Olivier Espéli

Le Centre interdisciplinaire de recherche en biologie (CIRB), créé en 2009 à l’initiative d’Alain Prochiantz, est situé sur le site Marcelin Berthelot du Collège de France. Le CIRB est actuellement composé de 18 équipes, dont les thématiques de recherche couvrent aussi bien la microbiologie, la biologie cellulaire, la biologie du développement, les neurosciences et l’évolution que la biologie du cancer. Le CIRB offre un environnement intégré et original pour mener des recherches sur des quest...

Recherche Page web : https://www.college-de-france.fr/chromosome-dynamics. Notre groupe étudie l’adaptation des bactéries aux changements de leur environnement. Bien que les bactéries soient parmi les organismes vivants les plus simples, formés d’une seule cellule, elles font preuve d’une énorme capacité d’adaptation à la présence de nutriments ou de composés toxiques dans leur environnement. Cette capacité d’adaptation leur permet de survivre à des périodes d’épuisement des nutriments, à des...

During transcription, RNA polymerase (RNAP) continuously unwinds and rewinds DNA, generating negative and positive supercoils upstream and downstream, respectively. Using single-particle cryo-EM, we elucidated how bacterial RNAP and DNA topoisomerase I (TopoI), which relaxes negative supercoils, operate in close spatial proximity. TopoI binds to relaxed DNA upstream of RNAP, and this involves a conformational switch in the TopoI functional domains. This suggests that TopoI exerts a sensing role before the formation of negative supercoils. On DNA substrates mimicking negatively supercoiled DNA, TopoI threads one strand into the active site for cleavage and binds the complementary strand with an auxiliary domain. Transcriptomic and phenotypic analyses suggest that mutations affecting conformational changes in TopoI impact gene expression and operon polarity in bacteria. In summary, we propose a comprehensive model for DNA relaxation in the proximity of active bacterial transcription.

Patients with Crohn's disease exhibit abnormal intestinal colonization by Proteobacteria, particularly adherent-invasive Escherichia coli (AIEC). These bacteria predominate in the mucus, adhere to epithelial cells, colonize them, and survive inside macrophages. We recently demonstrated that the AIEC strain LF82 adapts to phagolysosomal stress through a two-step process: initial replication arrest generating stress-tolerant persisters, followed by the resumption of replication, leading to the formation of intracellular bacterial communities (IBCs) embedded in a biofilm-like matrix. Given the significant genomic diversity among strains with the AIEC phenotype, we performed a comparative genomic and functional analysis of 13 AIEC isolates from Crohn's disease patients in France and Spain. Our results demonstrate that IBCs are replicative niches for all AIEC strains within THP-1 macrophages, yet their formation relies on distinct mechanisms, including variations in phagosome detoxification, biofilm architecture, and macrophage responses. Our study identifies a strong positive correlation between vacuole acidification and persister induction, which underlies the intracellular survival of the different strains. Furthermore, we revealed distinct AIEC dissemination strategies outside macrophages, potentially contributing to the propagation of inflammation in the human host. These findings highlight that research on pathogens and pathobionts with dynamic genomes should extend beyond classical bacterial models.

In September 2023, the Biology and Physics of Prokaryotic Chromosomes meeting ran at the Lorentz Center in Leiden, The Netherlands. As part of the workshop, those in attendance developed a series of discussion points centered around current challenges for the field, how these might be addressed, and how the field is likely to develop over the next 10 years. The Lorentz Center staff facilitated these discussions via tools aimed at optimizing productive interactions. This Perspective article is a summary of these discussions and reflects the state‐of‐the‐art of the field. It is expected to be of help to colleagues in advancing their own research related to prokaryotic chromosomes and inspiring novel interdisciplinary collaborations. This forward‐looking perspective highlights the open questions driving current research and builds on the impressive recent progress in these areas as represented by the accompanying reviews, perspectives, and research articles in this issue. These articles underline the multi‐disciplinary nature of the field, the multiple length scales at which chromatin is studied in vitro and in and highlight the differences and similarities of bacterial and archaeal chromatin and chromatin‐associated processes.

