PXD000319

PXD000319 is an original dataset announced via ProteomeXchange.

Title	Maniupulating root water supply elicits major shifts in the shoot proteome
Description	Detailed information: Rice (*Oryza sativa* L. cv. Nipponbare) is a drought-susceptible species which is well suited for studies of abiotic stress response because of the comprehensive bioinformatics resource available. By withholding water from the entire root system of young rice plants, or half the root system only, it was possible to infer the relative impact of signals arriving from roots growing in wet and dry soil on the shoot proteome. The global proteome of shoots had 685 proteins in common to all three drought treatments but there were major shifts in abundance of individual proteins within 16 functional categories. The dominant changes were analyzed more deeply. First, we investigated transport and cell component organization, where some proteins were up-regulated by drought but many more down-regulated. Proteins involved in protein metabolism were up-regulated in general by drought when they were responsible for protein degradation but those involved in protein synthesis were down-regulated when water was withheld. Stress-related proteins behaved very consistently by increasing in droughted plants but notably some proteins were most abundant when roots of the same plant were growing in both wet and dry soil. This suggests that drought signals are complex interactions and not simply the additive effect of water supply to the roots. Changes in carbohydrate-processing proteins were consistent with the passive accumulation of soluble sugars in shoots under drought, with hydrolysis of sucrose and starch synthesis both enhanced. Data analysis information: The result raw files were converted to mzXML format and processed through the global proteome machine (GPM) software (version 2.1.1) of the X!Tandem algorithm (freely available at http://www.thegpm.org). The 16 gel fractions were processed serially for each experiment and the output files were generated as non-redundant, merged files with protein identifications with log (e) values less than -1, for each individual gel fraction. A protein database compiled from NCBI *O*. *sativa* with 26938 protein sequences (August 2011) was used in GPM to search the tandem mass spectra; the database also included common trypsin and human peptide contaminants. False discovery rates (FDR) were evaluated by searching against a reversed sequence database. Search parameters included MS and MS/MS tolerances of +2 Da and +0.2 Da, carbamidomethylation of cysteine as fixed modifications, oxidation of methionine as variable modifications and tolerance of two missed tryptic cleavages and K/R-P cleavages.
HostingRepository	PRIDE
AnnounceDate	2020-01-22
AnnouncementXML	Submission_2020-01-22_05:23:10.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Mehdi mirzaei
SpeciesList	scientific name: Oryza sativa (Rice); NCBI TaxID: 4530;
ModificationList	monohydroxylated residue; deamidated residue
Instrument	LTQ

Revision	Datetime	Status	ChangeLog Entry
0	2013-07-04 04:16:21	ID requested
⏵ 1	2020-01-22 05:23:12	announced

Mirzaei M, Soltani N, Sarhadi E, George IS, Neilson KA, Pascovici D, Shahbazian S, Haynes PA, Atwell BJ, Salekdeh GH, Manipulating root water supply elicits major shifts in the shoot proteome. J Proteome Res, 13(2):517-26(2014) [pubmed]

submitter keyword: Rice, Drought, Split-root, Shotgun proteomics

Ghasem Hosseini Salekdeh
contact affiliation	Department of Molecular Systems Biology at Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
contact email	h_salekdeh@abrii.ac.ir
lab head
Mehdi mirzaei
contact affiliation	Australian School of Advanced Medicine
contact email	mehdi.mirzaei@mq.edu.au
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD000319
     1. Label: PRIDE project
     2. Name: Maniupulating root water supply elicits major shifts in the shoot proteome