Data from: Spatial and temporal distribution of ribosomes in single cells reveals aging differences between old and new daughters of Escherichia coli
Data files
Nov 21, 2024 version files 120.08 KB
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Elife_Ribo_Paper_Data_Corrected_and_submitted.xlsx
118.11 KB
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README.md
1.97 KB
Abstract
Lineages of rod-shaped bacteria such as Escherichia coli exhibit a temporal decline in elongation rate in a manner comparable to cellular or biological aging. The effect results from the production of asymmetrical daughters, one with a lower elongation rate, by the division of a mother cell. The slower daughter compared to the faster daughter, denoted respectively as the old and new daughters, has more aggregates of damaged proteins and fewer expressed gene products. We have examined further the degree of asymmetry by measuring the density of ribosomes between old and new daughters and between their poles. We found that ribosomes were denser in the new daughter and also in the new pole of the daughters. These ribosome patterns match the ones we previously found for expressed gene products. This outcome suggests that the asymmetry is not likely to result from properties unique to the gene expressed in our previous study, but rather from a more fundamental upstream process affecting distribution of ribosomal abundance. Because damage aggregates and ribosomes are both more abundant at the poles of E. coli cells, we suggest that competition for space between the two could explain the reduced ribosomal density in old daughters. Using published values for aggregate sizes and the relationship between ribosomal number and elongation rates, we show that the aggregate volumes could in principle displace quantitatively the amount of ribosomes needed to reduce the elongation rate of the old daughters.
https://doi.org/10.5061/dryad.59zw3r2jg
Description of the data and file structure
Data provided report values of elongation rates and ribosome densities of old and new daughters of single cell E. coli mothers. The elongation rates were obtained by measuring the length of growing cells from microscopy images of single cells. The difference between the length of a cell over time estimated the growth rate. The ribosome densities were obtained by attaching to the ribosomes a fluorescent protein reporter and recording the emitted fluorescence by microscopy images of single cells. Both the measurements of ribosome density and elongation rates were quantified from the microscopy images with the aid of the image processing package ImageJ from the National Institutes of Health.
Files and variables
File: Elife_Ribo_Paper_Data_A.xlsx
Description: The values of elongation rates and ribosome densities analyzed in the publication are presented in separate Excel spreadsheets, each correspondingly labeled to match the Figures in the published manuscript. The columns in each sheet are also labeled to match the axes of graphs or values grouped for analysis. Each spread sheet will indicate if the data presented are normalized or not. The normalization consisted of converting elongation rates and ribosome densities into relative percentage so that the data from different cells could be combined into one data pool. For example, if two single cells had different total or absolute ribosome densities but their normalized densities increased by the same amount (e.g. 23.5%), their response was interpreted to be identical from a normalized perspective.
Variables
Ribosome density and Elongation rates (See above for description).