2025
Summary
- It is with deep sadness that we inform you of the passing of Jean-Luc Férat, which occurred on Friday, January 3, 2025.
It is with deep sadness that we inform you of the passing of Jean-Luc Férat, which occurred on Friday, January 3, 2025.
It was with great sadness that we learned of the death of our colleague Jean-Luc Ferat on January 3, at the age of 59, after a 10-year fight against cancer. During these years, Jean-Luc showed extraordinary courage in continuing his teaching and research.
Recruited by the University of Versailles Saint-Quentin-en-Yvelines in 1997, Jean-Luc Ferat was appointed Professor of Molecular Biology and Genetics at the UFR Sciences du Vivant of the Université Paris Cité in September 2022. Throughout his career, he has pursued his research and teaching activities with passion and determination.
Jean-Luc’s research in bacterial biology and molecular genetics has always included a phylogenetic and bioinformatics component, which he has never abandoned and which makes his work so original. During his thesis at the CGM in Gif/Yvette, under the supervision of François Michel, he discovered the presence of group II introns in bacteria, at the origin of the eukaryotic RNA splicing machinery. He then worked with Nancy Kleckner at Harvard University on the coordination between replication initiation and the cell cycle in Escherichia coli.
Back in France at the CGM in 2001, Jean-Luc developed an original approach to comparing organisms based on the presence of protein domains. This enabled him to propose the existence of links between genes involved in DNA maintenance and the methylation machinery of certain bacteria, links that were confirmed experimentally by other teams. Using the same approach, Jean-Luc identified the ancestral protein responsible for bacterial replicative helicase activity at initiation, DciA, and experimentally confirmed his discovery. Then, as part of François-Xavier Barre’s team at I2BC, he showed that DciA ensures bidirectionality of replication initiation and that unidirectional initiation leads to a topological catastrophe, suggesting why initiation is bidirectional in all 3 domains of life. This is the work he has been developing since joining Marie-Noëlle Prioleau’s team at the Institut Jacques Monod.
Jean-Luc applied the same high standards to his teaching as to his research. At the Université de Versailles Saint-Quentin-en-Yvelines, Jean-Luc taught in all years of training. In particular, he was in charge of the first-year students in Biochemistry and Molecular Biology for about ten years. He has initiated or participated in the creation of a large number of courses from L1 to M2. In particular, he has been a driving force behind the creation of courses combining molecular biology, genomics, genetics, bioinformatics and phylogeny.
Thanks to this multidisciplinary approach, he played a key role in the creation of the first master’s degree in “Bioinformatics and Genomics”. As part of the merger of the Master’s programs of the 3 sites UEVE, UVSQ and the Faculty of Science Orsay under the banner of the Université Paris-Saclay, he was also behind the creation and inauguration in 2015 of an original Master’s program entitled “Biodiversity, Genomics and the Environment”. To achieve this, he was able to convince and involve members of AgroParisTech and INRAE. He was in charge of this program until 2022 when he was recruited by the Université Paris Cité. After his new appointment as university professor, Jean-Luc immediately became involved in the teaching teams, sharing his experience and scientific vision and contributing to the development of certain courses. He was also a driving force behind the revision of the L3 molecular biology courses and the changes to the BMC Masters curriculum, making a significant contribution to the improvement of the curricula.
Jean-Luc was passionate about his work and eager to share his scientific enthusiasm. He cared about the future of his students and guided them with a rigor that pushed them to be the best they could be. His vast scientific knowledge led to discussions that were often passionate and fascinating. We will also remember him for his general knowledge, his concern for the common good, and his freedom of thought.
Finally, for almost 10 years, Jean-Luc faced his illness with great clarity, strength of character and admirable courage. He spent his last moments caring for his daughter, his family, his students and his colleagues.
Our thoughts are with his daughter and his family, to whom we offer our full support and our sincerest condolences.
Regulation of DNA Topology in Archaea: State of the Art and Perspectives
How do Archaea manage entangled DNA in their cells? This review summarizes current knowledge of the molecular mechanisms involved, with a focus on topoisomerases, and explores future research directions to address this fundamental question.
DNA topology is a direct consequence of the double helical nature of DNA and is defined by how the two complementary DNA strands are intertwined. Virtually every reaction involving DNA is influenced by DNA topology or has topological effects. It is therefore of fundamental importance to understand how this phenomenon is controlled in living cells. DNA topoisomerases are the key actors dedicated to the regulation of DNA topology in cells from all domains of life. While significant progress has been made in the last two decades in understanding how these enzymes operate in vivo in Bacteria and Eukaryotes, studies in Archaea have been lagging behind. This review article aims to summarize what is currently known about DNA topology regulation by DNA topoisomerases in main archaeal model organisms. These model archaea exhibit markedly different lifestyles, genome organization and topoisomerase content, thus highlighting the diversity and the complexity of DNA topology regulation mechanisms and their evolution in this domain of life. The recent development of functional genomic assays supported by next-generation sequencing now allows to delve deeper into this timely and exciting, yet still understudied topic.
More information: http://doi.org/10.1111/mmi.15328
Contact : Tamara BASTA <tamara.basta@i2bc.paris-saclay.fr>
Epigenetic control of T-DNA during transgenesis and pathogenesis
T-DNAs are mobile elements transferred from pathogenic Agrobacterium to plants that reprogram host cells into hairy roots or tumors, and which are used as disarmed forms to deliver transgenes in plants. Here we review the mechanisms that silence the expression of T-DNAs in transgenic plants as well as during pathogenesis.
Mobile elements known as T-DNAs are transferred from pathogenic Agrobacterium to plants and reprogram the host cell to form hairy roots or tumors. Disarmed nononcogenic T-DNAs are extensively used to deliver transgenes in plant genetic engineering. Such T-DNAs were the first known targets of RNA silencing mechanisms, which detect foreign RNA in plant cells and produce small RNAs that induce transcript degradation. These T-DNAs can also be transcriptionally silenced by the deposition of epigenetic marks such as DNA methylation and the dimethylation of lysine 9 (H3K9me2) in plants. Here, we review the targeting and the roles of RNA silencing and DNA methylation on T-DNAs in transgenic plants as well as during pathogenesis. In addition, we discuss the crosstalk between T-DNAs and genome-wide changes in DNA methylation during pathogenesis. We also cover recently discovered regulatory phenomena, such as T-DNA suppression and RNA silencing-independent and epigenetic-independent mechanisms that can silence T-DNAs. Finally, we discuss the implications of findings on T-DNA silencing for the improvement of plant genetic engineering.
More information: https://academic-oup-com.insb.bib.cnrs.fr/plphys/advance-article/doi/10.1093/plphys/kiae583/7876130
Contact : Angélique DELERIS <angelique.deleris@i2bc.paris-saclay.fr>