{"database":"FAIRDOMHub","file_versions":[],"scores":null,"additional":{"omics_type":["Models"],"submitter":["Thomas Millat"],"full_dataset_link":["https://fairdomhub.org/models/99?version=1"],"ModelFormat":["Matlab package"],"submitter_affiliation":["University of Rostock"],"repository":["FAIRDOMHub"],"pubmed_abstract":["In response to changing extracellular pH levels, phosphate-limited continuous cultures of Clostridium acetobutylicum reversibly switches its metabolism from the dominant formation of acids to the prevalent production of solvents. Previous experimental and theoretical studies have revealed that this pH-induced metabolic switch involves a rearrangement of the intracellular transcriptomic, proteomic and metabolomic composition of the clostridial cells. However, the influence of the population dynamics on the observations reported has so far been neglected. Here, we present a method for linking the pH shift, clostridial growth and the acetone-butanol-ethanol fermentation metabolic network systematically into a model which combines the dynamics of the external pH and optical density with a metabolic model. Furthermore, the recently found antagonistic expression pattern of the aldehyde/alcohol dehydrogenases AdhE1/2 and pH-dependent enzyme activities have been included into this combined model. Our model predictions reveal that the pH-induced metabolic shift under these experimental conditions is governed by a phenotypic switch of predominantly acidogenic subpopulation towards a predominantly solventogenic subpopulation. This model-driven explanation of the pH-induced shift from acidogenesis to solventogenesis by population dynamics casts an entirely new light on the clostridial response to changing pH levels. Moreover, the results presented here underline that pH-dependent growth and pH-dependent specific enzymatic activity play a crucial role in this adaptation. In particular, the behaviour of AdhE1 and AdhE2 seems to be the key factor for the product formation of the two phenotypes, their pH-dependent growth, and thus, the pH-induced metabolic switch in C. acetobutylicum."],"pubmed_title":["A shift in the dominant phenotype governs the pH-induced metabolic switch of Clostridium acetobutylicumin phosphate-limited continuous cultures."],"pubmed_authors":["Millat Thomas T, Janssen Holger H, Thorn Graeme J GJ, King John R JR, Bahl Hubert H, Fischer Ralf-Jörg RJ, Wolkenhauer Olaf O"],"name_synonyms":["Shift, Estimate, School-Age Populations, Populations, School-Age, Estimation, Optical, Optics, Observed, School Age, ESTIMATED, School-Age Population, School Age Population, Population, Forward, Estimated, Physical Shift, Statistical Estimation, School Age Populations, Displacement."],"description_synonyms":["Shift, Estimate, School-Age Populations, Populations, School-Age, Estimation, Optical, Optics, Observed, School Age, ESTIMATED, School-Age Population, School Age Population, Population, Forward, Estimated, Physical Shift, Statistical Estimation, School Age Populations, Displacement."],"pubmed_abstract_synonyms":["biochemical pathways, Metabolic Process, Residential, Transitions, nucleocytoplasm, Mobility, postnatal development., Stable Population, postnatal development, Metabolic Concepts, Metabonomic, Metabonomics, growth and development, Visible Light, Aging, Pi, 1-hydroxyethane, Solvent, DmelCG6383, alcohol, 2-Propanone, Techniques, Decreases, Stationary, Population Pressures, Roles, Method, Alkohol, Concepts, Population Replacement, Metabolism Concept, Phenomenon, methyl ketone, IKKg, multicellular organismal biosynthetic process, KEY, Key, tetraoxophosphate(V), single-organism biosynthetic process, Theory, Orthophosphate, PHOSPHATE ION, catabolism, tetraoxidophosphate(3-), ethanol anabolism during fermentation, crumb, Phosphate, metabolic process