Chromosome dynamics

Principal Investigator: Olivier ESPELI, DR2 Cnrs

Our group studies the adaptation of bacteria to changes in their environments. Although bacteria are among the simplest living organisms, formed of a single cell, they display a huge adaptability to the presence of nutrients or toxic compounds in their environment. This adaptability allows them to survive periods of nutrient depletion, treatment with antibiotics or survival within their host in the context of an infection.

The first line of adaptation goes through the modulation of gene expression. This characteristic is known for decades. Since the pioneer work of Francois Jacob, Jacques Monod and their colleagues on the lactose operon in 1961, this field has been revolutionized by the development of genomic methods. In the laboratory we use these assays to analyze the expression of thousands of genes in response to various stimuli, the binding of proteins to multiple sites on the bacterial chromosome and even the 3D folding of the chromosome in various growing conditions. More and more we and others, observe that chromosome folding and genome expression are tightly connected (Lioy et al 2018, Planchenault et al 2020). We study various aspects of the interplay between chromosome folding and gene expression; first in collaboration with the group of Olivier Rivoire (CIRB) we analyze of the role of the physics of the DNA molecule in transcription initiation and second in collaboration with Romain Koszul (Pasteur Institute, Paris) we analyze the role of transcription on long range DNA folding. A second aspect of bacterial adaptation relies in modification of the growing regime and life style of the bacteria. In the presence of a stress bacteria can halt their cell cycle to limit the extent of the damages; in the harshest conditions, some bacteria may enter in a dormancy state, where metabolic activities are limited. This state confer them a high tolerance to antibiotic for example. In other conditions bacteria cooperate to form communities, also called biofilm, that favor their adherence and tolerance to stresses.


Figure 1: Localisation of a gene (green) in the bacterial chromosome (red)

In the recent years we have observed, with commensal E. coli, that chemotherapeutics drugs such as Mitomycine C, Bleomycin or AZT severely change the cell cycle. This is linked to the sudden expression of dozen of genes from the SOS regulon. One protein from this regulon caught our attention, RecN. This protein belongs to the SMC family that also contain eukaryotic cohesins and condensins . When a particular type of DNA Damage repair is engaged, RecN is able to block chromosome segregation and to promote the regression of already segregated sister chromatids. RecN act as a DNA damage specific cohesin, this is the first bacterial cohesin described (Vickridge et al 2017). In E. coli, sister chromatid cohesion is a transient step usually mediated by topological link between sister chromatids. Our group contributed to the discovery of this topological cohesion process (Lesterlin et al 2012) and characterized some aspect of its regulation (El Sayyed et al 2016). In collaboration with the group of Romain Koszul (Pasteur Institute, Paris), we are currently studying the impact of the sister chromatid cohesion step on global chromosome folding in normal or pathological cell cycles.
Our interest for bacterial adaptation to the environment brought us to study bacterial pathogens whose environment is shaped by their host. We work with E. coli, Shigella and Listeria that are intracellular pathogens. They can survive and multiply within macrophages or epithelial cells. Adherent Invasive E. coli (AIEC) have been identified in Crohn disease patients. They colonize the digestive tract, adhere to epithelium and multiply within macrophages that are supposed to eliminate bacterial pathogens. AIEC present an original colonization of macrophages, they do not escape from the phagolytic vacuole and they do not detoxify it instead they multiply in a toxic environment (acidic, oxidative, nutrient poor). To do so they have to adapt permanently. We demonstrated that this adaptation is in two steps (Demarre et al 2020), first AIEC halt their cell cycle to become dormant for 10 hours and, during this period, they change their gene expression program to construct a protective matrix around them. Once the matrix program is initiated, bacterial multiplication start again and bacterial communities are formed (Prudent et al 2020). These intracellular bacterial communities can serve as a long-term survival niche for AIEC. In this frame, we are involved in the European Community COST action EuromicropH. Our current work explores different paths. In collaboration with the group of Nicolas Barnich at the University of Clermont Auvergne, our project evaluate the relevance of IBC during animal model infection and the available strategies to fight again these recalcitrant bacteria. In collaboration with the groups of Marie Agnès Petit (INRA, Jouy en Josas) and Ivan Matic (Cochin Institute, Paris) we are characterizing the DNA management (replication, segregation, repair of DNA) of dormant persistant bacteria.


Figure 2: Human macrophages infected by AIEC bacteria (red). The bacteria form intracellular communities inside toxic phagolysosomes labeled by Lamp1 (green)

We also study various aspects of Shigella flexneri and Listeria monocytogenes infections of epithelial cells in collaboration with the groups of Alice Lebreton (IBENS, Paris), Guy Tran Van Nhieu (ENS Paris Saclay) and Lionel Navaro (IBENS, Paris).
Our project are funded by The Agence Nationale de la Recherche , by the Labex Memolife from PSL university, the ARC foundation and the Association Francois Aupetit (AFA) and the European Community COST action EuromicropH.

Impact of chemotherapeutic drugs on E. coli growth in the absence of RecN

The E. coli chromosome is labelled with the HU-mCherry fluorescent protein, mitomycine C is  added  for 5 minutes to the growing medium then washed. The total length of the experiment is 4 hours.

Selected publications

- Conin, B., Billault-Chaumartin, I., El Sayyed, H., Quenech’Du, N., Cockram, C., Koszul, R., and Espéli, O. (2022). Extended sister-chromosome catenation leads to massive reorganization of the E. coli genome. Nucleic Acids Res gkac105.

