DOI: 10.5281/zenodo.18059845
title: Data of the article "E. coli prepares for starvation by dramatically remodeling its proteome in the first hours after loss of nutrients"

description: This repository contains the data and code used to generate the figures of the article written by Gervais et al. entitled "E. coli prepares for starvation by dramatically remodeling its proteome in the first hours after loss of nutrients".
description: The following datasets are available in this archive:



myframes_starvation : dataset containing the data of the hard-switch and overflow experiments (multiple strains going from exponential growth to carbon starvation, either abruptly or gradually)



length_um : length of the cells in micrometer, as estimated by (deep)MoMA software.

strain : name of the strain.

fluo_ampl_ch_1 : total fluorescence in the first fluorescence channel coming from the the cell, as estimated by (deep)MoMA software.

fluo_ampl_ch_2 : total fluorescence in the second fluorescence channel coming from the the cell, as estimated by (deep)MoMA software. Only relevant when the strain carries a dual fluorescent reporter.

Fluo1 : name of the fluorescence protein used in the channel 1.

Fluo2 : name of the fluorescence protein used in the channel 2.

prom : name of the promoter whose expression is reported by the fluorescence signal in channel 1.

prom2 : name of the promoter whose expression is reported by the fluorescence signal in channel 2.

DrpoS : boolean indicating whether the strain has a rpoS-knockout background (TRUE) or wild type (FALSE).

condition : short descriptive name of the experimental condition.

SP_entry : time of entry into starvation (in sec).

m_start : start time of the different phases within one experiment (in sec).

m_end : end time of the different phases within one experiment (in sec).

start_time : start time of the cell cycle (in sec).

end_time : end time of the cell cycle (in sec).

end_type : the event causing the cell’s time series to terminate (div, exit, or eod for end of data).

plasmid : boolean indicating whether the reporter is carried on a plasmid (TRUE) or is chromosally integrated (FALSE).

c_step : condition step, describing the nature of the experimental step (GM = growth media, SPM = stationary phase media) and the occurence (1 : first encounter, 2 second encounter).

date : date of the experiment in the yyyymmdd format.

gl_id : unique identifier of the growth lane.

cell : unique identifier of the cell.

b_rank : rank of the cells from bottom to top, starting with rank 0 (the mother cell).

time_sec : time in second.

acq_freq_sec : acquisition frequency in second. Corresponds to the distance to the next time point, in seconds.

overflow : boolean indicating whether the experimental setup was the overflow (TRUE) or the hard-switch (FALSE).



myframes_RealTrace : output of RealTrace software (https://doi.org/10.1101/2025.09.12.675772) for the data found in myframes_starvation



condition : short descriptive name of the experimental condition.

c_step : condition step, describing the nature of the experimental step (GM = growth media, SPM = stationary phase media) and the occurence (1 : first encounter, 2 second encounter).

cell : unique identifier of the cell

Fluo1 : name of the fluorescence protein used in the channel 1.

DrpoS : boolean indicating whether the strain has a rpoS-knockout background (TRUE) or wild type (FALSE).

prom : name of the promoter whose expression is reported by the fluorescence signal in channel 1.

plasmid : boolean indicating whether the reporter is carried on a plasmid (TRUE) or is chromosally integrated (FALSE).

time_sec : time in second.

mean_x : logarithm of the inferred cell length.

mean_l : inferred instantaneous growth rate.

mean_g : inferred total fluorescence in the cell.

mean_q : inferred instantaneous volumic production rate.

Q_Fluo1 : degradation-corrected instantaneous volumic production rate.

Q_Fluo1_maturation : degradation and maturation-corrected instantaneous volumic production rate.

Corr_conc : degradation and photobleaching-corrected fluorescence concentration, obtained by integrating Q_Fluo1.

Corr_conc_maturation : degradation and maturation and photobleaching-corrected fluorescence concentration, obtained by integrating Q_Fluo1_maturation.

cov_xx : variance of the cell length estimate distribution.

cov_ll : variance of the growth rate estimate distribution.

cov_gg : variance of the total fluorescence estimate distribution.

cov_qq : variance of the volumic production rate estimate distribution.

Corr_tot_Fluo : corrected total fluorescence.

C_steady_corr : degradation-corrected steady-state concentration estimate.

C_steady_corr_maturation : degradation and maturation-corrected steady-state concentration estimate.



myframes_stress_exp : dataset containing the data of the oxidative stress experiments (addressing the survival of cells to oxidative stress as a function of perturbing the expression of their genes at different time point and for various duration during starvation)



condition : short descriptive name of the experimental condition.

