Plastids pp 395-406 | Cite as

AT_CHLORO: The First Step When Looking for Information About Subplastidial Localization of Proteins

  • Daniel Salvi
  • Sylvain Bournais
  • Lucas Moyet
  • Imen Bouchnak
  • Marcel Kuntz
  • Christophe Bruley
  • Norbert RollandEmail author
Part of the Methods in Molecular Biology book series (MIMB, volume 1829)


Plastids contain several key subcompartments. The two limiting envelope membranes (inner and outer membrane of the plastid envelope with an intermembrane space between), an aqueous phase (stroma), and an internal membrane system terms (thylakoids) formed of flat compressed vesicles (grana) and more light structures (lamellae). The thylakoid vesicles delimit another discrete soluble compartment, the thylakoid lumen. AT_CHLORO ( is a unique database supplying information about the subplastidial localization of proteins. It was created from simultaneous proteomic analyses targeted to the main subcompartments of the chloroplast from Arabidopsis thaliana (i.e., envelope, stroma, thylakoid) and to the two subdomains of thylakoid membranes (i.e., grana and stroma lamellae). AT_CHLORO assembles several complementary information (MS-based experimental data, curated functional annotations and subplastidial localization, links to other public databases and references) which give a comprehensive overview of the current knowledge about the subplastidial localization and the function of chloroplast proteins, with a specific attention given to chloroplast envelope proteins.

Key words

Chloroplast Subcellular localization Envelope Stroma Thylakoid Plant Proteomics 



D.S., S.B., L.M., I.B., M.K, C.B., and N.R acknowledge support from the ANR project ANR-15-IDEX-02. I.B. is supported by a joint PhD fellowship from the INRA Plant Biology and Breeding Division and from the Labex GRAL (ANR-10-LABX-49-01).


