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

Publications

• Batista M*, Langendijk-Genevaux P*, Kwapisz M, Canal I, Phung DK, Plassart L, Capeyrou R, Moalic Y, Jebbar M, Flament D, Fichant G, Bouvier M, Clouet-d'Orval B.
  Batista M, Langendijk-Genevaux P, Kwapisz M, Canal I, Phung DK, Plassart L, Capeyrou R,Evolutionary and functional insights into the Ski2-like helicase family in Archaea: a comparison of Thermococcales ASH-Ski2 and Hel308 activities
  NAR Genom Bioinform.
  2024 Mar 6(1):lqae026. doi: 10.1093/nargab/lqae026. PMID: 38500564
• Yiying Yang, Haoxiang Chen, Robin A. Corey, Violette Morales, Yves Quentin, Carine Froment, Anne Caumont-Sarcos, Cécile Albenne, Odile Burlet-Schiltz, David Ranava, Phillip J. Stansfeld, Julien Marcoux, Raffaele Ieva.
  LptM promotes oxidative maturation of the lipopolysaccharide translocon by substrate binding mimicry.
  Nature Communications
  2023 Oct
• Xu X, Usher B, Gutierrez C, Barriot R, Arrowsmith TJ, Han X, Redder P, Neyrolles O, Blower TR, Genevaux P..
  MenT nucleotidyltransferase toxins extend tRNA acceptor stems and can be inhibited by asymmetrical antitoxin binding
  Nat Commun.
  2023 Aug 14(1):4644. doi: 10.1038/s41467-023-40264-3. PMID: 37591829
• Soussan Diane, Salze Marine, Ledormand Pierre, Sauvageot Nicolas, Boukerb Amine, Lesouhaitier Olivier, Fichant Gwennaele, Rincé Alain, Quentin Yves, Muller Cécile.
  The NagY regulator: A member of the BglG/SacY antiterminator family conserved in Enterococcus faecalis and involved in virulence
  Frontiers in Microbiology
  2023 Feb doi: 10.3389/fmicb.2022.1070116
• 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)

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Funding

Alumni

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