PXD019140-2

PXD019140 is an original dataset announced via ProteomeXchange.

Title	Comparison between the proteome of Escherichia coli single colony and during liquid culture
Description	Most of the proteomic studies done so far uses bacterial cells harvested from liquid culture media. However it is widely accepted that many important determinants associated with virulence and host cell adhesion are exclusively expressed during growth on solid media. As an attempt to complement previous studies, in this study we compare the proteome coverage of Escherichia coli K12 from a single colony on solid media with those at different growth phases in liquid culture; i.e. early log, mid log, early - and late stationary growth phases. A total of 2044 protein groups covering approximately 47% of the total proteome were identified across all studied conditions; 1650 number of proteins identified from single colonies and 1679 proteins from liquid cultured cells. Label-free quantitative analysis revealed that single colony proteome in a solid agar differs largely from that in liquid culture. The presence of the Suf-operon, involved in iron mobilisation and swarming motility were associated exclusively with single colony profiles. Whereas proteins involved in motility such as MotA, MotB, fliH, flip, fliD and fliJ were associated exclusively to cells grown in liquid culture. The data presented here provide a valuable resource for understanding the role of key proteins within microenvironments surrounding E.coli single colonies.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_05:27:48.662.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	john Iradukunda
SpeciesList	scientific name: Escherichia coli; NCBI TaxID: 562;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Q Exactive HF

Revision	Datetime	Status	ChangeLog Entry
0	2020-05-12 19:03:16	ID requested
1	2021-09-08 23:32:20	announced
⏵ 2	2024-10-22 05:27:50	announced	2024-10-22: Updated project metadata.

10.1016/j.mex.2021.101277;

Fortuin S, Iradukunda J, Nel AJ, Blackburn JM, Soares NC, single colony. MethodsX, 8():101277(2021) [pubmed]

submitter keyword: protein extraction, bacterial proteome, Ecoli, Mass spectrometry,Single-colony, Proteomics

Jonathan Blackburn
contact affiliation	Department:Intergrated biomedical sciences,Division:Chemical biology,Institute of infectious diseases and Molecular medicine(IDM),Faculty of health science, University of Cape Town, South Africa
contact email	Jonathan.blackburn@uct.ac.za
lab head
john Iradukunda
contact affiliation	University of Cape Town
contact email	irdjoh001@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/2021/09/PXD019140

PRIDE project URI

• PRIDE
  1. PXD019140
     1. Label: PRIDE project
     2. Name: Comparison between the proteome of Escherichia coli single colony and during liquid culture