PXD008075-2

PXD008075 is an original dataset announced via ProteomeXchange.

Title	Cell wall enrichment unveils proteomic changes in the cell wall during treatment of Mycobacterium smegmatis with sub-lethal concentrations of Rifampicin
Description	In this study, we successfully developed two gel-free approaches to specifically look at cell wall proteins in Mycobacterium smegmatis. The cell wall was subjected to differential centrifugation, differential detergent solubilisation and phase separation to yield the genuine cell wall proteome. The protein extracts were digested by filter-assisted sample preparation for LC-MS/MS analysis on a Q-Exactive mass spectrometer and identified proteins subjected to a strict bioinformatics pipeline. This resulted in the unprecedented coverage of 96 lipoproteins, 475 membrane proteins containing at least one transmembrane helix and 73 secreted proteins. We used this gel-free approach to study the changes in the cell wall proteome during exposure of M. smegmatis to sub-lethal concentration of Rifampicin in a quantitative manner. This enabled us to characterise in detail the dysregulation of transporters such as TatB and ABC transporters, virulence factors such as MCE proteins and PknG, as well as proteins involved in cell wall and lipid synthesis.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_04:41:17.005.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Alexander Giddey
SpeciesList	scientific name: Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155); NCBI TaxID: 246196;
ModificationList	iodoacetamide derivatized residue
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2017-10-30 04:17:30	ID requested
1	2019-04-09 08:39:41	announced
⏵ 2	2024-10-22 04:41:25	announced	2024-10-22: Updated project metadata.

10.1016/j.jprot.2018.02.019;

Hermann C, Giddey AD, Nel AJM, Soares NC, Blackburn JM, Cell wall enrichment unveils proteomic changes in the cell wall during treatment of Mycobacterium smegmatis with sub-lethal concentrations of rifampicin. J Proteomics, 191():166-179(2019) [pubmed]

curator keyword: Biological

submitter keyword: Cell wall proteomics, Mycobacteria, Mass spectrometry, Rifampicin, TB drugs, TB, sub lethal

Jonathan M Blackburn
contact affiliation	Division of Chemical and Systems Biology, Department of Integrative Biomedical Science, Institute for Infectious Disease and Molecular Medicine, Faculty of Health Science, University of Cape Town, South Africa.
contact email	jonathan.blackburn@uct.ac.za
lab head
Alexander Giddey
contact affiliation	University of Cape Town
contact email	gddale001@myuct.ac.za
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2019/04/PXD008075

PRIDE project URI

• PRIDE
  1. PXD008075
     1. Label: PRIDE project
     2. Name: Cell wall enrichment unveils proteomic changes in the cell wall during treatment of Mycobacterium smegmatis with sub-lethal concentrations of Rifampicin