Work Package 4

Tuesday 5 June 2012
by  daubin
popularity : 0%

Coordinator: Daniel Kahn (INRA,LBBE)

Contributions: LBBE, ISEM

Objectives:

Ancestral gene repertoires will serve as a basis for the reconstruction of ancestral metabolic networks in order to investigate the patterns underlying metabolic diversification from a combined evolutionary and functional perspective. The objectives of this work package are 3-fold:

  1. To investigate principles of metabolic network evolution. Concerted subsets of metabolic genes will be identified from the co-evolution analyses performed in WP2. Unlike previous related studies (e.g., (Yamada, Kanehisa, et Goto 2006; Peregrín-Alvarez et al. 2009) our approach will, by design, take phylogenetic inertia, i.e. the propensity of genes to have similar histories due to common descent, into account. Other approaches considered modules as communities in metabolic graphs, not as evolutionary stable functional subsets (e.g. (Guimerà et Nunes Amaral 2005; Kreimer et al. 2008). Ultimately we aim at a functional interpretation of the structure of metabolic networks in the light of their evolution, and to describe their evolution on the basis of their structure.
  2. To use network information in the reconstruction of the histories of metabolic genes. Reconstructed structures of ancestral metabolic networks will be used to infer correlated reaction fluxes. The resulting functional proximity between metabolic genes will contribute to the reconstruction of their histories in WP1, so that maximum likelihood scenarios will take into account this functional coupling.
  3. To evaluate hypotheses about ancestral environments. Reconstructed metabolic networks will serve to infer prototypes of ancestral life-sustaining environments, which could provide clues on the events associated with the emergence of ancestral phyla (WP6).