Metabolism & Systems Biology

From annotation and analysis of microbial genomes, Genome-Scale Metabolic Networks (GSMN) can be obtained and contain all of the known metabolic reactions in a given organism and the genes that encode each enzyme. Part of our research activities are focused on the curation of GSMN and the development of databases and methods to improve their reconstruction.

Two main bottlenecks limit the understanding of metabolic consequences encoded in a genome: the difficulty in associating correct functions to genes and the lack of experimental characterization of enzyme activities for which proteins are sometimes unknown, i.e. orphan enzymes. In the light of enzymatic screening and metabolomics experiments, we develop bioinformatics methods and perform bioanalysis for the discovery of new enzyme families and the exploration of their functional diversity. Methods are mainly based on sequence analysis, genomic and metabolic context exploration and structural bioinformatics.

 

Discovery of the complete catabolic pathway for red algal carrageenans in marine bacteria

Discovery of the complete catabolic pathway for red algal carrageenans in marine bacteria An international consortium coordinated by the Marine Glycobiology team (UMR8227 – CNRS/UPMC) has just published the discovery of the complete system for the utilization of carrageenans, sulfated polysaccharides which are a major component of the cell walls ...
Read More

NetSyn – Exploring Syntenies Networks of Genes

We developed a method to classify proteins of a family based on their conserved genomic contexts. Each protein genomic context is compared against all others to determine syntenies. A graph is generated where nodes are input proteins connected by edges when a synteny is observed. Edges weight represent the mean ...
Read More

Mining secondary metabolites in cyanobacterial genomes

Cyanobacteria are an ancient lineage of photosynthetic bacteria, which are prolific producers of secondary metabolites. Hundreds of bioactive compounds with diverse chemical structures , such as toxins and molecules of pharmaceutical interest, have been characterized from cyanobacteria ...
Read More