PXD009722-1

PXD009722 is an original dataset announced via ProteomeXchange.

Title	In vivo, Quantitative label free proteomics and microscopy analysis highlights the central role of the endomembrane system during barley grain filling development.
Description	Abstract Barley is a cereal crop of worldwide importance for brewing industry, animal and in lesser extent humannutrition. Grain development is a tightly controlled process which predominantly contributes to the final grain quality. To understand molecular changes occurring in the early seed development stage up to the initial storage phase, proteome profiling of developing barley seed at 8, 10 18 and 20 days after flowering was analyzed. In vivo label free quantification approach allowed the quantification of more than 1200 proteins across the different stages. Confirmation of the reproducibility of the developmental data obtained in our proteomics analysis was performed using western-blot technics to validate the specific pattern of selected proteins and comparison with previously published data. Multi- and uni-variates statistics were used to unravel the biochemical dynamics underlying the grain filling process. Seed storage proteins (SSPs) were found to accumulate during the grain filling process suggesting a higher activity of the endoplasmic reticulum playing a major role in protein synthesis. This hypothesis was supported by a spatio-temporal analysis of the ER marker protein-disulfide-isomerase (PDI) at both transcript and protein level coupled with microscopic study of the ER dynamics. Results indicates that ER is predominantly active in the starchy endosperm up to 18 DAP and is subsequently degraded while the cells undergo program cell death. The central role of the ER was further strengthening by the analysis of all ER related proteins. Similarly, the pattern of vacuolar H+ ATPases suggested a decrease of the vacuolar acidity, microscopic analysis of the endosperm unravel a concomitant decrease of both vacuolar size and acidity associated with an abundance switch in different class of vacuolar annotated proteins (eg: Sucrose related metabolism proteins). Observed endomembrane system dynamics were supported by specific abundance changes of ESCRT related proteins such as VPS4 and SNF7 or VPS5 a protein associated to the retromer complex. Collectively, our results provide insight into endomembrane molecular processes taking place during barley early grain development, additionally the proteome dataset provide a comprehensive overview of a wide range of metabolic pathway which will be helpful for the cereal community.
HostingRepository	PRIDE
AnnounceDate	2018-07-02
AnnouncementXML	Submission_2018-07-02_01:14:54.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Valentin Roustan
SpeciesList	scientific name: Hordeum vulgare (Barley); NCBI TaxID: 4513;
ModificationList	monohydroxylated residue; acetylated residue; iodoacetamide derivatized residue
Instrument	LTQ Orbitrap Elite

Revision	Datetime	Status	ChangeLog Entry
0	2018-05-09 00:03:56	ID requested
⏵ 1	2018-07-02 01:14:58	announced
2	2018-10-01 08:33:20	announced	Updated publication reference for PubMed record(s): 29951075, 30250475.
3	2024-10-22 04:45:10	announced	2024-10-22: Updated project metadata.

Shabrangy A, Roustan V, Reipert S, Weidinger M, Roustan PJ, Stoger E, Weckwerth W, Ibl V, Using RT-qPCR, Proteomics, and Microscopy to Unravel the Spatio-Temporal Expression and Subcellular Localization of Hordoindolines Across Development in Barley Endosperm. Front Plant Sci, 9():775(2018) [pubmed]

curator keyword: Biological

submitter keyword: endomembrane system. barley caryopsis development, ESCRT, shotgun proteomics, microscopy, qRT-PCR

Verena Ibl
contact affiliation	Department of Ecogenomics and Systems Biology, University of Vienna, Althanstrasse 14, 1090 Vienna, Austria
contact email	verena.ibl@univie.ac.at
lab head
Valentin Roustan
contact affiliation	University of Vienna
contact email	valentin.roustan@univie.ac.at
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/2018/07/PXD009722

PRIDE project URI

• PRIDE
  1. PXD009722
     1. Label: PRIDE project
     2. Name: In vivo, Quantitative label free proteomics and microscopy analysis highlights the central role of the endomembrane system during barley grain filling development.