Section: New Results

Host-symbiont metabolic dialog

The methodological work done has covered one main question concerning what we called metabolic stories. Given a subset of metabolites representing those monitored as being under- or over-produced in some condition (e.g., interaction with a parasite) and a metabolic network represented as a compound graph, metabolic stories are maximal directed acyclic graphs (DAGs) that cover all the metabolites in the subset of interest, and have all sources and targets among these metabolites. One exact algorithm (Touché , [24] ) was developed to enumerate all metabolic stories that improved on our previous method (Gobbolino ).

The algorithm above was validated on biological data [16] in a study of the response of yeast to cadmium exposure. We used this system as a proof of concept for our method and we showed that we are able to find a story that reproduces very well the current knowledge about the yeast response to cadmium. We further showed that this response is mostly based on enzyme activation. We also provided a framework for exploring the alternative pathways or side effects this local response is expected to have in the rest of the network. Finally, we discussed several interpretations for the changes we see and we suggest hypotheses which could in principle be experimentally tested.