  1. 1.
    MacFadden GI (2014) Origin and evolution of plastids and photosynthesis in eukaryotes. Cold Spring Harb Perspect Biol 6(4):a016105CrossRefGoogle Scholar
  2. 2.
    Martin W, Rujan T, Richly E et al (2002) Evolutionary analysis of Arabidopsis, cyanobacterial, and chloroplast genomes reveals plastid phylogeny and thousands of cyanobacterial genes in the nucleus. Proc Natl Acad Sci U S A 99(19):12246–12251CrossRefPubMedPubMedCentralGoogle Scholar
  3. 3.
    Jarvis P, López-Juez E (2013) Biogenesis and homeostasis of chloroplasts and other plastids. Nat Rev Mol Cell Biol 14:787–802CrossRefPubMedGoogle Scholar
  4. 4.
    Ferro M, Brugière S, Salvi D, Seigneurin-Berny D et al (2010) AT_CHLORO, a comprehensive chloroplast proteome database with subplastidial localization and curated information on envelope proteins. Mol Cell Proteomics 9(6):1063–1084CrossRefPubMedPubMedCentralGoogle Scholar
  5. 5.
    Rolland N, Curien G, Finazzi G et al (2012) The biosynthetic capacities of the plastids and integration between cytoplasmic and chloroplast processes. Annu Rev Genet 46:233–264CrossRefPubMedGoogle Scholar
  6. 6.
    Emanuelsson O, Nielsen H, von Heijne G (1999) ChloroP, a neural network-based method for predicting chloroplast transit peptides and their cleavage sites. Protein Sci 8(5):978–984CrossRefPubMedPubMedCentralGoogle Scholar
  7. 7.
    Emanuelsson O, Nielsen H, Brunak S, von Heijne G (2000) Predicting subcellular localization of proteins based on their N-terminal amino acid sequence. J Mol Biol 300:1005–1016CrossRefGoogle Scholar
  8. 8.
    Agrawal GK, Bourguignon J, Rolland N et al (2011) Plant organelle proteomics: collaborating for optimal cell function. Mass Spectrom Rev 30(5):772–853PubMedGoogle Scholar
  9. 9.
    Kleffmann T, Hirsch-Hoffmann M, Gruissem W et al (2006) plprot: a comprehensive proteome database for different plastid types. Plant Cell Physiol 47(3):432–436CrossRefPubMedGoogle Scholar
  10. 10.
    Sun Q, Zybailov B, Majeran W et al (2009) PPDB, the plant proteomics database at Cornell. Nucleic Acids Res 37(Database issue): D969–D974CrossRefPubMedGoogle Scholar
  11. 11.
    Joshi HJ, Hirsch-Hoffmann M, Baerenfaller K et al (2011) MASCP gator: an aggregation portal for the visualization of Arabidopsis proteomics data. Plant Physiol 155(1):259–270CrossRefPubMedGoogle Scholar
  12. 12.
    Heazlewood JL, Verboom RE, Tonti-Filippini J et al (2007) SUBA: the Arabidopsis subcellular database. Nucleic Acids Res 35(Database issue):D213–D218CrossRefPubMedGoogle Scholar
  13. 13.
    Tanz SK, Castleden I, Hooper CM et al (2013) SUBA3: a database for integrating experimentation and prediction to define the SUBcellular location of proteins in Arabidopsis. Nucleic Acids Res 41:1185–1191CrossRefGoogle Scholar
  14. 14.
    Hooper CM, Castleden IR, Tanz SK et al (2017) SUBA4: the interactive data analysis centre for Arabidopsis subcellular protein locations. Nucleic Acids Res 45(D1):D1064–D1074CrossRefPubMedGoogle Scholar
  15. 15.
    Bruley C, Dupierris V, Salvi D et al (2012) AT_CHLORO: a chloroplast protein database dedicated to sub-plastidial localization. Front Plant Sci 3:205CrossRefPubMedPubMedCentralGoogle Scholar
  16. 16.
    Tomizioli M, Lazar C, Brugière S et al (2014) Deciphering thylakoid sub-compartments using a mass spectrometry-based approach. Mol Cell Proteomics 13(8):2147–2167CrossRefPubMedPubMedCentralGoogle Scholar
  17. 17.
    Salvi D, Rolland N, Joyard J et al (2008) Purification and proteomic analysis of chloroplasts and their sub-organellar compartments. Methods Mol Biol 432:19–36CrossRefPubMedGoogle Scholar
  18. 18.
    Seigneurin-Berny D, Salvi D, Dorne AJ et al (2008) Percoll-purified and photosynthetically active chloroplasts from Arabidopsis thaliana leaves. Plant Physiol Biochem 46(11):951–955CrossRefPubMedGoogle Scholar
  19. 19.
    Salvi D, Moyet L, Seigneurin-Berny D et al (2011) Preparation of envelope membrane fractions from Arabidopsis chloroplasts for proteomic analysis and other studies. Methods Mol Biol 775:189–206CrossRefPubMedGoogle Scholar
  20. 20.
    Moyet L, Salvi D, Tomizioli M et al (2018) Preparation of membrane fractions (envelope, thylakoids, grana and stroma lamellae) from Arabidopsis chloroplasts for quantitative proteomic investigations and other studies. Methods Mol Biol 1696:117–136CrossRefPubMedGoogle Scholar
  21. 21.
    Joyard J, Ferro M, Masselon C et al (2009) Chloroplast proteomics and the compartmentation of plastidial isoprenoid biosynthetic pathways. Mol Plant 2:1154–1180CrossRefPubMedGoogle Scholar
  22. 22.
    Joyard J, Ferro M, Masselon C et al (2010) Chloroplast proteomics highlights the subcellular compartmentation of lipid metabolism. Prog Lipid Res 49:128–158CrossRefPubMedGoogle Scholar
  23. 23.
    Gloaguen P, Bournais S, Alban C et al (2017) ChloroKB: a Web application for the integration of knowledge related to chloroplast metabolic network. Plant Physiol 174(2):922–934CrossRefPubMedPubMedCentralGoogle Scholar
  24. 24.
    Dell'Aglio E, Giustini C, Salvi D et al (2013) Complementary biochemical approaches applied to the identification of plastidial calmodulin-binding proteins. Mol BioSyst 9(6):1234–1248CrossRefPubMedGoogle Scholar
  25. 25.
    Seigneurin-Berny D, Gravot A, Auroy P et al (2006) HMA1, a new Cu-ATPase of the chloroplast envelope, is essential for growth under adverse light conditions. J Biol Chem 281:2882–2892CrossRefPubMedGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2018

Authors and Affiliations

  • Daniel Salvi
    • 1
  • Sylvain Bournais
    • 2
  • Lucas Moyet
    • 1
  • Imen Bouchnak
    • 1
  • Marcel Kuntz
    • 1
  • Christophe Bruley
    • 2
  • Norbert Rolland
    • 1
    Email author
  1. 1.Laboratoire de Physiologie Cellulaire et VégétaleUniversité Grenoble Alpes, Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique, Commissariat à l’Energie Atomique et aux Energies AlternativesGrenobleFrance
  2. 2.Laboratoire de Biologie à Grande EchelleUniversité Grenoble Alpes, Commissariat à l’Energie Atomique et aux Energies Alternatives, Institut National de la Santé et de la Recherche MédicaleGrenobleFrance

Personalised recommendations