, 6C, I-2Dm, succinate, metabolite, common, whole genome, CG4299, ion(2-), citrate oxaloacetate-lyase ((pro-3S)-CH(2)COO(-)->acetyl-CoA) activity, Carbon 12, I-2PP1, CT12113, dSET/TAF-Ibeta, wide, Vitreous Carbon, 2610030F17Rik, TAF-IBETA, Material, citrogenase activity, metabolites, carbonium, Cistron, oxaloacetate transacetase activity, TAF-Ibeta, assay, (-)OOC-CH2-CH2-COO(-), AA407739, Strains and Sprains, i2pp2a, 2-Ethanedicarboxylic Acid, condensing enzyme activity, Anabolismscale tissue, primary metabolites, Materials, Genetic, scale, Genomes, Material, plant peltate hair, peltate hair, Genetic Materials, Cistron, secondary metabolites, metabolite, Gene, whole genome, scales, metabolites., Cistrons, Genetic MaterialfalseKulyashov2020 - Genome-Scale Metabolic Model for Geobacillus icigianusHere we present a genome-scale metabolic model iMK1321 for Geobacillus icigianus constructed using an auto-generating pipeline with consequent thorough manual curation. The model contains 1321 genes and includes 1676 reactions and 1589 metabolites, representing the most-complete and publicly available model of the genus Geobacillus.2024-08-122024-10-152022-04-15MODEL220415000132635563MODEL2204150001