STRESS : description of the stress applied on the cells in the experiment.

strain : name of the strain.

prom : name of the promoter whose expression is reported by the fluorescence signal in channel 1.

prom2 : name of the promoter whose expression is reported by the fluorescence signal in channel 2.

CAM_C_INIT_SP : concentration of chloramphenicol used in the first 5 hours of starvation, in micromolar.

date : date of the experiment in the yyyymmdd format.

cell_rank : rank of the cells from bottom to top, starting with rank 0 (the mother cell).

end_type : the event causing the cell’s time series to terminate (div, exit, or eod for end of data).

fluo_ampl_ch_1 : total fluorescence in the first fluorescence channel coming from the the cell, as estimated by (deep)MoMA software.

fluo_ampl_ch_2 : total fluorescence in the second fluorescence channel coming from the the cell, as estimated by (deep)MoMA software. Only relevant when the strain carries a dual fluorescent reporter.

m_start : start time of the different phases within one experiment (in sec).

m_end : end time of the different phases within one experiment (in sec).

time_sec : time in second.

c_step : condition step, describing the nature of the experimental step (GM = growth media, SPM = stationary phase media, STRESS = stress phase) and the occurence (1 : first encounter, 2 second encounter).

cell : unique identifier of the cell

ugl : unique identifier of the growth lane.

length_um : length of the cells in micrometer, as estimated by (deep)MoMA software.

time_start : start time of the cell cycle (in sec).

time_end : end time of the cell cycle (in sec).

Fluo1 : name of the fluorescence protein used in the channel 1.

Fluo2 : name of the fluorescence protein used in the channel 2.

DrpoS : boolean indicating whether the strain has a rpoS-knockout background (TRUE) or wild type (FALSE).

plasmid : boolean indicating whether the reporter is carried on a plasmid (TRUE) or is chromosally integrated (FALSE).

acq_freq_sec : acquisition frequency in second. Corresponds to the distance to the next time point, in seconds.

SP_entry : time of entry into starvation (in sec).



myframes_RealTrace_stress_exp : output of RealTrace software for the data found in myframes_stress_exp



condition : short descriptive name of the experimental condition.

c_step : condition step, describing the nature of the experimental step (GM = growth media, SPM = stationary phase media) and the occurence (1 : first encounter, 2 second encounter).

cell : unique identifier of the cell

Fluo1 : name of the fluorescence protein used in the channel 1.

DrpoS : boolean indicating whether the strain has a rpoS-knockout background (TRUE) or wild type (FALSE).

prom : name of the promoter whose expression is reported by the fluorescence signal in channel 1.

plasmid : boolean indicating whether the reporter is carried on a plasmid (TRUE) or is chromosally integrated (FALSE).

time_sec : time in second.

mean_x : logarithm of the inferred cell length.

mean_l : inferred instantaneous growth rate.

mean_g : inferred total fluorescence in the cell.

mean_q : inferred instantaneous volumic production rate.

Q_Fluo1 : degradation-corrected instantaneous volumic production rate.

Q_Fluo1_maturation : degradation and maturation-corrected instantaneous volumic production rate.

Corr_conc : degradation and photobleaching-corrected fluorescence concentration, obtained by integrating Q_Fluo1.

Corr_conc_maturation : degradation and maturation and photobleaching-corrected fluorescence concentration, obtained by integrating Q_Fluo1_maturation.

cov_xx : variance of the cell length estimate distribution.

cov_ll : variance of the growth rate estimate distribution.

cov_gg : variance of the total fluorescence estimate distribution.

cov_qq : variance of the volumic production rate estimate distribution.

Corr_tot_Fluo : corrected total fluorescence.

C_steady_corr : degradation-corrected steady-state concentration estimate.

C_steady_corr_maturation : degradation and maturation-corrected steady-state concentration estimate.



myframes_degradation : dataset containing the data used to measure the degradation rate, by using very low frequency of illumination and measuring the decrease of fluorescence due to degradation on strain carrying an inducible promoter.



strain : name of the strain.

date : date of the experiment in the yyyymmdd format.

condition : short descriptive name of the experimental condition.

time_sec : time in second.

length_um : length of the cells in micrometer, as estimated by (deep)MoMA software.

end_type : the event causing the cell’s time series to terminate (div, exit, or eod for end of data).

cell : unique identifier of the cell.

gl_id : unique identifier of the growth lane.

m_start : start time of the different phases within one experiment (in sec).

m_end : end time of the different phases within one experiment (in sec).

start_time : start time of the cell cycle (in sec).

end_time : end time of the cell cycle (in sec).

b_rank : rank of the cells from bottom to top, starting with rank 0 (the mother cell).

c_step : condition step, describing the nature of the experimental step (GM = growth media, SPM = stationary phase media) and the occurence (1 : first encounter, 2 second encounter).

acq_freq_sec : acquisition frequency in second. Corresponds to the distance to the next time point, in seconds.

