PXD000798

PXD000798 is an original dataset announced via ProteomeXchange.

Title	Effects of Campylobacter jejuni CJIE1 prophage on protein expression experiment 1
Description	Temperate bacteriophages (prophages) have recently been demonstrated in Campylobacter jejuni. However, what they do there is largely unknown. In the series of studies that are the subject of these submissions we have investigated the relative expression levels of proteins in C. jejuni isolates that differ in the presence or absence of the CJIE1 prophage. At the time of the initial investigations whole genome sequence data were not available for the isolates used, though DNA microarray data indicated that the isolates were very closely related. The overall project was carried out through four separate experiments. The first set of experiments (experiment 1) therefore compared protein expression in 4-plex iTRAQ experiments using three isolates carrying the (previously sequenced) prophage with a fourth isolate that was epidemiologically and genetically related to these isolates but which naturally lacked the CJIE1 prophage. Three replicate experiments were done. These isolates were grown on medium containing blood to obtain optimal growth and determine whether any differences were found. Three replicate experiments were done. However, since these growth conditions may not mimic in vivo growth of the organism the results may not be considered relevant or very interesting. Previous work in the scientific literature indicated that growth on medium lacking blood but containing sodium deoxycholate induced the expression of at least some proteins associated with virulence and provided data thought to be of relevance to the virulence of the bacterium. Therefore two isolates were chosen, one with and one without the CJIE1 prophage. Each of three replicates of a 4-plex iTRAQ experiment compared protein expression of the two isolates (00-2425 and 00-2426) after growth on Mueller-Hinton agar with and without 0.1% sodium deoxycholate. There was pretty good overlap between the proteins expressed in the first two experiments but, because all results were expressed as log2 change values, it was difficult to determine whether the expression of some proteins was completely absent in one or the other isolate. As well, protein expression overall showed quite extensive differences compared with the first experiment that we attributed to the lack of blood in the growth medium; we thought we might be seeing a response to limited iron as well. Finally, the response to the deoxycholate was extensive, and we wished to further explore this phenomenon as a means of determining or verifying what effects were due to the presence of the CJIE1 prophage and which were due to other differences. Further 4-plex iTRAQ experiments compared protein expression for each of isolate after growth on medium containing blood, without blood, without blood plus sodium deoxycholate, and without blood plus 2.5% Oxgall. Comparison of the results for isolate 00-2425 (with the CJIE1 prophage) and 00-2426 (without the prophage) identified a small number of proteins that could not be detected in one or the other isolate and allowed discrimination of the effects of the prophage from the responses to iron limitation and bile salt preparations. This dataset is associated with the first experiment, experiment 1, which compares C. jejuni isolates carrying the CJIE1 prophage (00-2425, 00-2538, 00-2544) with a very closely related isolate lacking the prophage (00-2426)
HostingRepository	PRIDE
AnnounceDate	2014-12-02
AnnouncementXML	Submission_2014-12-02_00:31:14.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Clifford Clark
SpeciesList	scientific name: Campylobacter jejuni 10227; NCBI TaxID: 1327986;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue; iTRAQ4plex-116 reporter+balance reagent acylated residue
Instrument	LTQ Orbitrap Velos

Revision	Datetime	Status	ChangeLog Entry
0	2014-03-06 01:15:10	ID requested
1	2014-07-31 03:36:39	announced
⏵ 2	2014-12-02 00:31:15	announced	Updated project metadata.

Clark CG, Chong PM, McCorrister SJ, Simon P, Walker M, Lee DM, Nguy K, Cheng K, Gilmour MW, Westmacott GR, The CJIE1 prophage of Campylobacter jejuni affects protein expression in growth media with and without bile salts. BMC Microbiol, 14():70(2014) [pubmed]

curator keyword: Biological

submitter keyword: LC-MSMS

Campylobacter jejuni

CJIE1 prophage

iTRAQ;

Garrett R. Westmacott
contact affiliation	Mass Spectrometry and Proteomics Core Facility, National Microbiology Laboratory, Public Health Agency of Canada 1015 Arlington Street, Winnipeg, Manitoba, Canada R3E 3R2
contact email	garrett.westmacott@phac-aspc.gc.ca
lab head
Clifford Clark
contact affiliation	National Microbiology Laboratory, Public Health Agency of Canada
contact email	clifford.clark@phac-aspc.gc.ca
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD000798
     1. Label: PRIDE project
     2. Name: Effects of Campylobacter jejuni CJIE1 prophage on protein expression experiment 1