As part of the ANR Glyco-Chloroplast project (Genoplante; 2007-2009), in collaboration with Norbert Rolland's team, we established a database for the Arabidopsis thaliana chloroplast. The database listed over 1300 proteins found in the chloroplast or associated with it. Sub-chloroplast localisation information is available for all these proteins (see description of the AT_Chloro database). The database was made available on a specially designed web site (Ferro et al., Molecular and Cellular Proteomics, 2010).

Among the envelope components of the chloroplast, the protein ceQORH has the specificity of containing a central transit sequence which is not cleaved after the protein has been imported into the chloroplast. This is in contrast with the majority of chloroplast proteins which lose their transit peptides upon import (Miras et al., 2002, 2007; patents FR0207729 and WO2004/001050 A1). Study of ceQORH revealed a previously unknown mechanism controlling protein trafficking between the cytosol and the chloroplast.

Chloroplast proteome dynamics is currently studied through two ANR projects and the GRAL project. Label-free quantitative proteomics approaches, particularly the AMT method, are used.

Coordinator:
Norbert Rolland (PCV, UMR5168, CEA/Grenoble)
EDyP correspondent:
Myriam Ferro
Funded by:
ANR Blanc, 2010-2014 (French National Research Agency)

The Chloro-Pro project aims to:
- Identify the chloroplast proteins regulated by an import mechanism similar to that used by ceQORH
- Identify signals controlling protein trafficking through the chloroplast envelope
- Use quantitative proteomics to determine how deregulation of this mechanism affects chloroplast physiology.

Coordinator:
Norbert Rolland (PCV, UMR5168, CEA/Grenoble)
EDyP correspondent:
Myriam Ferro
Funded by:
ANR genomics and plant biotechnology call, 2011-2014 (French National Research Agency)

The Chloro-types project aims to:
- Identify abiotic stressors affecting protein targeting to the chloroplast
- Determine the regulatory mechanisms induced by abiotic stress and controlling sub-cellular localisation of some proteins
- Understand how regulatory mechanisms, induced by stress, affect chloroplast physiology.

Coordinator:
Gilles Peltier (iBEB/SBVME/LB3M, UMR6191, CEA/Cadarache)
EDyP correspondent:
Myriam Ferro
Funded by:
ANR Bioenergy, 2008-2012 (French National Research Agency)

Chlamydomonas reinhardtii is a unicellular photosynthetic alga which has developed a metabolic capacity to produce hydrogen or accumulate lipid stores using water, CO₂, and solar energy as its main resources. In some unfavourable situations (e.g. starvation), Chlamydomonas adapts its cellular metabolism to accumulate energy stores (starch, lipids). As part of the ALGOMICS project, EDyP is undertaking the proteomics part of a multidisciplinary project combining a wide range of "omics" approaches: proteomics, transcriptomics, genomics, metabolomics, and fluxomics. ALGOMICS aims to develop a "Systems biology" strategy to characterise Chlamydomonas mutants defective for reserve metabolism. The aim is to determine the points of control and regulation for algal metabolism.
For ALGOMICS, EDyP performed quantitative proteomics experiments on metabolically labelled Chlamydomonas cells (¹⁵N). In collaboration with the Cellular & Plant Physiology laboratory, and Michael Hippler's laboratory, a sub-project is underway to develop a software tool predicting subcellular protein localisation specifically in algae. The tool, PredAlgo, recognises "signal" pre-sequences found at the N-terminal extremity of proteins. Development of PredAlgo is possible thanks to the use of proteomics analysis methods specifically targeting N-terminal peptides from Chlamydomonas proteins.


Publication :
Nguyen HM, Baudet M, Cuiné S, Adriano JM, Barthe D, Billon E, Bruley C, Beisson F, Peltier G, Ferro M and Li-Beisson Y
Proteomic profiling of oil bodies isolated from the unicellular green microalga Chlamydomonas reinhardtii: With focus on proteins involved in lipid metabolism.
Proteomics, 2011, 11(21): 4266-4273

Coordinator:
Jacques Bourguignon (PCV, UMR5168, CEA/Grenoble)
EDyP correspondent:
Yves Vandenbrouck
Funded by:
Programme Transversal de Toxicologie du CEA

Plants are sessile organisms incapable of escaping from environmental pressure. To cope with this, they have developed a range of mechanisms and strategies to counteract stressful environmental conditions. This project is based on two main axes:

1 - Study of what becomes of uranyl, its speciation and the metabolites it induces in higher plants. Analysis will focus on the speciation of uranyl in the whole plant, and its distribution in plant cells. We will also analyse the impact of this toxin on metabolites, to identify compounds involved in its chelation. The proteins targeted by uranyl will also be identified.

2 - Study of the Arabidopsis thaliana response to uranyl-induced stress using CATMA DNA chips and bioinformatics approaches. The metabolic pathways affected or exacerbated by uranium, and the molecular and cellular mechanisms implemented by the plant to deal with this toxin will be identified. This approach should reveal genes (coding for transporters, transcription factors, etc.) likely to play an important role in this response.
This project will provide an overview of the plant response to uranyl-induced stress, and will characterise metabolic and/or protein biomarkers of uranyl exposure.

Development:
Boyer F, Combes F, Bourguignon J and Vandenbrouck Y
A graph-based approach for extracting transcriptional regulatory modules from a large microarray compendium: An application to the transcriptional response of Arabidopsis thaliana under stress condition in TIC Signal Processing Proceedings Series, 2009, vol. 48. pp 23-27

Boyer F, Combes F, Lindlöf A, Bourguignon J and Vandenbrouck Y
Exploring the transcriptional response of Arabidopsis under stress conditions by a graph-mining approach highlights new insights into key metabolic pathways. Journées Ouvertes de Biologie, Informatique et Mathématiques (JOBIM). Montpellier, France, 7-9th Sept 2010