Topoisomerases are the main enzymes capable of resolving the topological constraints imposed by DNA transactions such as transcription or replication. All bacteria possess topoisomerases of different types. Although bacteria with circular replicons should encounter similar DNA topology issues, the distribution of topoisomerases varies from one bacterium to another, suggesting polymorphic functioning. Recently, several proteins restricting, enhancing or modifying the activity of topoisomerases were discovered, opening the way to a new area of understanding DNA topology management during the bacterial cell cycle. In this review, we discuss the distribution of topoisomerases across the bacterial phylum and current knowledge on the interplay among the different topoisomerases to maintain topological homeostasis.

When DNA is transcribed to RNA, the DNA double helix is constantly unwound and rewound to provide access for RNA polymerase (RNAP). This induces DNA supercoiling as a function of transcript length due to over- and under-twisting of the DNA downstream and upstream of RNAP, respectively. Using single-particle cryo-EM and in vivo assays we investigated the relationship between bacterial RNAP and DNA Topoisomerase I (TopoI), which removes negative supercoils accumulating upstream of RNAP. TopoI binds to relaxed DNA upstream of RNAP in a manner suggesting a sensory role awaiting the formation of negative supercoils and involving a conformational switch in the functional domains of TopoI. On DNA substrates mimicking negatively supercoiled DNA, TopoI threads one strand into the active site for cleavage while binding the complementary strand with an auxiliary domain. We propose a comprehensive model for DNA relaxation in the context of a transcribing RNAP.

Patients with Crohn’s disease exhibit abnormal colonization of the intestine by Proteobacteria, particularly the adherent-invasive Escherichia coli (AIEC) group. These bacteria are predominant in the mucus, adhere to epithelial cells, colonize them, and survive inside macrophages. We recently demonstrated that the acclimation of strain LF82 to phagolysosomal stress occurs in two distinct steps: first, a replication halt producing stress- tolerant persisters, and second, a replication phase that leads to the formation of Intracellular Bacterial Communities (IBC) organized with a biofilm-like matrix. Given the significant genomic diversity among strains with the AIEC phenotype, we conducted a comparative analysis of the genomes and macrophage colonization characteristics of 13 AIEC strains collected from patients during a clinical study conducts by the CHU of Clermont-Ferrand. Our results demonstrate that IBCs serve as replicative niches for all AIEC strains within macrophages. However, these strains form IBCs using different strategies, including varying levels of phagosome detoxification, distinct biofilm characteristics, and diverse macrophage responses. Our study reveals a strong positive correlation between vacuole acidification and persister induction that explains intracellular survival of the different strains. In addition, we revealed distinct AIEC dissemination strategies outside macrophages, which may contribute to the propagation of inflammation in the human host. These findings highlight that research on pathogens and pathobionts with plastic genomes should not rely solely on a few laboratory models.

Transcription generates local topological and mechanical constraints on the DNA fiber, leading to the generation of supercoiled chromosome domains in bacteria. However, the global impact of transcription on chromosome organization remains elusive, as the scale of genes and operons in bacteria remains well below the resolution of chromosomal contact maps generated using Hi-C (~5–10 kb). Here we combined sub-kb Hi-C contact maps and chromosome engineering to visualize individual transcriptional units. We show that transcriptional units form discrete three-dimensional transcription-induced domains that impose mechanical and topological constraints on their neighboring sequences at larger scales, modifying their localization and dynamics. These results show that transcriptional domains constitute primary building blocks of bacterial chromosome folding and locally impose structural and dynamic constraints.

Le Centre interdisciplinaire de recherche en biologie (CIRB), créé en 2009 à l’initiative d’Alain Prochiantz, est situé sur le site Marcelin Berthelot du Collège de France. Le CIRB est actuellement composé de 18 équipes, dont les thématiques de recherche couvrent aussi bien la microbiologie, la biologie cellulaire, la biologie du développement, les neurosciences et l’évolution que la biologie du cancer. Le CIRB offre un environnement intégré et original pour mener des recherches sur des quest...