DOI: 10.5061/dryad.t76hdr894
title: Data from: Peptidoglycan-tethered and free forms of the Braun lipoprotein are in dynamic equilibrium in Escherichia coli

description: 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.
description: # **Mass spectra data of muropeptides (Tri-KR isotopologues) described in
 the paper "Peptidoglycan-tethered and free forms of the Braun
 lipoprotein are in dynamic equilibrium in *Escherichia
 coli*"** Yucheng Liang, Jean-Emmanuel Hugonnet, Filippo
 Rusconi and Michel Arthur Elife 2024. Dryad DOI for this dataset
 : [https://doi.org/10.5061/dryad.t76hdr894](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/](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](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.