BBSRC iCase - Development of an automated, high-resolution analysis pipeline for bacterial peptidoglycan structural analyses
Lead Research Organisation:
University of Sheffield
Department Name: Molecular Biology and Biotechnology
Abstract
This project will build on our preliminary work to develop a novel pipeline for PG structure analysis that combines high mass accuracy LC-MS/MS and automated analysis of fragmentation spectra.
People |
ORCID iD |
| Stéphane MESNAGE (Primary Supervisor) |
Publications
Bublitz DC
(2019)
Peptidoglycan Production by an Insect-Bacterial Mosaic.
in Cell
Sandoz K
(2020)
ß-Barrel proteins tether the outer membrane in many Gram-negative bacteria
in Nature Microbiology
Sibinelli-Sousa S
(2020)
A Family of T6SS Antibacterial Effectors Related to l,d-Transpeptidases Targets the Peptidoglycan.
in Cell reports
Studentship Projects
| Project Reference | Relationship | Related To | Start | End | Student Name |
|---|---|---|---|---|---|
| BB/M011151/1 | 01/10/2015 | 30/09/2023 | |||
| 2058718 | Studentship | BB/M011151/1 | 01/10/2017 | 30/11/2021 |
| Title | Automated data analysis of tandem mass spectrometry of non linear molecules (branched or crosslinked) |
| Description | Optimised pipeline for data acquisition using liquid chromatography and tandem mass spectrometry coupled to data analysis software to automate data analysis. |
| Type Of Material | Improvements to research infrastructure |
| Year Produced | 2018 |
| Provided To Others? | No |
| Impact | One manuscript in favourable review in Nature Microbiology & one paper in Cell. |
| Description | Analysis of peptidoglycan bound proteins in gram negative pathogens |
| Organisation | National Institute of Allergy and Infectious Diseases (NIAID) |
| Department | Rocky Mountain Laboratories |
| Country | United States |
| Sector | Public |
| PI Contribution | Using the peptidoglycan (PG) analysis pipeline designed during this PhD project, we showed that several gram negative pathogens produce beta barrel proteins that are covalently anchored to PG. These proteins have been shown to be essential for cell envelope integrity in the model organism Coxiella burnetii. |
| Collaborator Contribution | Our partners provided biological samples that we analysed. |
| Impact | One manuscript in favourable revision in Nature microbiology. |
| Start Year | 2018 |
| Description | Characterisation of L-D Transpeptidase activity from a novel type 6 secretion system effector |
| Organisation | Universidade de São Paulo |
| Country | Brazil |
| Sector | Academic/University |
| PI Contribution | Data analysis of peptidoglycan treated with a novel T6SS effector |
| Collaborator Contribution | Provided biological material |
| Impact | Paper in review in EMBO |
| Start Year | 2019 |
| Description | Data analysis on provided peptidoglycan samples. |
| Organisation | University of Montana |
| Country | United States |
| Sector | Academic/University |
| PI Contribution | Performed data analysis on peptidoglycan samples sent by collaborators confirming a symbiotic relationship between a fly species and two bacteria in its gut. |
| Collaborator Contribution | Provides biological samples. |
| Impact | Paper in Cell. DOI: 10.1016/J.CELL.2019.08.054 |
| Start Year | 2019 |
| Title | Automated analysis of tandem mass spectrometry data fron nojn linear molecules |
| Description | Software enables the analysis of non linear molecules (branched or crosslinked) such as peptidoglycan, antibodies and cyclic molecules without sample processing to generate short linear peptides. This is achieved by representing the molecule in silico as a graph comprising nodes that represent the building blocks of the molecule and edges describing the bonds between nodes. |
| Type Of Technology | Software |
| Year Produced | 2019 |
| Impact | Software is still in development but has shown the ability to analyse peptidoglycan monomers and dimers. |
| Title | Automated identification of muropeptides from MS1 data |
| Description | Automated identification of muropeptides within MS1 data using a simple initial search library and optional 'smart' in silico modification generation to minimise false positives and facilitate removal of search space bias due to time requirements in manual analysis. |
| Type Of Technology | Webtool/Application |
| Year Produced | 2021 |
| Open Source License? | Yes |
| Impact | Software currently in final form is using python code. Jupyter notebook interface near completion. Publication of software and its application in journal currently in work. |