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

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 <em>S. cerevisiae </em>with that from<em>Yarrowia lipolytica. </em>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 <em>S. cerevisiae </em>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.

本数据集关联论文《通过通路移植揭示的糖酵解协同调控机制》（Synergistic regulatory mechanisms in glycolysis revealed by pathway transplantation）。本研究通过将酿酒酵母（S. cerevisiae）的完整糖酵解通路替换为解脂耶氏酵母（Yarrowia lipolytica）的同源通路，探究了蛋白质别构效应在酵母糖酵解调控中的作用。研究采用完整通路互补与单基因互补两种实验策略，确定了糖酵解的核心调控步骤为葡萄糖激酶、磷酸果糖激酶与丙酮酸激酶。实验进一步发现，即便在酿酒酵母自身的糖酵解通路背景下共表达上述三种酶，仍会引发糖酵解失衡，仅通过降低葡萄糖激酶活性方可纠正该失衡。本存储库包含改编自Van Heerden等人2014年研究的动力学模型，该模型用于探究单个调控步骤对糖酵解通路的影响（对应图6A）；同时还包含用于单细胞代谢反应微流控数据分析的全套文件与代码（对应图7），其中包括用于细胞识别与显微镜图像处理的代码（存放于code目录下）、以.pickle格式存储的处理后微流控数据、用于数据分析与绘图的Jupyter笔记本，以及最终生成的可视化图表。