Our main focus is to understand the regulation of gene expression in organelles.
In parallel, the OGE team develops functional genomics tools
Understanding plant organellar functions and regulations, which are at the core of the plant metabolism, is a major challenge towards improving agriculture of crops with better yields and a better adaptability to a fluctuating environment.
The organelles, plastids and mitochondria, are the main places of energy metabolism of eukaryotic cells, but they also play a key role in many metabolic pathways.
Throughout evolution and after the ancestral events of endosymbiosis at their origins, organelles have lost much of their original genomes by the transfer of genetic material to the nucleus.
However, they have retained small genomes encoding key proteins and RNAs necessary for their biology. Many proteins encoded by the nucleus are required for organelle gene expression or metabolism and need to be targeted to the organelles, creating a requirement for coordinate regulation of nuclear and organellar gene expression.
Many nuclear proteins are needed for a wide range of transcriptional and post-transcriptional processes including DNA replication, RNA transcription, RNA processing, RNA editing, RNA splicing and translation. Among these nuclear factors, the large family of pentatricopeptide repeat proteins (PPR), which is currently the main object of study of the team, is a key component of the regulation of these two organellar genomes.
These nuclear encoded proteins are almost exclusively targeted to mitochondria and/or chloroplasts where they bind to specific RNAs and are involved in all steps of gene expression from transcription to translation, including splicing, editing and processing of mRNAs.
Roles for PPR proteins in organellar gene expression : from transcription (1) to translation (5). (2) RNA clivage, (3) splicing, (4) editing.
The team was involved in the discovery of the PPR family in 2000, in the genomic characterization of the family in Arabdopsis, rice and Physcomitrella and in several genetic and functional characterizations of members of the Arabidopsis family. Recently, we have been mainly involved in 4 projects :
Systematic study of sub-cellular localization of Arabidopsis PPR proteins (Obando et al, RNA Biology 2013).
Molecular and functional characterization of the DYW1 protein in the chloroplast editing complex of Arabidopsis thaliana (Boussardon et al, Plant Cell 2012).
TAP tag purification of a complex containing 3 PPR proteins involved in editing (Obando et al, in prep).
The main goal of the IPS2 Transcriptomic Platform
is to offer an expertise on development and analysis of transcriptomic data in model and non-model plant species to the plant science community. We offer a large panel of transcriptomic technologies suited to the biological questions and plant material provided by the users (from regular DNA and tiling microarrays to high throughput sequencing (HTS).
The ORFeomics platform was developed
in order to accelerate the functional characterization
of Arabidopsis proteins.
Started in 2002, the purpose of the ATOME project was to begin the construction of the Arabidopsis ORFeome by systematically cloning thousands of ORFs.
During the last 10 years, through targeted projects, a total of c.5000 Arabidopsis ORFs have been cloned in a Gateway vector and a dedicated database was constructed.
The ATOME collection is now available for distribution at CNRGV (Toulouse, France) and at the ABRC (Ohio State University, USA) stock centers.
Downstream of these cloning projects, we are developing “clone-based proteomics” approaches. In particular, we identified the development of systematic protein-protein interaction maps as crucial for Arabidopsis functional genomics.
In the frame of the AGRONOMICS European project, the team set up a collaboration with the NSF funded project “A Plant Interactome Network Map” (NSF#0703905) coordinated by Pr Joseph Ecker (Salk Institute, San Diego) and Pr Marc Vidal (DFCI, Boston).
The first data set from this project was published in July 2011 with a proteome-wide binary protein-protein interaction map containing about 6200 high quality interactions between about 2700 proteins.
We are currently setting up a similar tool at IPS2.