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Phages / Petit
RESEARCH PROJECTS
The team focus is on the estonishing plasticity of bacteriophage genomes, studied using three complementary approaches: bio-informatics, molecular biology and ecology. The project is funded in part by an INRA “Jeune Equipe” grant, for the period 2010-2012.
Combining predictive and experimental approaches, the kind of questions asked are:
- What is the role of phage-encoded recombinases in the structure of temperate phage genomes (Martinsohn et al., 2008, Lopes et al., 2010)?
- What kind of factors control temperate phage propagation and horizontal gene transfer mediated by such phages infecting Escherichia coli, in one of its natural environment, the mouse gut?
- The co-evolution of lambdoid phages of E. coli and their cognate receptor: is it as simple as predicted by the red-queen theory?
- Is it possible to predict the function of the overwhelming mass of unknown phage genes using adapted cutting-edge methods for far distance homology detection (Lopes et al., 2010)?
This team is the follow-up of the former team of Meriem El Karoui which was initially concentrated on bacterial genome dynamics. Genome comparisons at the intra-species level have lead to the conclusion that bacterial genomes are composed of a backbone, shared by all strains of the species, and variable segments, that are present or absent depending on each strain ( Chiapello et al, 2005). The backbone is likely to be inherited vertically from the common ancestor of all strains of the species, while the variable segments are for the most part recently acquired by horizontal transfer.
We have set up a general strategy of multiple genome alignments, in collaboration with the Mathématique Informatique et Génome laboratory (INRA). A Web site gives access to the partition between backbone and variable segments for numerous species (149 species available in 2010), and allows to visualize the alignments ( http://genome.jouy.inra.fr/mosaic). Moreover, an original method to calculate rapidly within-species genomic distances has been set up ( Deloger et al., 2009).
We have shown that the bacterial backbone is enriched in small DNA motifs that contribute to genome maintenance, such as Chi ( Halpern et al., 2007), KOPS ( Bigot et al., 2005, Val et al., 2008), and matS ( Romain et al., 2008).
A systematic study of variable segments has shown that most of them are small in size (less than 500 bp), and often present within genes. They constitute a new type of diversity, called micro-diversity ( Touzain et al., 2010). This work is presently being continued along the following axes :
- Prediction of motifs structuring the other E. coli macrodomains
- Understanding the origin of microdiversity
FUNDING
- Jeune Equipe INRA (2010-2012)
- Fondation pour la Recherche Médicale (2010-2012)
See also
- The web site for the MOSAIC database, dedicated to intra-species whole genome alignments and analysis
- The MUMI web site for Mumi distance calculation between two genomes belonging to the same, or very related species.
- The VIRFAM web site of our collaborator Raphaël Guerois for predicting phage-encoded recombinase function.
Writing:
Micalis
Creation date: 02 April 2011
Update: 09 November 2011
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