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NADH-driven poly-3-hydroxybutyrate accumulation in Escherichia coli: Data from enzymatic assays and oxygen-limited continuous cultures

Biosynthesis of poly-3-hydroxybutyrate (PHB) as a fermentation product enables the coupling of growth and product generation. Moreover, the reduction of oxygen supply should reduce operative cost and increase product yield. Generation of PHB as a fermentation product depends on the in vivo activity...

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Autores principales: Olavarria, Karel, Quakkelaar, Caspar, van Renselaar, Joachim, Langerak, Dennis, van Loosdrecht, Mark C.M., Wahl, S.A.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Elsevier 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7726675/
https://www.ncbi.nlm.nih.gov/pubmed/33318976
http://dx.doi.org/10.1016/j.dib.2020.106588
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author Olavarria, Karel
Quakkelaar, Caspar
van Renselaar, Joachim
Langerak, Dennis
van Loosdrecht, Mark C.M.
Wahl, S.A.
author_facet Olavarria, Karel
Quakkelaar, Caspar
van Renselaar, Joachim
Langerak, Dennis
van Loosdrecht, Mark C.M.
Wahl, S.A.
author_sort Olavarria, Karel
collection PubMed
description Biosynthesis of poly-3-hydroxybutyrate (PHB) as a fermentation product enables the coupling of growth and product generation. Moreover, the reduction of oxygen supply should reduce operative cost and increase product yield. Generation of PHB as a fermentation product depends on the in vivo activity of an NADH-preferring acetoacetyl-CoA reductase. Proof of this concept requires (i) quantification of the cofactor preference, in physiologically relevant conditions, of a putative NADH-preferring acetoacetyl-CoA reductase and (ii) verification of PHB accumulation using an NADH-preferring acetoacetyl-CoA reductase in a species naturally incapable of doing so, for example, Escherichia coli. This dataset contains kinetic data obtained by spectrophotometry and data from a continuous culture of an engineered E. coli strain accumulating PHB under oxygen-limiting conditions. In this dataset it is possible to find (1) enzyme stability assays; (2) initial rates and progress curves from reactions catalyzed by two acetoacetyl-CoA reductases; (3) estimations of the relative use of NADH and NADPH by two acetoacetyl-CoA reductases; (4) estimations of the flux capacity of the reaction catalyzed by an acetoacetyl-CoA reductase; (5) biomass composition of an engineered E. coli strain transformed with a plasmid; (6) calculation of reconciled specific rates of this engineered strain growing on sucrose as the sole carbon source under oxygen limitation and (7) metabolic fluxes distributions during the continuous growth of this engineered strain. Because a relatively small number of acetoacetyl-CoA reductases have been kinetically characterized, data and scripts here provided could be useful for further kinetic characterizations. Moreover, the procedure described to estimate biomass composition could be interesting to estimate plasmid and protein burden in other strains. Application of data reconciliation to fermentations should help to obtain specific rates consistent with the principle of mass and electron conservation. All the required data and scripts to perform these analyses are deposited in a Mendeley Data repository. This article was co-submitted with the manuscript entitled “An NADH preferring acetoacetyl-CoA reductase is engaged in poly-3-hydroxybutyrate accumulation in Escherichiasia. coli”.
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spelling pubmed-77266752020-12-13 NADH-driven poly-3-hydroxybutyrate accumulation in Escherichia coli: Data from enzymatic assays and oxygen-limited continuous cultures Olavarria, Karel Quakkelaar, Caspar van Renselaar, Joachim Langerak, Dennis van Loosdrecht, Mark C.M. Wahl, S.A. Data Brief Data Article Biosynthesis of poly-3-hydroxybutyrate (PHB) as a fermentation product enables the coupling of growth and product generation. Moreover, the reduction of oxygen supply should reduce operative cost and increase product yield. Generation of PHB as a fermentation product depends on the in vivo activity of an NADH-preferring acetoacetyl-CoA reductase. Proof of this concept requires (i) quantification of the cofactor preference, in physiologically relevant conditions, of a putative NADH-preferring acetoacetyl-CoA reductase and (ii) verification of PHB accumulation using an NADH-preferring acetoacetyl-CoA reductase in a species naturally incapable of doing so, for example, Escherichia coli. This dataset contains kinetic data obtained by spectrophotometry and data from a continuous culture of an engineered E. coli strain accumulating PHB under oxygen-limiting conditions. In this dataset it is possible to find (1) enzyme stability assays; (2) initial rates and progress curves from reactions catalyzed by two acetoacetyl-CoA reductases; (3) estimations of the relative use of NADH and NADPH by two acetoacetyl-CoA reductases; (4) estimations of the flux capacity of the reaction catalyzed by an acetoacetyl-CoA reductase; (5) biomass composition of an engineered E. coli strain transformed with a plasmid; (6) calculation of reconciled specific rates of this engineered strain growing on sucrose as the sole carbon source under oxygen limitation and (7) metabolic fluxes distributions during the continuous growth of this engineered strain. Because a relatively small number of acetoacetyl-CoA reductases have been kinetically characterized, data and scripts here provided could be useful for further kinetic characterizations. Moreover, the procedure described to estimate biomass composition could be interesting to estimate plasmid and protein burden in other strains. Application of data reconciliation to fermentations should help to obtain specific rates consistent with the principle of mass and electron conservation. All the required data and scripts to perform these analyses are deposited in a Mendeley Data repository. This article was co-submitted with the manuscript entitled “An NADH preferring acetoacetyl-CoA reductase is engaged in poly-3-hydroxybutyrate accumulation in Escherichiasia. coli”. Elsevier 2020-11-28 /pmc/articles/PMC7726675/ /pubmed/33318976 http://dx.doi.org/10.1016/j.dib.2020.106588 Text en © 2020 The Authors http://creativecommons.org/licenses/by-nc-nd/4.0/ This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).
spellingShingle Data Article
Olavarria, Karel
Quakkelaar, Caspar
van Renselaar, Joachim
Langerak, Dennis
van Loosdrecht, Mark C.M.
Wahl, S.A.
NADH-driven poly-3-hydroxybutyrate accumulation in Escherichia coli: Data from enzymatic assays and oxygen-limited continuous cultures
title NADH-driven poly-3-hydroxybutyrate accumulation in Escherichia coli: Data from enzymatic assays and oxygen-limited continuous cultures
title_full NADH-driven poly-3-hydroxybutyrate accumulation in Escherichia coli: Data from enzymatic assays and oxygen-limited continuous cultures
title_fullStr NADH-driven poly-3-hydroxybutyrate accumulation in Escherichia coli: Data from enzymatic assays and oxygen-limited continuous cultures
title_full_unstemmed NADH-driven poly-3-hydroxybutyrate accumulation in Escherichia coli: Data from enzymatic assays and oxygen-limited continuous cultures
title_short NADH-driven poly-3-hydroxybutyrate accumulation in Escherichia coli: Data from enzymatic assays and oxygen-limited continuous cultures
title_sort nadh-driven poly-3-hydroxybutyrate accumulation in escherichia coli: data from enzymatic assays and oxygen-limited continuous cultures
topic Data Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7726675/
https://www.ncbi.nlm.nih.gov/pubmed/33318976
http://dx.doi.org/10.1016/j.dib.2020.106588
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