Gene loci fluctuations reveal bacterial chromosome dynamical organization
Data files
Nov 04, 2025 version files 16.45 MB
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Data_Fig1.opju
330.14 KB
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Data_Fig4.zip
16.06 MB
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Data_Fig5.zip
48.66 KB
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README.md
3.74 KB
Abstract
Chromosomal sites in rod-like bacteria move sub-diffusely, driven by the out-of-equilibrium nature of the viscoelastic, crowded intracellular environment. Furthermore, it has been shown that there is a pronounced dynamical asymmetry between longitudinal (long-axis) and transverse (radial) motions, manifested in different exponents in the mean square displacements,
and
respectively. Here, using polymer simulations and experimental observations of a locus in Bacillus subtilis, we substantiate the notion that asymmetric dynamics are a result of the asymmetric structure of the bacterial chromosome modelled as a bottlebrush polymer in a poor solvent. Our simulations recapitulate the observed asymmetry as well as the range of the observed exponent values that are related to scaling models of polymer dynamics, lending support to the notion that asymmetric dynamics is a consequence of the bottlebrush structure of the bacterial chromosome.
Dataset DOI: 10.5061/dryad.g1jwstr4d
Description of the data and file structure
Description of the data and file structure
Deposited data includes the following data files used to generate different figures in the main text, with their respective description (in Origin, Notepad and Excel files).
File: Data_Fig1.opju
Description: This dataset contains experimental raw data of the anisotropic mean square displacement (MSD) of a chromosomal locus as a function of time. The measurements were obtained from time-lapse microscopy tracking in the image plane.
File structure:
The data are organized into three worksheets of an Origin file corresponding to different displacement components:
- MSDX — Mean square displacement in the transversal (x) direction
- MSDY — Mean square displacement in the longitudinal (y) direction
- MSDr — Mean square displacement in the radial (r) direction
Each worksheet contains:
- Column 1: Time in seconds (s)
- Columns 2–96: Individual MSD traces for separate trajectories in nano-meters square.
File: Data_Fig4.zip
Description: Simulation raw data of longitudinal (Data_Fig4a) and transverse (Data_Fig4b) mean square displacement (MSD) as a function of time for full regions, middle regions, and end regions of the chromosome chains.
Folder Structure
The ZIP archive includes 10 folders, each corresponding to an individual simulation run.
Each simulation folder contains three text files (Notepad), representing the MSD results for different regions along the chromosome chain:
File description:
full_region.txt, MSD for the full region of the chromosome chain
middle_region.txt, MSD for the middle region of the chromosome chain
end_region.txt, MSD for the end region of the chromosome chain
Data Format:
Each text file contains three columns:
1 Time (τ)
2 Longitudinal mean square displacement (MSD)
3 Transverse mean square displacement (MSD)
Units:
- Time (τ): simulation time units
- MSD: simulation length units
File: Data_Fig5.zip
Description:
Simulation raw data of longitudinal MSD exponents 𝛼ℓ (Data_Fig5a, alpha_l), transverse MSD exponents α𝑟 (Data_Fig5b, alpha_r), and the ratio of longitudinal to transverse exponents α𝑟/𝛼ℓ (Data_Fig5c) as functions of confinement radius and interaction strength.
Folder Structure
The ZIP archive contains three sub-folders of data for panels Fig5a, Fig5b, with two Excel files each (allbeads representing 60-bead loops and topbeads representing beads 25–35 of each 60-bead loop). Folder Fig5c contains two Excel files each, with the ratio α𝑟/𝛼ℓ.
File description:
Fig5a:
alpha_l_allbeads.xlsx
alpha_l_topbeads.xlsx
Fig5b:
alpha_r_allbeads.xlsx
alpha_r_topbeads.xlsx
Fig5c:
alpha_ratio_allbeads.xlsx
alpha_ratio_topbeads.xlsx
Data Format:
Each Excel file contains a table with columns corresponding to different values of the confinement radius R (units of beads) while rows correspond to the indicated values of epsilon (units of kBT)
Units:
- Simulation units
- All beads: 60-bead loop
- Top beads: 25–35 of each 60-bead loop
Code/software
All custom analysis and visualization scripts developed for this study are included in the Zenodo repository (https://doi.org/10.5281/zenodo.17307615).
The molecular dynamics simulations were performed using LAMMPS (open-source, GPLv2 license), and data analysis was carried out using standard Python and MATLAB environments.