AT_CHLORO Database

AT_CHLORO is database dedicated to the chloroplast proteome from Arabidopsis thaliana.
An AMT database gathers protein identifications related to a given biological system. LC-MS/MS analyses performed on a high resolution mass spectrometer are used to generate the AMT database where analytical coordinates (RT = retention time, Mr = molecular weight) of the peptides are stored. Using this analytical information an AMT database is meant to be used for label-free quantification experiments at the scale of the chosen biological system.

The AT_CHLORO database stores information for proteins that have been identified in different sub-fractions obtained from A. thaliana chloroplasts (Ferro et al., 2010). Several types of information can be found in the AT_CHLORO database:

subplastidial localization (Envelope, Stroma, Thylakoids) as revealed by spectral counting
analytical coordinates (RT, Mr) of all the peptides corresponding to the proteins stored in the database
curated localization and function of proteins that were identified in envelope fractions
links to public web sites (TAIR, PPDB, AtProteome, SUBA, Aramemnon)

Key features of the AT_CHLORO database

controlled chloroplast sub-fractionation
~ 500 LC-MS/MS analyses
~ 12 000 non redundant peptides
1323 protein groups
819 protein groups with subcellular localization based on spectral counting

$chloroplast sub-fractionation$

Subplastidial localization

To obtain subplastidial localization, highly purified fractions of envelope, stroma and thylakoids were obtained and spectral counting was used to classify proteins according to their sub-plastidial localization. Using statistical analysis, the localization of 819 proteins, that are present in the AT_CHLORO, was determined.

How to use the AT_CHLORO database

Users can (i) consult the whole database, (ii) retrieve proteins that are localized in a sub-plastidial compartment (xxx) (iii) or choose a set of proteins with their AGI accession numbers.

Users can customize the display and export the results in xls or PDF files. Each protein has a dedicated page where all related information can be found, including the AMT specific coordinates (RT, Mr).

List of the features that can be retrieved is described here. Some information were retrieved from TAIR (http://www.arabidopsis.org/) and PPDB (http://ppdb.tc.cornell.edu/) in march 2010.

Disclaimer

When using the AT_CHLORO database please cite the following reference :

Ferro M, Brugière S, Salvi D, Seigneurin-Berny D, Court M, Moyet L, Ramus C, Miras S, Mellal M, Le Gall S, Kieffer-Jaquinod S, Bruley C, Garin J, Joyard J, Masselon C, Rolland N. AT_CHLORO, a comprehensive chloroplast proteome database with subplastidial localization and curated information on envelope proteins. Mol Cell Proteomics. 2010 Jun;9(6):1063-84. Epub 2010 Jan 10.

The AT_Chloro database was used to explore the subplastidial localization of specific metabolic pathways:

Joyard J, Ferro M, Masselon C, Seigneurin-Berny D, Salvi D, Garin J, Rolland N. Chloroplast proteomics and the compartmentation of plastidial isoprenoid biosynthetic pathways. Mol Plant. 2009 Nov;2(6):1154-80.
Joyard J, Ferro M, Masselon C, Seigneurin-Berny D, Salvi D, Garin J, Rolland N. Chloroplast proteomics highlights the subcellular compartmentation of lipid metabolism. Prog Lipid Res. 2010 Apr;49(2):128-58.

EDyP laboratory
PCV laboratory
Web Master : veronique.dupierris@cea.fr
Contacts: norbert.rolland@cea.fr; myriam.ferro@cea.fr