ATPGrowth

Code for the manuscript: Glycolytic ATP production enables rapid cell growth

Key words: Glycolysis, ATP Production, and Cell Growth

Description: This repository contains the data and analysis scripts associated with the manuscript examining ATP production, glycolysis, and OXPHOS capacity and demand across E. coli, S. cerevisiae, and mammalian cell lines.

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Repository Structure

Final/
├── Data/              # All raw and processed data files (.csv)
├── Figures/           # Output figures (.pdf)
├── Scripts/           # Analysis notebooks and utility scripts
└── README.md

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Scripts

mammalian_atp_growth.ipynb

Processes and analyzes mammalian cell data. Computes ATP production rates from oxygen consumption (OCR) and lactate secretion, bootstraps confidence intervals, and generates figures relating ATP production to cell growth rate across conditions (baseline, GSK, Antimycin, Cyclophosphamide, Gobble).

Key inputs: oxygen_consumption_output_hr.csv, lactate_output.csv, growth_output_hr_clean.csv
Key outputs: Mammalian ATP production summary, bootstrap CI figures

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ecoli_and_yeast_atp_growth.ipynb

Analyzes ATP production and growth for E. coli and S. cerevisiae. Computes ATP production from acetate/ethanol secretion and oxygen consumption, and relates ATP flux to growth rate across carbon-limited and nitrogen-limited conditions.

Key inputs: ecoli_experimental.csv, yeast_experimental.csv, atp_production_ecoli.csv, atp_production_yeast.csv
Key outputs: E. coli and yeast ATP production vs. growth figures

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atp_demand_glycolysis_respiration.ipynb

Estimates maximum ATP production capacity from glycolysis and OXPHOS using proteome occupancy and specific enzyme activities. Bootstraps capacity estimates and compares them against measured ATP demand across E. coli, yeast, and mammalian cells. Generates the ATP fraction (glycolysis vs. OXPHOS) figures.

Key inputs: atp_production_ecoli.csv, atp_production_yeast.csv, mammalian_atp_production_all_conditions_summary.csv, cellular rates, occupancy, and specific activity files
Key outputs: ATP capacity vs. demand figures, fraction ATP figures

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atp_demand_biomass.ipynb

Calculates ATP cost of biomass synthesis and relates it to cellular growth. Uses cell composition, volume, and protein concentration data to derive the theoretical ATP demand for biosynthesis.

Key inputs: 2025_08_12_cell_composition.csv, 20260327_cell_volume.csv, 20260330_protein_concentration.csv
Key outputs: ATP demand vs. biomass figures

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export_data_to_excel.py

Utility script that compiles all .csv files in Data/ into a single formatted Excel workbook (Supplementary_Data.xlsx) for publication. Generates a README tab with descriptions of each dataset, and styles each sheet with headers and alternating row shading.

Output: Data/Supplementary_Data.xlsx

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Data Files

Mammalian

File	Description
mammalian_atp_production_all_conditions_summary.csv	Bootstrap summary of mammalian ATP production (glycolysis + OXPHOS) across all conditions
mammalian_cellular_rates.csv	Cellular metabolic rates for mammalian cells (growth, lactate, OCR)
growth_output_hr_clean.csv	Cleaned growth rate output (hr⁻¹) across cell lines and conditions
lactate_output.csv	Lactate secretion rates across cell lines and conditions
oxygen_consumption_output_hr.csv	Oxygen consumption rates (OCR, hr⁻¹) across cell lines and conditions
2024_02_26_mammalian_atp_total_core.csv	Total ATP production estimates, core metabolic reactions
2024_02_26_mammalian_specific_actvity_ferm.csv	Specific activity of fermentation enzymes
2024_02_26_mammalian_specific_actvity_resp_core.csv	Specific activity of core respiratory enzymes
20260327_cell_volume.csv	Cell volume measurements
20260330_protein_concentration.csv	Protein concentration measurements

E. coli

File	Description
ecoli_experimental.csv	Experimental measurements for ATP and growth analyses
atp_production_ecoli.csv	ATP production rates across growth conditions
ecoli_cellular_rates.csv	Cellular metabolic rates (growth, glucose uptake, etc.)
2024_08_13_ecoli_atp_total.csv	Total ATP production estimates
2024_08_13_ecoli_specific_activity_fermentation.csv	Specific activity of Pta-AckA pathway enzymes
2024_08_13_ecoli_specific_activity_respiration.csv	Specific activity of respiratory enzymes
2024_10_07_ecoli_ptaack_occupancy.csv	Proteome occupancy of the Pta-AckA glycolytic pathway
2024_10_07_ecoli_respiration_occupancy_all_data.csv	Proteome occupancy of the respiratory chain, all conditions

S. cerevisiae

File	Description
yeast_experimental.csv	Experimental measurements for ATP and growth analyses
atp_production_yeast.csv	ATP production rates across growth conditions
yeast_cellular_rates.csv	Cellular metabolic rates (growth, glucose uptake, etc.)
2024_08_13_yeast_atp_total_core.csv	Total ATP production estimates, core metabolic reactions
2024_08_13_yeast_specific_activity_fermentation.csv	Specific activity of fermentation enzymes
2024_08_13_yeast_specific_activity_resp_core.csv	Specific activity of core respiratory enzymes
2024_10_07_yeast_fermentation.csv	Proteome occupancy of fermentation enzymes
2024_10_07_yeast_resp_occupancy.csv	Proteome occupancy of the respiratory chain

Shared

File	Description
2025_08_12_cell_composition.csv	Cell composition data used for ATP cost and biomass calculations
Supplementary_Data.xlsx	All datasets compiled into a single formatted Excel workbook for publication

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Dependencies

Analysis was performed in Python 3. Required packages:

numpy
pandas
matplotlib
seaborn
scipy
statsmodels
tqdm
openpyxl

Install with:

pip install numpy pandas matplotlib seaborn scipy statsmodels tqdm openpyxl

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Running the Analysis

Each notebook in Scripts/ is self-contained and reads data from ../Data/ relative to the script location. Run notebooks in Jupyter from the Scripts/ directory:

cd Scripts/
jupyter notebook

To regenerate the supplementary Excel file:

cd Scripts/
python export_data_to_excel.py