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Genoscope Unit UMR 8030 Genomics Metabolics

UMR 8030 Génomique Métabolique du Genoscope

Director : Patrick Wincker (DR, CEA)

Deputy director : Véronique de Berardinis  (DR, CEA)

Published on 27 April 2023

UMR 8030 "Metabolic Genomics" is the Genoscope's own research structure - National Sequencing Centre

Genoscope conducts its research activity within the mixt unit research UMR Metabolic Genomics (CEA/CNRS/University of Evry, Paris-Saclay), which has a staff of around 110, including 83 permanent staff. 

Through various projects, both internal and conducted in the form of national or international collaborations, we explore the biodiversity of organisms by analysing their genomes, thus making a significant contribution to the global exploration of the tree of life. The unit develops interdisciplinary approaches ranging from genomics to the "supervised" evolution of micro-organisms via molecular biology, metabolic engineering, biochemistry, bioinformatics and analytical chemistry. It is involved in several international consortia such as Tara Oceans (marine metagenomic exploration) and ERGA (genomic catalogue of European biodiversity).

The unit is organised into 6 laboratories:

  • Laboratoire d'Analyses Génomiques des Eucaryotes (LAGE, Dir Patrick Wincker)
  • Laboratoire de Bio-informatique en Génomique et Métabolisme (LABGeM, Dir David Vallenet)
  • Laboratoire de Bioinformatique pour la Génomique et la Biodiversité (LBGB, Dir Jean-Marc Aury)
  • Laboratoire de Génomique et Biochimie du Métabolisme (LGBM, Dir Véronique de Berardinis)
  • Laboratoire de Biocatalyse, Biorémédiation et Métabolisme Synthétique (L2BMS, Dir Anne Zaparucha)
  • Laboratoire de Biologie Synthétique et Systémique (LiSSB, Dir Valérie Pezo)

Recently, the emergence of new sequencing technologies has revolutionised genomics research, giving access not only to new genomes belonging to largely under-explored areas of life, but also to the global study of the biodiversity of consortia of organisms derived from environmental samples, in particular marine eukaryotes (TARA Oceans project), soil organisms (MetaTAXOMIC project), and the bacterial flora of the human gastrointestinal tract (metaHIT project). 

The deluge of de novo sequence data is also accompanied by an increase in the number of genes whose functions remain completely unknown. The Genoscope UMR has therefore decided to extend the study of genome biodiversity to the study of chemical reactions carried out by living organisms, by tackling the elucidation of the function of genes with unknown functions through systematic approaches, often on a large scale, combining genomics and experimental validation (e.g. BKACE projects). The exploitation of sequencing data and the resulting identification of biological functions, particularly in biocatalysis and synthetic biology via the diversification of the chemical capacities of living organisms, has opened up new development horizons in industrial biotechnologies. From a sustainable development perspective, the unit is looking for biological solutions in chemical synthesis to contribute to the green chemistry paradigm which aims to reduce the use of fossil fuels, pollution and energy consumption.

The research is organised around several topics which are often interconnected:

  • Evolutionary and comparative genomics of prokaryotic and eukaryotic genomes with meta-omics approaches to study communities (e.g. the global Tara Ocean project studying consortia of organisms derived from marine environmental samples).
  • Bioinformatics methods for the assembly, annotation and comparative analysis of eukaryotic genomes and expert annotation of prokaryotic genomes via the MicroScope platform.
  • In silico and experimental approaches for the elucidation of the function of genes of unknown function through the discovery of new enzymatic activities, new metabolites and discovery/completion of metabolic pathways. The unit is also concerned with the identification of degradation pathways of recalcitrant molecules such as chlordecone with a view to bioremediation.
  • Interactions between the methylome, transcriptome and bacterial virulence/adaptation to better understand the key players and epigenetic pathways to develop more effective treatments against some bacterial pathogens.
  • Large-scale in silico and experimental exploration via an enzymatic screening platform of the metabolic diversity of micro-organisms for the identification of new biocatalysts and exploitation of their chemistry for synthetic chemistry applications.
  • Diversification of the chemistry of living organisms through synthetic biology and metabolic engineering approaches for the assimilation of molecules in C1 , the valorisation of biomass by microorganisms to produce molecules of biotechnological interest or xenobiology to create new bacterial chassis with a genetic artificial information system.
  • Reconstitution of gene regulation networks involved in the morpho-spatial architecture of tissues using systems biology approaches: study of cell evolution through spatio-temporal studies combining 3D brain organoid culture strategies with functional genomics data  (team LiSSB/Sysfate).

The flood of de novo sequencing data is also accompanied by an increase in the number of genes whose functions remain totally unknown. Genoscope and the UMR have therefore decided to expand the study of the biodiversity of genomes to that of the chemical reactions conducted by the living worlds with four orientations:

This evolution is resolutely in line with a sustainable chemistry approach and contributes to the setup of chemistry using less fossil fuel, generating less pollution and consuming less energy.