resulting in cell growth, Aethanol, [CH2Me(OH)], Population Theory, Dehydrated ethanol, TNFSF14, Methodological Studies, Propanon, Role Concepts, biotransformation, Theories, Catabolism, Inorganic, spiritus vini, single-organism behavior, Radiation, Process, CG6383, UNQ391/PRO726, dimethylketone, metabolism resulting in cell growth, acid, Stationary Populations, Light, Ethyl alcohol, Procedure, Aceton, results, DmIKKgamma, LIGHT, Role Concept, Pyroacetic ether, Playthings and Play, dIKK, Kenny, Role, Plaything, secretion, Population Decrease, Decrease, internal to cell, [OEtH], Population Replacements, Phosphates, Visible Radiations, Acid, Populations, Replacements, ethanol synthesis during fermentation, Visible Radiation, HVEML, EtOH, growth pattern, PO4(3-), acide, non-developmental growth, IKK-gamma, Toys, acids, acido, Rural-Urban Migration, Methodological, Methodological Study, beta-Ketopropane, alcohol etilico, Methylcarbinol, experimental procedures, Phenotypes, Migrations, DmelCG16910, phosphate, phosphate ions, Replacement, Aldehyde, Biocatalyst, l(3)S050920, Crbs, Rural-Urban Migrations, tetraoxophosphate(3-), Mobilities, Stable Populations, Migration, Plays, Demographic Transitions, Procedures, experimental, Processes, Biocatalysts, etanol, Clostridium acetobutyricum, Rural-Urban, solventogenesis, far, Metabolic Processes, Population Theories, Population Decreases, dIKK-gamma, Ly113, Aethylalkohol, method, propanone, Crumbs, Metabolism, Clostridium acetonobutylicum, method used in an experiment, DmIKK-gamma, dimethylcetone, Studies, dmIKKgamma, Metabolomic, IKK[[gamma]], Metabolism Phenomena, Technique, Neomalthusianism, Toy, protoplasm, ethanol formation during fermentation, CT19912, 0509/20, methods, pattern, protoplast, Playthings, distribution, experimental section, 1384/04, Inorganic Phosphates, Granulobacter pectinovorum, Metabolic Concept, Visible, Population, Study, acidogenesis, Malthusianism, C2H5OH, Enzyme, Puppets, IKK, Stable, Optimum, Play, Optimum Population, TR2, Azeton, Transition, Saeure, Dimethyl ketone, Puppet, l(3)j1B5, [PO4](3-), Dimethylketon, degradation, ethanol biosynthetic process involved in glucose fermentation to ethanol, CD258, Cell, Demographic Transition, Concept, Metabolic Phenomena, l(3)07207, development, Metabolism Concepts, IKKgamma, Pressure, Phenomena, alcool ethylique, Demographic, CRB, Crb, Optimum Populations, l(3)S058104, metabolism, Metabolic Phenomenon, Inorganic Phosphate, Radiations, multicellular organism metabolic process, Rural Urban Migration, biodegradation, Metabolic, Residential Mobility, Saeuren, HVEM-L, Dmikkgamma, postnatal growth, Photoradiation, Residential Mobilities, Stationary Population, Dynamics, CG16910, LTg, plan specification, extracellular, hydroxyethane, Population Pressure, Photoradiations, Pressures, Demographic Aging, phosphates, growth, alcoholic fermentation, Anabolism"],"pubmed_title_synonyms":["Inorganic Phosphate, Phosphates, [PO4](3-), Phenotypes, tetraoxophosphate(3-), tetraoxophosphate(V), Anaerobacter, Orthophosphate, Inorganic., phosphate, phosphate ions, PHOSPHATE ION, tetraoxidophosphate(3-), PO4(3-), Inorganic Phosphates, Phosphate, phosphates, Pi, Anaerobacter Duda et al. 1996, Inorganic"],"additional_accession":[]},"is_claimable":false,"name":"Estimation of an acidogenic and solventogenic population from optical density data observed in 'forward'-shift experiments using continuous cultures of C. acetobutylicum","description":"Estimation of an acidogenic and solventogenic population from optical density data observed in 'forward'-shift experiments using continuous cultures of C. acetobutylicum","dates":{"created":"2013-01-05","publication":"2014-06-11","submission":"2013-01-05","last_modified":"2014-06-11"},"accession":"99","cross_references":{"pubmed":["23640360"]}}