Subject |
Biological Sciences. Biotechnology |
Specific subject area |
Continuous production of poly-3-hydroxybutyrate as a fermentation product under oxygen limitation. |
Type of data |
Figure: Product concentration versus Enzyme concentration times Time. |
Figure: Initial rates versus acetoacetyl-CoA concentration |
Figures: Progress curves of reactions catalyzed by acetoacetyl-CoA reductases. |
Figure: Relative consumption of NADH and NADPH in the reactions catalyzed by two acetoacetyl-CoA reductases. |
Figure: Flux capacity of a reaction catalyzed by an acetoacetyl-CoA reductase at different NADH/NAD+ ratios. |
Table: Biomass composition of the E. coli strain ((F– λ– ilvG– rfb-50 rph-1 (DE3) ΔadhE ΔadhP ΔldhA Δpta ΔmhpF)) transformed with the plasmid pCOLA-phaCAphaB-cscABK. |
Table: Non-balanced and reconciled specific rates during the continuous growth of that engineered strain, using sucrose as the sole carbon source, at a dilution rate of 0.1 h−1, and oxygen limitation. |
Table: Metabolic fluxes distributions during the continuous growth of that engineered strain, using sucrose as the sole carbon source, at a dilution rate of 0.1 h−1, and oxygen limitation. |
How data were acquired |
In the case of kinetic data, product concentrations were estimated by spectrophotometry and enzyme concentrations were estimated using the Biorad Protein Assay kit. Time and initial rates were automatically recorded/calculated by the spectrophotometer Synergy HTX plate-reader (Biotek) with the software Gen5 (Biotek). Scripts to read and analyze the kinetic data were written and tested with the software DYNAFIT [1] version 4 for Windows (Biokin). |
Other scripts were written and tested with MATLAB 2020a. |
Data format |
Data from the Selwyn tests are available as Microsoft Excel files where the columns corresponding to Product concentrations and to Enzyme concentration times Time are clearly identified. |
Data from reaction progress curves are available as .txt files where the first column contains the time (in seconds) and the second column contains the corresponding substrate concentrations (in micromolar). |
Initial rates are available as a .txt file where the first column contains the concentrations of acetoacetyl-CoA (in micromolar) and the second column contains the initial rates (in micromole of product/micromole of enzyme/second). |
Data from biomass composition is provided as a Microsoft Excel file. |
Parameters for data collection |
Kinetic data were recorded at 30 °C. Continuous cell cultures were studied at 37 °C. Further details are explained in the section Experimental Design, Materials and Methods. |
Description of data collection |
Kinetic data were obtained by spectrophotometry in a plate reader equipped with monochromator, temperature control and a built-in software controlled by the user through the software Gen5. Data from continuous cultures were obtained by the integration of data obtained by different means. More details in the section Experimental Design, Materials and Methods. |
Data source location |
Institution: Department of Biotechnology, Delft University of Technology |
City/Town/Region: Delft, Zuid Holland |
Country: Netherlands |
Data accessibility |
Repository name: |
NADH-driven polyhydroxybutyrate accumulation in E. coli dataset 2 |
Data identification number: 10.17632/954dxdncrv.1 |
Direct URL to data: http://dx.doi.org/10.17632/954dxdncrv.1
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Instructions for accessing these data: Freely available in Mendeley Database. |
Related research article |
Olavarria K., Carnet A., van Ranselaar J., Quakkelaar C., Cabrera R., Guedes da Silva L., Smids A.L., Villalobos P., van Loosdrecht M.C.M., and Wahl S.A.. An NADH preferring acetoacetyl-CoA reductase is engaged in poly-3-hydroxybutyrate accumulation in E. coli. Journal of Biotechnology. Accepted on October 18, 2020. https://doi.org/10.1016/j.jbiotec.2020.10.022
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