Fluo : name of the fluorescence protein used to measure degradation.

Ampl : total fluorescence coming from the the cell, as estimated by (deep)MoMA software.



myframes_bleaching : dataset containing the data used to measure the bleaching rates from the decay of degradation-corrected fluorescence observed in strains carrying an inducible promoter.



strain : name of the strain.

date : date of the experiment in the yyyymmdd format.

condition : short descriptive name of the experimental condition.

time_sec : time in second.

idx : index used to separate the experiment in different phase (growth and starvation)

Fluo_sig : name of the fluorescence protein used to measure degradation.

signal : total fluorescence coming from the the cell, as estimated by (deep)MoMA software.

exp_series : describe the series of experiment the data comes from.

cell : unique identifier of the cell.



myframes_control : dataset containing the data used to control the plasmid copy number and effect of phototoxicity on the cell viability.



condition : short descriptive name of the experimental condition.

strain : name of the strain.

prom : name of the promoter whose expression is reported by the fluorescence signal in channel 1.

prom2 : name of the promoter whose expression is reported by the fluorescence signal in channel 2.

date : date of the experiment in the yyyymmdd format.

b_rank : rank of the cells from bottom to top, starting with rank 0 (the mother cell).

end_type : the event causing the cell’s time series to terminate (div, exit, or eod for end of data).

fluo_ampl_ch1 : total fluorescence in the first fluorescence channel coming from the the cell, as estimated by (deep)MoMA software.

fluo_ampl_ch2 : total fluorescence in the second fluorescence channel coming from the the cell, as estimated by (deep)MoMA software. Only relevant when the strain carries a dual fluorescent reporter.

m_start : start time of the different phases within one experiment (in sec).

m_end : end time of the different phases within one experiment (in sec).

time_sec : time in second.

c_step : condition step, describing the nature of the experimental step (GM = growth media, SPM = stationary phase media, STRESS = stress phase) and the occurence (1 : first encounter, 2 second encounter).

cell : unique identifier of the cell

gl_id : unique identifier of the growth lane.

length_um : length of the cells in micrometer, as estimated by (deep)MoMA software.

time_start : start time of the cell cycle (in sec).

time_end : end time of the cell cycle (in sec).

Fluo1 : name of the fluorescence protein used in the channel 1.

Fluo2 : name of the fluorescence protein used in the channel 2.

DrpoS : boolean indicating whether the strain has a rpoS-knockout background (TRUE) or wild type (FALSE).

plasmid : boolean indicating whether the reporter is carried on a plasmid (TRUE) or is chromosally integrated (FALSE).

acq_freq_sec : acquisition frequency in second. Corresponds to the distance to the next time point, in seconds.

SP_entry : time of entry into starvation (in sec).

mean_x : logarithm of the RealTrace-inferred cell length.

mean_l : RealTrace-inferred instantaneous growth rate.

mean_g : RealTrace-inferred total fluorescence in the cell.

mean_q : RealTrace-inferred instantaneous volumic production rate.

Q_Fluo1 : degradation-corrected instantaneous volumic production rate.

Corr_conc : degradation and photobleaching-corrected fluorescence concentration, obtained by integrating Q_Fluo1.

cov_xx : variance of the cell RealTrace-length estimate distribution.

cov_ll : variance of the RealTrace-growth rate estimate distribution.

cov_gg : variance of the RealTrace-total fluorescence estimate distribution.

cov_qq : variance of the RealTrace-volumic production rate estimate distribution.

Corr_tot_Fluo : corrected total fluorescence.

C_steady_corr : degradation-corrected steady-state concentration estimate.



myframes_control_RealTrace : output of RealTrace software for the data found in myframes_control



condition : short descriptive name of the experimental condition.

c_step : condition step, describing the nature of the experimental step (GM = growth media, SPM = stationary phase media) and the occurence (1 : first encounter, 2 second encounter).

cell : unique identifier of the cell

Fluo1 : name of the fluorescence protein used in the channel 1.

prom : name of the promoter whose expression is reported by the fluorescence signal in channel 1.

plasmid : boolean indicating whether the reporter is carried on a plasmid (TRUE) or is chromosally integrated (FALSE).

time_sec : time in second.

mean_x : logarithm of the inferred cell length.

mean_l : inferred instantaneous growth rate.

mean_g : inferred total fluorescence in the cell.

mean_q : inferred instantaneous volumic production rate.

Q_Fluo1 : degradation-corrected instantaneous volumic production rate.

