Genomics of integrated systems

Presentation

Biological systems result from a complex evolutionary history, as partners and/or relationships between them may have been gained, lost or replaced during evolution. Our main research interest is to use genomic data to clarify the history that shaped key cellular process (ancestral genes, horizontal gene transfers, gene gains/losses) but also to provide functional information for experimental work. We address these issues by conducting comparative genomic analyses with phylogenomics approaches.

For several years, through different collaborations with experimental biologists, we have focused our studies on the evolution of RNA degradation and processing machineries in bacteria and archaea by conducting many phylogenomics analyses on the different partners (ribonuclease, helicases, …). More recently, we have initiated a collaboration with Peter Redder's group to understand RNase J-mediated RNA degradation in Firmicutes with S. aureus as a model organism, and to assess the contribution of secondary structures and 5' epi-transcriptomic modifications of RNA substrates to the regulation of this process. In addition to phylogenomics approaches on the partners of the degradation machinery, this project focuses on RNA substrates and requires the development of original workflows and statistical analyses to integrate the specificity of the RNA-Seq data produced by P. Redder's team.

Gwennaele Fichant Professor, UT3	Yves Quentin Researcher, CNRS	Roland Barriot Associate Professor, UT3	Petra Langendijk-Genevaux Engineer, CNRS	Tomas Caetano PhD student, UT3

Projets

Genome-wide analyses of multigenic families

RNA homeostasis in Firmicutes

RNA processing machineries in Archaea

Publications

• Hajj M+, Langendijk-Genevaux P+, Batista M, Quentin Y, Laurent S, Capeyrou R, Abdel-Razzak Z, Flament D, Chamieh H, Fichant G*, Clouet-d'Orval B*, Bouvier M.
  Phylogenetic Diversity of Lhr Proteins and Biochemical Activities of the Thermococcales aLhr2 DNA/RNA Helicase
  Biomolecules
  2021 Jun 11(7):950. doi: 10.3390/biom11070950. PMID: 34206878 (+ co-first authors, * correspondence)
• Tejada-Arranz A, Matos RG, Quentin Y, Bouilloux-Lafont M, Galtier E, Briolat V, Kornobis E, Douché T, Matondo M, Arraiano CM, Raynal B, De Reuse H.
  RNase R is associated in a functional complex with the RhpA DEAD-box RNA helicase in Helicobacter pylori
  Nucleic Acids Res.
  2021 May 49(9):5249-5264. doi: 10.1093/nar/gkab283. PMID: 33893809
• Barriot R, Latour J, Castanié-Cornet MP, Fichant G, Genevaux P.
  J-Domain Proteins in Bacteria and Their Viruses
  J Mol Biol.
  2020 Apr S0022-2836(20)30301-6. doi:10.1016/j.jmb.2020.04.014
• D.K. Phung, C. Etienne, M. Batista, P. Langendijk-Genevaux, Y. Moalic, S. Laurent, S. Liuu, V. Morales, M. Jebbar, G. Fichant, M. Bouvier, D. Flament, B. Clouet-d’Orval.
  RNA processing machineries in Archaea: the 5′-3′ exoribonuclease aRNase J of the β-CASP family is engaged specifically with the helicase ASH-Ski2 and the 3′-5′ exoribonucleolytic RNA exosome machinery
  Nucleic Acids Research
  2020 Feb
• Manon Batista1, Petra Langendijk-Genevaux1, Mirna Hajj1,Duy Khanh Phung2, Laura Plassart3, Marie Bouvier1, Gwennaële Fichant1, and Béatrice Clouet-d’Orval1*.
  The Archaeal Specific Helicase of the Ski2-like family, ASH-Ski2, is an authentic RNA helicase
  2019 Dec en préparation

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Funding

     

Alumni

Kathy DE SOUSA
Michael CHANDLER
Mathias WEYDER
Arnaud FRECHE
Virginie CALDERON
Claire GAUGAIN
Bénédicte WIRTH
Marie-Jeanne BASSE