Data from: Peptidoglycan-tethered and free forms of the Braun lipoprotein are in dynamic equilibrium in Escherichia coli
Abstract
Peptidoglycan (PG) is a giant macromolecule that completely surrounds bacterial cells and prevents lysis in hypo-osmotic environments. This net-like macromolecule is made of glycan strands linked to each other by two types of transpeptidases that form either 4→3 (PBPs) or 3→3 (LDTs) cross-links. Previously, we devised a heavy isotope-based PG full labeling method coupled to mass spectrometry to determine the mode of insertion of new subunits into the expanding PG network (Atze et al., 2022). We showed that PG polymerization operates according to different modes for the formation of the septum and of the lateral cell walls, as well as for bacterial growth in the presence or absence of β-lactams in engineered strains that can exclusively rely on LDTs for PG cross-linking when drugs are present. Here, we apply our method to the resolution of the kinetics of the reactions leading to the covalent tethering of the Braun lipoprotein (Lpp) to PG and the subsequent hydrolysis of that same covalent link. We find that Lpp and disaccharide-peptide subunits are independently incorporated into the expanding lateral cell walls. Newly synthesized septum PG appears to contain small amounts of tethered Lpp. LDTs did mediate intense shuffling of Lpp between PG stems leading to a dynamic equilibrium between the PG-tethered and free forms of Lpp.
Yucheng Liang, Jean-Emmanuel Hugonnet, Filippo Rusconi and Michel Arthur
Elife 2024.
Dryad DOI for this dataset : https://doi.org/10.5061/dryad.t76hdr894
Description of the data and file structure
Mass spectrometry raw data of the Tri-KR isotopologues of Escherichia coli strain BW25113 and strain BW25113 delta YafK.
The data are provided in the Mass Spectrometer Output File Format (mzML) format, an open XML-based format for encoding mass spectrometer output files (1)
The files can be opened with the open-source free software MineXpert2 accessible at this adress: http://msxpertsuite.org/ (2)
Files and variables
File: DYafK.zip
Description: Raw data files from the TriKR muropeptide species of the strain BW25113 delta Yafk.
15 files. replicate X indicate the number of the biological replicate (1 to 4). Xmins indicate the time point when the culture was harvested after the switch from heavy to light medium (0 to 60 minutes).
File: WT.zip
Description: Raw data files from the TriKR muropeptide species of the strain BW25113
16 files. replicate X indicate the number of the biological replicate (1 to 5). Xmins indicate the time point when the culture was harvested after the switch from heavy to light medium (0 to 60 minutes).
References
(1) Deutsch, E.W. (2010). Mass Spectrometer Output File Format mzML. In: Hubbard, S., Jones, A. (eds) Proteome Bioinformatics. Methods in Molecular Biology™, vol 604. Humana Press. https://doi.org/10.1007/978-1-60761-444-9_22
(2) Langella O, Rusconi F. mineXpert2: Full-Depth Visualization and Exploration of MSn Mass Spectrometry Data. J Am Soc Mass Spectrom. 2021 Apr 7;32(4):1138-1141. doi: 10.1021/jasms.0c00402. Epub 2021 Mar 8. PMID: 33683899.