Data and code underlying the publication: Synergistic regulatory mechanisms in glycolysis revealed by pathway transplantation

DOI:10.4121/79f009a8-f098-4135-ab03-fc3c97c7ef19.v1
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DOI: 10.4121/79f009a8-f098-4135-ab03-fc3c97c7ef19

Datacite citation style

Ewout Knibbe; Francine J. Boonekamp; Rachel Stuij; Savakis, Philipp; Pelsma, Koen et. al. (2025): Data and code underlying the publication: Synergistic regulatory mechanisms in glycolysis revealed by pathway transplantation . Version 1. 4TU.ResearchData. dataset. https://doi.org/10.4121/79f009a8-f098-4135-ab03-fc3c97c7ef19.v1
Other citation styles (APA, Harvard, MLA, Vancouver, Chicago, IEEE) available at Datacite

Dataset

Data and code associated with the paper Synergistic regulatory mechanisms in glycolysis revealed by pathway transplantation. In this study the role of protein allostery in the regulation of yeast glycolysis is studied by replacing the complete pathway in S. cerevisiae with that fromYarrowia lipolytica. By using complete pathway complementation, as well as single gene complementation, the essential regulatory steps were identified to be glucokinase, phosphofructokinase and pyruvate kinase. Expression of these enzymes together, even in the context of the S. cerevisiae pathway led to imbalances in glycolysis which could only be overcome by lowering the glucokinase activity. In this repository, the adapted kinetic model is included (which was adapted from Van Heerden et al. 2014) used to study the effect of single regulatory steps on the glycolytic pathwya (figure 6A). Also included are the files and code used for the microfluidics data analysis for the single cell metabolic responses (shown in figure 7). This contains the code used to recognize cells and process the microscope pictures (under code), the processed microfluidics data in the form of .pickle files, a jupyter notebook where these are analyzed and plotted and the resulting figures.

History

  • 2025-10-21 first online, published, posted

Publisher

4TU.ResearchData

Format

One python script containing the adapted kinetic model and a .zip file containing a directory with all files pertaining to the microfluidics analysis, which contains .pickle files, a Jupyter notebook, .pdf figures and a code directory with the the processing algorithm (.py) used on the microscopy data

Organizations

TU Delft, Faculty of Applied Sciences, Department of Biotechnology, Industrial Microbiology

Vrije Universiteit Amsterdam, Amsterdam Institute of Molecular and Life Sciences, Systems Biology Lab

Instituto de Investigaciones Biomédicas “Alberto Sols”, CSIC-UAM, Department of Experimental Models of Human disease

DATA

Files (2)