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2 results on '"plastidial localization"'

1. AT_CHLORO: a chloroplast protein database dedicated to sub-plastidial localization

Author

Christophe eBruley, Véronique eDupierris, Daniel eSalvi, Norbert eRolland, Myriam eFerro, Institut de Biosciences et de Biotechnologies de Grenoble (ex-IRTSV) (BIG), Institut National de la Santé et de la Recherche Médicale (INSERM)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Joseph Fourier - Grenoble 1 (UJF)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019]), Laboratoire de Biologie à Grande Échelle (BGE - UMR S1038), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Laboratoire de physiologie cellulaire végétale (LPCV), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de la Recherche Agronomique (INRA)-Université Joseph Fourier - Grenoble 1 (UJF)-Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (INSERM)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Joseph Fourier - Grenoble 1 (UJF)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA)-Université Grenoble Alpes (UGA), Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Grenoble Alpes (UGA), Université Joseph Fourier - Grenoble 1 (UJF)-Institut National de la Recherche Agronomique (INRA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS), Université Joseph Fourier - Grenoble 1 (UJF)-Institut National de la Recherche Agronomique (INRA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019]), Université Joseph Fourier - Grenoble 1 (UJF)-Institut National de la Recherche Agronomique (INRA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), and Martin-Laffon, Jacqueline

Subjects
0106 biological sciences, Proteomics, Arabidopsis thaliana, proteome, review, plant, Review Article, Computational biology, Plant Science, lcsh:Plant culture, computer.software_genre, 01 natural sciences, Chloroplast membrane, envelope membrane, chloroplast, database, protein, plastidial localization, proteomics, 03 medical and health sciences, Stroma, [SDV.BBM] Life Sciences [q-bio]/Biochemistry, Molecular Biology, SDV:BBM, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, lcsh:SB1-1110, 030304 developmental biology, sub-plastidial localization, 0303 health sciences, biology, biology.organism_classification, Chloroplast, Chloroplast envelope, Thylakoid, Proteome, Data mining, Chloroplast Proteins, computer, 010606 plant biology & botany
Abstract

International audience; AT_CHLORO (www.grenoble.prabi.fr/at_chloro) is a database dedicated to sub-plastidial localization of A. thaliana chloroplast proteins. This information was infered from proteomics experiments obtained from a comprehensive study that allowed the identification of proteins from envelope, stroma, and thylakoid sub-compartments Ferro et al., 2010. In addition to current knowledge regarding sub-plastidial localization, AT_CHLORO provides experimental data that allowed curated information regarding subcellular localizations of chloroplast proteins to be given. A specific focus was given to proteins that were identified in envelope fractions and for which expert functional annotation was provided. The present mini review shows the specificities of AT_CHLORO with respect to available information, data export options and recent improvements in data representation.

Published
2012

2. AT_CHLORO, a comprehensive chloroplast proteome database with subplastidial localization and curated information on envelope proteins

Author

Daniel Salvi, Jérôme Garin, Norbert Rolland, Stéphane Miras, Christophe Bruley, Sabine Brugière, Sylvie Kieffer-Jaquinod, Jacques Joyard, Lucas Moyet, Sophie Le Gall, Daphné Seigneurin-Berny, Christophe Masselon, Magali Court, Myriam Ferro, Claire Ramus, Mourad Mellal, Laboratoire d'étude de la dynamique des protéomes (LEDyP), Université Joseph Fourier - Grenoble 1 (UJF)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de la Santé et de la Recherche Médicale (INSERM), Laboratoire de physiologie cellulaire végétale (LPCV), Université Joseph Fourier - Grenoble 1 (UJF)-Institut National de la Recherche Agronomique (INRA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de chimie des protéines, Laboratoire de Glycobiologie et Matrice Extracellulaire Végétale (Glyco-MEV), Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-Normandie Université (NU), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Joseph Fourier - Grenoble 1 (UJF)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA), Université Joseph Fourier - Grenoble 1 (UJF)-Institut National de la Recherche Agronomique (INRA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), and Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)

Subjects
0106 biological sciences, Chloroplasts, Arabidopsis thaliana, thylakoid, Arabidopsis, plant, Proteomics, computer.software_genre, Thylakoids, 01 natural sciences, Biochemistry, Mass Spectrometry, Analytical Chemistry, Databases, Protein, database, chemistry.chemical_classification, 0303 health sciences, Database, Amino acid, Chloroplast, Thylakoid, Proteome, Subcellular Fractions, proteome, Blotting, Western, Biology, Cell Fractionation, envelope membrane, plastidial localization, 03 medical and health sciences, proteomics, Stroma, chloroplast, stroma, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Molecular Biology, 030304 developmental biology, Arabidopsis Proteins, Research, Reproducibility of Results, Intracellular Membranes, biology.organism_classification, Cell Compartmentation, chemistry, Chloroplast Proteins, Peptides, protein, computer, 010606 plant biology & botany
Abstract

International audience; Recent advances in the proteomics field have allowed a series of high throughput experiments to be conducted on chloroplast samples, and the data are available in several public databases. However, the accurate localization of many chloroplast proteins often remains hypothetical. This is especially true for envelope proteins. We went a step further into the knowledge of the chloroplast proteome by focusing, in the same set of experiments, on the localization of proteins in the stroma, the thylakoids, and envelope membranes. LC-MS/MS-based analyses first allowed building the AT_CHLORO database (http://www.grenoble.prabi.fr/protehome/grenoble-plant-proteomics/), a comprehensive repertoire of the 1323 proteins, identified by 10,654 unique peptide sequences, present in highly purified chloroplasts and their subfractions prepared from Arabidopsis thaliana leaves. This database also provides extensive proteomics information (peptide sequences and molecular weight, chromatographic retention times, MS/MS spectra, and spectral count) for a unique chloroplast protein accurate mass and time tag database gathering identified peptides with their respective and precise analytical coordinates, molecular weight, and retention time. We assessed the partitioning of each protein in the three chloroplast compartments by using a semiquantitative proteomics approach (spectral count). These data together with an in-depth investigation of the literature were compiled to provide accurate subplastidial localization of previously known and newly identified proteins. A unique knowledge base containing extensive information on the proteins identified in envelope fractions was thus obtained, allowing new insights into this membrane system to be revealed. Altogether, the data we obtained provide unexpected information about plastidial or subplastidial localization of some proteins that were not suspected to be associated to this membrane system. The spectral counting-based strategy was further validated as the compartmentation of well known pathways (for instance, photosynthesis and amino acid, fatty acid, or glycerolipid biosynthesis) within chloroplasts could be dissected. It also allowed revisiting the compartmentation of the chloroplast metabolism and functions.

Published
2010

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