Abstract
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 (http://at-chloro.prabi.fr/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.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
MacFadden GI (2014) Origin and evolution of plastids and photosynthesis in eukaryotes. Cold Spring Harb Perspect Biol 6(4):a016105
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):12246–12251
Jarvis P, López-Juez E (2013) Biogenesis and homeostasis of chloroplasts and other plastids. Nat Rev Mol Cell Biol 14:787–802
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):1063–1084
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 46:233–264
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):978–984
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 300:1005–1016
Agrawal GK, Bourguignon J, Rolland N et al (2011) Plant organelle proteomics: collaborating for optimal cell function. Mass Spectrom Rev 30(5):772–853
Kleffmann T, Hirsch-Hoffmann M, Gruissem W et al (2006) plprot: a comprehensive proteome database for different plastid types. Plant Cell Physiol 47(3):432–436
Sun Q, Zybailov B, Majeran W et al (2009) PPDB, the plant proteomics database at Cornell. Nucleic Acids Res 37(Database issue): D969–D974
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):259–270
Heazlewood JL, Verboom RE, Tonti-Filippini J et al (2007) SUBA: the Arabidopsis subcellular database. Nucleic Acids Res 35(Database issue):D213–D218
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 41:1185–1191
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–D1074
Bruley C, Dupierris V, Salvi D et al (2012) AT_CHLORO: a chloroplast protein database dedicated to sub-plastidial localization. Front Plant Sci 3:205
Tomizioli M, Lazar C, Brugière S et al (2014) Deciphering thylakoid sub-compartments using a mass spectrometry-based approach. Mol Cell Proteomics 13(8):2147–2167
Salvi D, Rolland N, Joyard J et al (2008) Purification and proteomic analysis of chloroplasts and their sub-organellar compartments. Methods Mol Biol 432:19–36
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):951–955
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 775:189–206
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 1696:117–136
Joyard J, Ferro M, Masselon C et al (2009) Chloroplast proteomics and the compartmentation of plastidial isoprenoid biosynthetic pathways. Mol Plant 2:1154–1180
Joyard J, Ferro M, Masselon C et al (2010) Chloroplast proteomics highlights the subcellular compartmentation of lipid metabolism. Prog Lipid Res 49:128–158
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):922–934
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):1234–1248
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 281:2882–2892
Acknowledgments
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).
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2018 Springer Science+Business Media, LLC, part of Springer Nature
About this protocol
Cite this protocol
Salvi, D. et al. (2018). AT_CHLORO: The First Step When Looking for Information About Subplastidial Localization of Proteins. In: Maréchal, E. (eds) Plastids. Methods in Molecular Biology, vol 1829. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-8654-5_26
Download citation
DOI: https://doi.org/10.1007/978-1-4939-8654-5_26
Published:
Publisher Name: Humana Press, New York, NY
Print ISBN: 978-1-4939-8653-8
Online ISBN: 978-1-4939-8654-5
eBook Packages: Springer Protocols