PXD010545-1

PXD010545 is an original dataset announced via ProteomeXchange.

Title	Unravelling hidden components of the chloroplast envelope proteome
Description	Chloroplast is a major plant cell organelle that fulfills essential metabolic and biosynthetic functions. Located at the interface between the chloroplast and other cell compartments, the chloroplast envelope system is a strategic barrier controlling exchanges of ions, metabolites and proteins, thus regulating essential metabolic functions (synthesis of hormones precursors, amino acids, pigments, sugars, vitamins, lipids, nucleotides…) of the plant cell. However, chloroplast envelope membranes remain the hidden part of the chloroplast proteome and many envelope proteins remain to be characterized (known but uncharacterized envelope proteins) or identified (orphan known envelope-associated functions carried by unidentified proteins) Indeed, the envelope contains only 1% of the chloroplast proteins (i.e. 0.25% of the whole cell proteome). When comparing the composition crude leaf extract and purified envelope vesicles, a high theoretical enrichment factor (EF) of specific envelope proteins is thus expected. This is especially true for minor envelope proteins (e.g. representing 1/100 or 1/1000 of the envelope protein content). Sensitivity of MS technique has been greatly improved during the last decade. Today, thanks to the continuous improvement of MS techniques, we are able to detect more components in a complex sample, to generate quantitative data and to statistically validate above-cited enrichment factor. Here, we have taken advantage of present-days better MS sensitivity towards a better definition (differentiate genuine envelope proteins from contaminants) of the chloroplast envelope proteome. This MS- and statistical-based analysis relied on an enrichment factor calculated for each protein identified in purified envelope fractions when compared to the value obtained for the same protein in crude cell extracts. Using this approach, a total of 1376 proteins was detected in purified envelope fractions, of which, more than 500 could be assigned an envelope localization combining MS-based statistical analyses and manual annotation using data from the literature or prediction tools. Interestingly, many of such proteins being unknown or unexpected envelope components, these data constitute a new resource of significant value to the broader plant science community aiming to define principles and molecular mechanisms controlling fundamental aspects of plastid biogenesis and functions.
HostingRepository	PRIDE
AnnounceDate	2019-04-15
AnnouncementXML	Submission_2019-04-15_08:26:45.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD010545
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Marianne Tardif
SpeciesList	scientific name: Arabidopsis thaliana (Mouse-ear cress); NCBI TaxID: 3702;
ModificationList	No PTMs are included in the dataset
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2018-07-24 07:48:50	ID requested
⏵ 1	2019-04-15 08:26:46	announced
2	2024-10-22 04:46:50	announced	2024-10-22: Updated project metadata.

Bouchnak I, Brugi, è, re S, Moyet L, Le Gall S, Salvi D, Kuntz M, Tardif M, Rolland N, Unraveling Hidden Components of the Chloroplast Envelope Proteome: Opportunities and Limits of Better MS Sensitivity. Mol Cell Proteomics, 18(7):1285-1306(2019) [pubmed]

curator keyword: Biological

submitter keyword: Arabidopsis, Chloroplast, Envelope, LC-MSMS

Norbert Rolland
contact affiliation	Univ. Grenoble Alpes, INRA, CNRS, CEA, BIG-LPCV, 38000 Grenoble, France
contact email	norbert.rolland@cea.fr
lab head
Marianne Tardif
contact affiliation	Univ. Grenoble Alpes, CEA, Inserm, BIG-BGE, 38000 Grenoble, France
contact email	marianne.tardif@cea.fr
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/2019/04/PXD010545

PRIDE project URI

• PRIDE
  1. PXD010545
     1. Label: PRIDE project
     2. Name: Unravelling hidden components of the chloroplast envelope proteome