From the Ectocarpus genome to its proteome and back

Andrés Ritter

The achievement of the Ectocarpus genome sequencing project*, has unravelled original features of a brown algal genome such as the high number of introns per gene, long 3’UTR, a high number of genes with unknown function and novel metabolic processes. These observations have made difficult to always proceed to an accurate gene annotation. In response to this difficulty, new emerging fields such as proteomics could provide new complementary insights to improve gene structure and identity. In the past years we have developed proteomic tools in Ectocarpus such as 2D gels analysis to study its proteome regulation**. Nowadays nanoLC-MS/MS shotgun proteomics offers the possibility of carrying high-throughput protein identification which can be confronted to the existing genomic data. In relation, we are currently constructing an extensive protein data set from different cellular fractions and life-stages (gametophyte and sporophyte) in Ectocarpus. Our aim is to constitute a global Ectocarpus proteome map that will establish protein localisation and metabolic processes. In a second time the data set will be confronted to the genome in order to validate predicted in-silico orphan genes and correct possible genome annotation errors such as non annotated genes, incorrect intron-exon split, translational start sites, stop codon read-troughs or programmed frame-shifts. This project is being developed in close collaboration with the Biogenouest proteomic platform in Rennes. The technological goal is to set up the technological chain of proteomic assisted genome annotation, by adapting bioinformatic tools such as the newly developed software Pepline*** into a LTQ-Obitrap MS. Future perspectives from this project will be to extend this technology to a wider number of marine organisms.


* Cock J.M. et al., Nature, in press
** Ritter A. et al., Proteomics, in press
*** Ferro et al., J. Proteomic research 2008

Ritter A.1-2, Lefeuvre R. 1-2, Cock J.M.1-2., Scornet D.-2, Marie D. 3, Dartevelle L. 1-2, Com E. 4, Pineau C. 4 and Potin P. 1

1UPMC Univ. Paris 06, The Marine Plants and Biomolecules Laboratory, UMR 7139, Station
Biologique de Roscoff, Place Georges Teissier, BP74, 29682 Roscoff Cedex, France.
2CNRS, UMR 7139, Laboratoire International Associé Dispersal and Adaptation in Marine Species, Station Biologique de Roscoff, Place Georges Teissier, BP74, 29682 Roscoff Cedex, France.
3UPMC (Paris-06) and CNRS, UMR 7144, Station Biologique de Roscoff, Roscoff, France
4Proteomics Core Facility BIOGENOUEST, Campus de Beaulieu, CS 2407, 35 042 Rennes cedex