Source data and representative raw data for "Peptidoglycan synthesis drives a single population of septal cell wall synthases during division in Bacillus subtilis"
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General information
Author: Kevin Whitley
Contact: kevin.whitley@newcastle.ac.uk
DOI: https://doi.org/10.25405/data.ncl.c.7078312
Related article: K.D. Whitley, J. Grimshaw, D.M. Roberts, E. Karinou, P.J. Stansfeld, S. Holden. Peptidoglycan synthesis drives a single population of septal cell wall synthases during division in Bacillus subtilis. Nature Microbiology (2024). https://doi.org/10.1038/s41564-024-01650-9
Introductory information
The following contain source data. This includes some of the figures in MATLAB .fig format, underlying data in .xlsx format, along with the videos and accompanying kymographs that are shown in the figures:
5) Supplementary Figure 1 source data
6) Supplementary Figure 2 source data
7) Supplementary Figure 3 source data
8) Supplementary Figure 4 source data
9) Supplementary Figure 5 source data
10) Supplementary Figure 6 source data
11) Supplementary Figure 7 source data
12) Supplementary Figure 8 source data
13) Supplementary Figure 9 source data
14) Supplementary Figure 10 source data
15) Supplementary Figure 11 source data
16) Extended Data Figure 2 source data
17) Extended Data Figure 3 source data
18) Extended Data Figure 4 source data
19) Extended Data Figure 5 source data
20) Extended Data Figure 6 source data
21) Extended Data Figure 7 source data
22) Extended Data Figure 8 source data
23) Extended Data Figure 9 source data
24) Extended Data Figure 10 source data
The following contain videos corresonding to the Supplementary Videos in the manuscript. They contain .avi files, as well as the more raw .tif or .nd2 files:
25) Supplementary Video 1 source data
26) Supplementary Video 2 source data
27) Supplementary Video 3 source data
28) Supplementary Video 4 source data
29) Supplementary Video 5 source data
30) Supplementary Video 6 source data
31) Supplementary Video 7 source data
32) Supplementary Video 8 source data
33) Supplementary Video 9 source data
34) Supplementary Video 10 source data
35) Supplementary Video 11 source data
36) Supplementary Video 12 source data
37) Supplementary Video 13 source data
38) Supplementary Video 14 source data
39) Supplementary Video 15 source data
40) Supplementary Video 16 source data
The following contain representative raw data (no processing) for the conditions used in the paper:
41) Representative raw data for rich media, 30C
42) Representative raw data for rich media, 30C with Penicillin G treatment
43) Representative raw data for rich media, 30C with fosfomycin treatment
44) Representative data for rich media, 37C
45) Representative data for minimal media, 30C
46) Representative raw data for minimal media, 37C
47) Representative raw data for rich media, 30C with PC190723 treatment
48) Representative raw data for rich media, 30C with FtsZ(G106S) expression
49) Representative raw data for FtsZ treadmilling in Dhag GFP-FtsZ HT-PBP2B strain
50) Representative raw data for rich media, 30C with 1 mM IPTG
51) Representative raw data for FtsZ treadmilling in rich media, 21C
52) Representative raw data for FtsZ(G106S) treadmilling in rich media, 30C
53) Representative raw data for HT-PBP2B motion horizontally in untreated cells
54) Representative raw data for HT-PBP2B motion in horizontal cells with PC190723 treatment
55) Representative raw data for HT-PBP2B motion in horizontal cells with FtsZ(G106S) expression
56) Representative raw data for HaloTag-FtsW motion in rich media, 30C
Methodological information
Most raw data in this repository is from fluorescence microscopy on bacteria. Many of the files are videos showing single-molecule dynamics of bacterial cell wall synthases inside live bacteria. Other files are data supporting these, such as characterizations of the bacterial strains used(growth, morphology, etc.).
Abbreviations: ROI = Region of Interest.
Instruments used: Bespoke single-molecule fluorescence microscope, Nikon Eclipse Ti, Nikon Eclipse Ti2, and Zeiss Elyra 7 Lattice SIM2.
Data acquisition software: Data collected using either Micro-Manager (v2.0gamma), NS-Elements (v5.42.02), or Zen Black 2.3 (v16.0.14.316).
Data analysis software: Videos analysed using Fiji (v1.54) with open-source plugins PureDenoise-GPU (v0.1.0) and PureDenoise-CPU (v0.1.0) (https://github.com/ZikaiSun/PureGpu/tree/main).
Extended Data Figures 4 and 6, along with Supplementary Videos 14-16 show data from molecules manually tracked using TrackMate (v7.10.2).
Further data analysis done using Matlab with custom code available on the Whitley lab Github page:
https://github.com/WhitleyLab/Vercini_spt_analysis
The divisome complex was modelled by AlphaFold2, using ColabFold (v1.3.0) and AlphaFold-Multimer (v2).
Date(s) of data collection: 15/12/2021 - 10/12/2023
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A single cell, single molecule microscopy platform for antibiotics research
Biotechnology and Biological Sciences Research Council
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AUTHORS (6)
- JGJames GrimshawDMDavid M. RobertsEKEleni KarinouPSPhillip J. StansfeldSHSéamus Holden