DOI: 10.5281/zenodo.15720128
title: Dataset for: The biophysical and functional characterization of the Dr fimbrial envelope in E. coli suggests its importance for pathogenesis and lithogenesis

description: Description

This dataset contains the raw experimental data supporting the article: The biophysical and functional characterization of the Dr fimbrial envelope in E. coli suggests its importance for pathogenesis and lithogenesis. This work was supported by National Science Centre, Poland, Grant 2021/41/B/NZ6/03088 to R. P.

Content and Structure

RP_all.7z. LC-MS analysis of DraE protein content in the Dr capsule encoded by E. coli AAEC191A/pCC90. Raw data were acquired using the Waters MClass/ZenoTOF 7600 high-resolution mass spectrometer (Sciex) equipped with an electrospray ionization (nanoESI) source and a time-of-flight (TOF) analyzer operating in Zeno mode. Mass spectra were collected in both data-dependent acquisition (DDA, also referred to as IDA – Information Dependent Acquisition) and data-independent acquisition (DIA, SWATH) modes. All raw files were saved in Sciex proprietary formats: .wiff and .wiff2. The dataset includes mass spectrometric profiles of protein digests derived from Dra family proteins (DraB, DraC, DraD, DraE) obtained from two Escherichia coli strains: AAEC191A carrying the plasmid pCC90 and AAEC191A carrying the control plasmid pACYC177. Additionally, calibration curves were generated using synthetic peptide standards, and the corresponding raw files are included. These data support both qualitative and quantitative proteomic analyses and were used to establish peptide identities, assess experimental reproducibility, and calibrate retention times and signal intensities.

Video6. Representative time lapse videos of detachment of Dr fimbriaeted and non-fimbriaeted bacteria from the glass surface under increasing shear stress. The beginning of the video shows the effect of 10 min accumulation of AAEC191A/pCC90 and AAEC191A/pACYC177 bacteria on the glass surface under static conditions. Then the bacterial suspensions were passing through the chamber with one minute flows generating shear stress of: 0.01, 0.05, 0.28, 0.6, 1.1, 2.8, 4.4 and 6.6 pN µm-². Bacteria were suspended in PBS buffer at pH 5.7, 7.0 and 8.0. The phase contrast microscopy videos show the entire 8 minute experiments accelerated 2.7-fold.

Video7. Representative time lapse videos of detachment of Dr fimbriaeted and non-fimbriaeted bacteria from the polystyrene surface under increasing shear stress. The beginning of the video shows the effect of 10 min accumulation of AAEC191A/pCC90 and AAEC191A/pACYC177 bacteria on the polystyrene surface under static conditions. Then the bacterial suspensions were passing through the chamber with one minute flows generating shear stress of: 0.01, 0.05, 0.28, 0.6, 1.1, 2.8, 4.4 and 6.6 pN µm-². Bacteria were suspended in PBS buffer at pH 5.7, 7.0 and 8.0. The phase contrast microscopy videos show the entire 8 minute experiments accelerated 2.7-fold.

Video8. Representative time lapse videos of accumulation of Dr fimbriaeted and non-fimbriaeted bacteria to the glass surface under shear stress. Accumulation of AAEC191A/pACYC177 and AAEC191A/pCC90 bacteria to glass surface. Bacteria suspended in the PBS pH 5.7 were washed through the flow chamber at shear stress of 0.01. 0.05 and 0.28 pN µm-2. The phase contrast microscopy videos show the 15 minutes experiments accelerated 5.3-fold.

Video9. Representative time lapse videos of accumulation of Dr fimbriaeted and non-fimbriaeted bacteria to the polystyrene surface under shear stress. Accumulation of AAEC191A/pACYC177 and AAEC191A/pCC90 bacteria to polystyrene surface. Bacteria suspended in the PBS pH 5.7 were washed through the flow chamber at shear stress of 0.01. 0.05 and 0.28 pN µm-2. The phase contrast microscopy videos show the 15 minutes experiments accelerated 5.3-fold.