PXD011345-2

PXD011345 is an original dataset announced via ProteomeXchange.

Title	Analysis of the Escherichia coli membrane vesicle proteome identifies markers of purity and culture conditions
Description	Bacteria release nano-sized membrane vesicles (MVs) into the extracellular milieu. Bacterial MVs contain molecular cargo originating from the parent bacterium and have important roles in bacterial survival and pathogenesis. Using 8-plex iTRAQ approaches, we profiled the MV proteome of two Escherichia coli strains - uropathogenic E. coli (UPEC) 536 and probiotic Nissle 1917. For these strains, we compared the difference in the MV proteome between a crude input MV prepared by ultracentrifugation alone with that from MVs that were further purified by either density gradient centrifugation (DGC) or size exclusion chromatography (SEC); and also compared MVs from bacterial cultures that were grown in iron-restricted (R) and ironsupplemented (RF) conditions. We found that overall, outer membrane components were highly enriched, and bacterial inner membrane components were significantly depleted in both UPEC and Nissle MVs, in keeping with an outer membrane origin. In addition, we found enrichment of ribosome-related Gene Ontology terms in UPEC MV, and proteins involved in glycolytic process and ligase activity in Nissle MV. We have identified that three proteins (RbsB of UPEC in R; YoeA of UPEC in RF; BamA of Nissle in R) were consistently enriched in the DGC- and SEC-purified MV samples in comparison to their crude input MV, whereas conversely the 60 kDa chaperonin GroEL was enriched in the crude input MVs for both UPEC and Nissle in R condition. Such proteins may have a potential utility as technical markers for assessing the purity from contaminating non-vesicular protein after MV purification. Several proteins were changed in their abundance depending on the iron availability in the media.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_04:49:11.926.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Leo Payne
SpeciesList	scientific name: Escherichia coli; NCBI TaxID: 562;
ModificationList	iTRAQ8plex-116 reporter+balance reagent acylated residue; iodoacetamide derivatized residue
Instrument	TripleTOF 6600

Revision	Datetime	Status	ChangeLog Entry
0	2018-10-12 01:17:30	ID requested
1	2019-07-15 01:29:53	announced
⏵ 2	2024-10-22 04:49:17	announced	2024-10-22: Updated project metadata.

Hong J, Dauros-Singorenko P, Whitcombe A, Payne L, Blenkiron C, Phillips A, Swift S, extracellular vesicle proteome identifies markers of purity and culture conditions. J Extracell Vesicles, 8(1):1632099(2019) [pubmed]

10.1080/20013078.2019.1632099;

curator keyword: Technical, Biological

submitter keyword: Membrane vesicles

extracellular vesicles

pathogen

microbe

proteomics

iron

Simon Swift
contact affiliation	Department of Molecular Medicine and Pathology, University of Auckland, Auckland, New Zealand
contact email	s.swift@auckland.ac.nz
lab head
Leo Payne
contact affiliation	School of Biological Sciences, University of Auckland
contact email	l.payne@auckland.ac.nz
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD011345
     1. Label: PRIDE project
     2. Name: Analysis of the Escherichia coli membrane vesicle proteome identifies markers of purity and culture conditions