AT_CHLORO
A database dedicated to the subplastidial localization of proteins

The AT_CHLORO database stores sub-plastidial (envelope, stroma, thylakoids; Ferro et al., Mol Cell Proteomics 2010; Bruley et al., Frontiers Plant Sci 2012) and sub-thylakoidal (Grana, stroma-lamellae) localization of Arabidopsis thaliana chloroplast proteins obtained from quantitative proteomics experiments as well as curated function and localization of proteins(Tomizioli et al, Mol Cell Proteomics 2014).

The AT_CHLORO database links to other public web sites (TAIR, PPDB, AtProteome, SUBA, POGs, Aramemnon)
The MASCP Gator (Joshi et al., Plant Physiol. 2011), the aggregation portal for the visualization of Arabidopsis proteomics data, gathers information from a variety of online proteomics resources including AT_CHLORO.

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).

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 (iii) or choose a set of proteins with their AGI accession numbers (Searching option).
A description of the features can be found in the help page.

Citation

If you find the AT_CHLORO database useful, please cite one of the following publications:

1. 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.
2. Tomizioli M, Lazar C, Brugiere S, Burger T, Salvi D, Gatto L, Moyet L, Breckels LM, Hesse AM, Lilley KS, Seigneurin-Berny D, Finazzi G, Rolland N, Ferro M. Deciphering thylakoid sub-compartments using a mass spectrometry-based approach. Mol Cell Proteomics. 2014 May 28. PubMed PMID: 24872594.
3. Bruley C, Dupierris V, Salvi D, Rolland N, Ferro M. AT_CHLORO: A Chloroplast Protein Database Dedicated to Sub-Plastidial Localization. Front Plant Sci. 2012 Sep 11;3:205.

In addition AT_CHLORO also stores plastidial calmodulin-binding proteins (Dell’Aglio et al., 2013)
4. Dell'Aglio E, Giustini C, Salvi D, Brugière S, Delpierre F, Moyet L, Baudet M, Seigneurin-Berny D, Matringe M, Ferro M, Rolland N, Curien G. Complementary biochemical approaches applied to the identification of plastidial calmodulin-binding proteins. Mol Biosyst. 2013 Jun;9(6):1234-48.

Methods used for subcellular and subplastidial fractionation of Arabidopsis chloroplast are described in the following publications:

• Salvi D, Moyet L, Seigneurin-Berny D, Ferro M, Joyard J, Rolland N. Preparation of envelope membrane fractions from Arabidopsis chloroplasts for proteomic analysis and other studies. Methods Mol Biol. 2011;775:189-206.
• Salvi D, Rolland N, Joyard J, Ferro M. Purification and proteomic analysis of chloroplasts and their sub-organellar compartments. Methods Mol Biol. 2008;432:19-36. doi: 10.1007/978-1-59745-028-7_2.

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.
• Rolland N, Curien G, Finazzi G, Kuntz M, Maréchal E, Matringe M, Ravanel S, Seigneurin-Berny D. The biosynthetic capacities of the plastids and integration between cytoplasmic and chloroplast processes. Annu Rev Genet. 2012;46:233-64.

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