Corr_conc : degradation and photobleaching-corrected fluorescence concentration, obtained by integrating Q_Fluo1.

cov_xx : variance of the cell length estimate distribution.

cov_ll : variance of the growth rate estimate distribution.

cov_gg : variance of the total fluorescence estimate distribution.

cov_qq : variance of the volumic production rate estimate distribution.

Corr_tot_Fluo : corrected total fluorescence.

C_steady_corr : degradation-corrected steady-state concentration estimate.



mydegrates : table of the degradation rates inferred from myframes_degradation data



Fluo1 : name of the fluorescence protein used in the channel 1.

gamma_dec_Fluo : exponential decay rate of the degradation rate

gamma_init : protein degradation rate inferred at the entry into starvation.



mypowers : dataset containing the batch-culture OD600 temporal dynamics associated with the overflow experiments from myframes_starvation



condition : short descriptive name of the experimental condition.

date : date of the experiment in the yyyymmdd format.

time_sec : time in second.

OD600 : optical density of the culture at 600 nm wavelength



myoverflows_SP_entry : table containing the starvation start time in the overflow experiments, inferred from the decrease of growth rate found in the overflow experiments data (myframes_starvation and myframes_RealTrace)



date : date of the experiment in the yyyymmdd format.

SP_entry : time of entry into starvation (in sec).



myproteomicsdata_multistrain : dataset containing the date of our quantitative proteomics experiments



Genes : name of the gene corresponding to the captured protein.

uniquePeptideCount : count of unique peptides belonging to the protein described by Genes.

Log_Quantity_MS : logarithm of the mass spectrometry signal for this protein.

sample : sample identifier.

GFP_prom : name of the promoter driving the expression of GFPmut2 in the strain used for the proteomics experiment.

mean_Log_Quantity_MS : mean of the logarithm of the mass spectrometry signal in the sample.

Log_Quantity_norm : normalized logarithm of the mass spectrometry signal for this protein.

time_h : experimental time at which the sample was taken, relative to starvation entry (time of starvation is defined as 0), in hour.



Fold_change_litterature : dataset containing the log fold change of various proteins between exponential phase and starvation, calculated from Caglar et al. 2017 (https://doi.org/10.1038/srep45303), Mori et al. 2021 (https://doi.org/10.15252/msb.20209536) and Schmidt et al. 2016 (https://doi.org/10.1038/nbt.3418)



gene_name : name of the gene corresponding to the captured protein.

Condition : identifier of the condition, defined to allow comparison of similar experimental conditions across different studies.

log_fold_change : logarithm of the fold change of normalized mass spectrometry signal from exponential growth to starvation for the protein described by gene_name.

Article : first author and date of publication of the article from which the proteomics data was extracted.



Urchueguia_et_al_data : dataset containing the data from Urchueguia et al. 2021 (https://doi.org/10.1371/journal.pbio.3001491) used here to select the promoters used in this study.



condition : condition in which the cells were grown before measuring their distribution of fluorescence.

plate : identifier of the 96 well plate containing the strain of interest, from Zaslaver library.

well : identifier of the well within the 96 well plate containing the strain of interest, from Zaslaver library.

gene_downstream : name of the gene from which the promoter used as reporter in the strain of interest was taken.

fl_mean : average fluorescence of the cells with the reporter described by gene_downstream in this experimental condition.

fl_var : variance of the fluorescence of the cells with the reporter described by gene_downstream in this experimental condition.



Galbusera_et_al_data : dataset containing the data from Galbusera et al. 2025 (https://doi.org/10.1103/nvk3-jsvm) used here to compare the homogeneity of single cell response to a different stress.



promoter : description of the promoter used as reporter.

medium : description of the growth medium used for the bacteria.

id : cell identifier.

lane_ID : growth lane identifier.

parent_id : identifier of the parent cell.

time_sec : time in second.

start_time : start time of the cell cycle (in sec).

end_time : end time of the cell cycle (in sec).

length_box : length of the binding box capturing the cell exported by MoMA software, in micrometer.

gfp_nb : total fluorescence in the cell, converted to fluorescent protein number.

experiment : name of the experiment.



Lempp_et_al_data : dataset containing the data from Lempp et al. 2019 (https://doi.org/10.1038/s41467-019-12474-1) used here to compare the changes of expression levels measured with transcriptomics or with the microfluidic coupled to time lapse-microscopy used in this study.



prom : name of the promoter whose expression is reported by the fluorescence signal in channel 1.

time : experimental time at which the sample was taken, relative to starvation entry (time of starvation is defined as 0), in hour.

F : expression signal.

method : description of the origin of the expression signal.

fraction : fraction of the expression signal across all genes represented by the promoter described by prom.