Nutrient sensors allow cells to adapt their metabolisms to match nutrient availability by regulating metabolic pathway expression. Many such sensors are cytosolic receptors that measure intracellular nutrient concentrations. One might expect that inducing the metabolic pathway that degrades a nutrient would reduce intracellular nutrient levels, destabilizing induction. In the galactose-responsive (GAL) pathway of S. cerevisiae, however, we find that induction is stabilized by flux sensing. Previously proposed mechanisms for flux sensing postulate the existence of metabolites whose concentrations correlate with flux. The GAL pathway flux sensor uses a different principle: the galactokinase Gal1p both performs the first step in galactose metabolism and reports on flux by signaling to the GAL repressor, Gal80p. Both Gal1p catalysis and Gal1p signaling depend on the concentration of the Gal1p-galactose complex and are therefore directly correlated. Given the simplicity of this mechanism, flux sensing is likely to be a general feature throughout metabolic regulation.

README: Data for: The galactokinase enzyme of yeast senses metabolic flux to stabilize GAL pathway regulation

https://doi.org/10.5061/dryad.t4b8gtj7b

File structure

The raw data is split into datasets that are stored in individual .7z archives. dataset_list.md contains a brief description of each dataset and which figures the dataset was used for.

For flow cytometry data, Flow Cytometry Standard (FCS) files are shared in the raw_data folders. These folders also include a meta.csv file that contains information about each FCS file, including the genotype of the analyzed strains and where applicable, the extracellular galactose concentrations (mM) and the extracellular doxycycline concentrations (ng/µL).

For extracellular galactose concentration measurements (dataset 2), absorbance measurements at 340 nm are included for culture medium (absorption_experimental_data.csv) and the standard curve used to infer galactose concentrations (absorption_standard_data.csv).

For optical density measurements (dataset 6), absorbance measurements at 600 nm at different time points are included in the od_data.csv file. meta.csv contains information about the genotype of the analyzed strains.

For microscopy data (dataset 5), images from different experiments are each located in separate archives to reduce the size of individual files. These experiments are indexed in microscopy_experiment_index.csv. For microscopy data, processing intermediates are also included: BFP images were segmented (using https://github.com/alexxijielu/yeast\_segmentation) and segmentation masks are deposited in the masks folder of each microscopy experiment. Segmented cells were tracked (using cell_tracking.ipynb) and cell tracks are saved as tracks.csv in the the folder of each microscopy experiment.

Code

The code.7z archive contains analysis.R which analyzes the data and saves the manuscript figures in the figures folder. The scripts assume the following folder structure.

.
├── code
│   ├── analysis.R
│   ├── utility_analysis.R
│   ├── utility_model.R
│   └── cell_tracking.ipynb
├── datasets
│   ├── dataset_1
│   ├── dataset_2
│   ├── dataset_3
│   ├── dataset_4
│   ├── dataset_5
│   │   ├── microscopy_experiment_index.csv
│   │   ├── 1
│   │   ├── ...
│   │   └── 16
│   ├── dataset_6
│   ├── dataset_7
│   ├── dataset_8
│   └── dataset_9
└── └── dataset_10

Note that microscopy_experiment_index.csv in the dataset_5 folder is used by analysis.R to annotate the microscopy folders.

Data for: The galactokinase enzyme of yeast senses metabolic flux to stabilize GAL pathway regulation

Data files

Abstract

README: Data for: The galactokinase enzyme of yeast senses metabolic flux to stabilize GAL pathway regulation

File structure

Code