- Prudent, V., Demarre, G., Vazeille, E., Wery, M., Quenech’Du, N., Ravet, A., Dauverd-Girault, J., van Dijk, E., Bringer, M.-A., Descrimes, M., Rimsky, S., Morillon, A., Espéli, O. (2021). The Crohn’s disease-related bacterial strain LF82 assembles biofilm-like communities to protect itself from phagolysosomal attack. Commun Biol 4, 627.

- Aubry, M., Wang, W.-A., Guyodo, Y., Delacou, E., Guignier, J.-M., Espeli, O., Lebreton, A., Guyot, F., and Gueroui, Z. (2020). Engineering E. coli for Magnetic Control and the Spatial Localization of Functions. ACS Synth Biol.

- Planchenault, C., Pons, M.C., Schiavon, C., Siguier, P., Rech, J., Guynet, C., Dauverd-Girault, J., Cury, J., Rocha, E.P., Junier, I., Cornet, F., Espéli, O. (2020). Intracellular positioning systems limit the entropic eviction of secondary replicons toward the nucleoid edges in bacterial cells. J. Mol. Biol.

- Demarre, G., Prudent, V., Schenk, H., Rousseau, E., Bringer, M.-A., Barnich, N., Tran Van Nhieu, G., Rimsky, S., De Monte, S., and Espéli, O. (2019). The Crohn’s disease-associated Escherichia coli strain LF82 relies on SOS and stringent responses to survive, multiply and tolerate antibiotics within macrophages. PLoS Pathog. 15, e1008123.

- Lioy, V.S., Cournac, A., Marbouty, M., Duigou, S., Mozziconacci, J., Espéli, O., Boccard, F., and Koszul, R. (2018), Multiscale Structuring of the E. coli Chromosome by Nucleoid-Associated and Condensin Proteins. Cell.172, 771-783.e18.

- El Sayyed, H., and Espéli, O. (2018), Mapping E. coli Topoisomerase IV Binding and Activity Sites. Methods Mol. Biol. 1703, 87–94.

- Demarre, G., Prudent, V. & Espéli, O. (2017), Imaging the Cell Cycle of Pathogen E. coli During Growth in Macrophage. Methods Mol. Biol. 1624, 227–236. 

- Vickridge, E., Planchenault, C., Cockram, C., Junceda, I.G. & Espéli, O. (2017a), Management of E. coli sister chromatid cohesion in response to genotoxic stress. Nat Commun 8, 14618.

- Vickridge, E., Planchenault, C. & Espéli, O. (2017b), Revealing Sister Chromatid Interactions with the loxP/Cre Recombination Assay. Methods Mol. Biol. 1624, 29–37.

- El Sayyed, H., Le Chat, L., Lebailly, E., Vickridge, E., Pages, C., Cornet, F., Cosentino Lagomarsino, M. & Espéli, O. (2016), Mapping Topoisomerase IV Binding and Activity Sites on the E. coli Genome. PLoS Genet. 12, e1006025.

- Lagomarsino M.C., Espéli O. & Junier I. (2015), From structure to function of bacterial chromosomes: Evolutionary perspectives and ideas for new experiments. FEBS Lett. 589, 2996–3004.

- Passot, F.M., Nguyen, H.H., Dard-Dascot, C., Thermes, C., Servant, P., Espéli, O. & and Sommer, S. (2015), Nucleoid Organization in the Radioresistant Bacterium Deinococcus radiodurans. Mol. Microbiol. 97, 759–774. 

- Junier I., Boccard F. & Espéli O. (2014), Polymer modeling of the E. coli genome reveals the involvement of locus positioning and macrodomain structuring for the control of chromosome conformation and segregation. Nucleic Acids Res. Feb 1;42(3):1461-73.

- Le Chat L. & Espéli O. (2012), Let's get 'Fisical' with bacterial nucleoid. Mol Microbiol. Dec;86(6):1285-90.

- Dame R.T., Espéli O., Grainger D.C. & Wiggins P.A. (2012), Multidisciplinary perspectives on bacterial genome organization and dynamics. Mol Microbiol. Dec;86(5):1023-30.

- Lesterlin C., Gigant E., Boccard F. & Espeli O. (2012), Sister chromatid interactions in bacteria revealed by a site specific recombination assay EMBO J, August 15. 31:3468-79.

- Espeli O., Borne R., Dupaigne P., Thiel A., Gigant E., Mercier R. & Boccard F. (2012), A MatP-divisome interaction coordinates chromosome segregation with cell division in E. coli. EMBO J, May 11. 31:3198-11.

- Possoz C., Junier I. & Espeli O. (2012), Bacterial chromosome segregation. Front Biosci 17: 1020-1034.

- Rabhi M., Espeli O., Schwartz A., Cayrol B., Rahmouni A.R., Arluison V. & Boudvillain M. (2011), The Sm-like RNA chaperone Hfq mediates transcription antitermination at Rho-dependent terminators. EMBO J, 30: 2805-2816.

- Mercier R., Petit M.A., Schbath S., Robin S., El Karoui M., Boccard F. & Espeli O. (2008), The MatP/matS site-specific system organizes the terminus region of the E. coli chromosome into a macrodomain. Cell 135(3): 475-485.

- Espeli O., Mercier R. & Boccard F. (2008), DNA dynamics vary according to macrodomain topography in the E. coli chromosome. Mol Microbiol 68(6): 1418-1427.


Group leader:
Espéli Olivier, DR1 CNRS
Senior researcher:
Rimsky Sylvie, DR2 CNRS

Postdoctoral fellows, PhD Students & Master student:
Singh Parul, Postdoctoral fellow
Borde Celine, Postdoctoral fellow
Camus Adrien, PhD student
Bruder Emma, PhD student

Technical staff:
Quenech’du Nicole, IEHC CDF