Olivier Espéli

Olivier Espéli
Collège de France · Center for Interdisciplinary Research in Biology

PhD

About

78
Publications
8,746
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Introduction
The work performed in the lab deals with chromosome dynamics in bacteria and yeast. We are analyzing changes affecting the conformation of DNA in response to stimuli such as replication, transcription and repair. Recently we focused mainly on the sister chromatid cohesion step and tried to characterize the role of specific proteins and DNA topology in the control of this key step of the cell cycle.
Additional affiliations
January 2014 - present
Collège de France
Position
  • Group Leader
January 2012 - present
CNRS - Université Paris-Sud 11
Position
  • Center for Molecular Genetics - CNRS- Paris-Sud University
February 2011 - December 2013
Center for Molecular Genetics
Position
  • Group Leader

Publications

Publications (78)
Article
Full-text available
The mechanisms that control chromosome conformation and segregation in bacteria have not yet been elucidated. In Escherichia coli, the mere presence of an active process remains an open question. Here, we investigate the conformation and segregation pattern of the E. coli genome by performing numerical simulations on a polymer model of the chromoso...
Article
Full-text available
The process of Sister Chromosome Cohesion (SCC), which holds together sister chromatids upon replication, is essential for chromosome segregation and DNA repair in eukaryotic cells. Although cohesion at the molecular level has never been described in E. coli, previous studies have reported that sister sequences remain co-localized for a period afte...
Article
Full-text available
Initiation of chromosome segregation in bacteria is achieved by proteins acting near the origin of replication. Here, we report that the precise choreography of the terminus region of the Escherichia coli chromosome is also tightly controlled. The segregation of the terminus (Ter) macrodomain (MD) involves the structuring factor MatP. We characteri...
Article
Full-text available
In bacteria, chromosome segregation occurs progressively from the origin to terminus within minutes of replication of each locus. Between replication and segregation, sister loci are held in an apparent cohesive state by topological links. The decatenation activity of topoisomerase IV (Topo IV) is required for segregation of replicated loci, yet li...
Article
Full-text available
Acute myeloid leukemia (AML) pathogenesis often involves a mutation in the NPM1 nucleolar chaperone, but the bases for its transforming properties and overall association with favorable therapeutic responses remain incompletely understood. Here we demonstrate that an oncogenic mutant form of NPM1 (NPM1c) impairs mitochondrial function. NPM1c also h...
Article
Full-text available
Patients with Crohn’s disease exhibit abnormal colonization of the intestine by adherent invasive E. coli (AIEC). They adhere to epithelial cells, colonize them and survive inside macrophages. It appeared recently that AIEC LF82 adaptation to phagolysosomal stress involves a long lag phase in which many LF82 cells become antibiotic tolerant. Later...
Preprint
Full-text available
In bacteria, chromosome segregation occurs progressively, from the origin to the terminus, a few minutes after the replication of each locus. In-between replication and segregation, sister loci are maintained in an apparent cohesive state by topological links. Whereas topoisomerase IV (Topo IV), the main bacteria decatenase, controls segregation, l...
Article
The fast-developing field of synthetic biology enables broad applications of programmed microorganisms including the development of whole-cell biosensors, delivery vehicles for therapeutics, or diagnostic agents. However, the lack of spatial control required for localizing microbial functions could limit their use and induce their dilution leading...
Preprint
Full-text available
Patients with Crohn's disease exhibit abnormal colonization of the intestine by proteobacteria, and among these bacteria, the adherent invasive E. coli (AIEC) family. They are predominant in the mucus, adhere to epithelial cells, colonize them and survive inside macrophages. We recently demonstrated that the acclimation of the AIEC strain LF82 to p...
Preprint
The fast-developing field of synthetic biology enables broad applications of programmed microorganisms including the development of whole-cell biosensors, delivery vehicles for therapeutics, or diagnostic agents. However, the lack of spatial control required for localizing microbial functions could limit their use and induce their dilution leading...
Article
Full-text available
Adherent Invasive Escherichia coli (AIEC) strains recovered from Crohn's disease lesions survive and multiply within macrophages. A reference strain for this pathovar, AIEC LF82, forms microcolonies within phagolysosomes, an environment that prevents commensal E. coli multiplication. Little is known about the LF82 intracellular growth status, and s...
Preprint
Full-text available
Adherent Invasive Escherichia coli (AIEC) strains recovered from Crohn's disease lesions survive and multiply within macrophages. A reference strain for this family, AIEC LF82, forms microcolonies within phagolysosomes, an environment that prevents commensal E. coli multiplication. Little is known about the LF82 intracellular growth status, and sig...
Article
Bacterial genomes, organized intracellularly as nucleoids, are composed of a main chromosome coexisting with different types of secondary replicons. Secondary replicons are major drivers of bacterial adaptation by gene exchange. They are highly diverse in type and size, ranging from less than 2 to more than 1000 kb, and must integrate with bacteria...
Article
Full-text available
In chromosome conformation capture experiments (Hi‐C), the accuracy with which contacts are detected varies due to the uneven distribution of restriction sites along genomes. In addition, repeated sequences or homologous regions remain indistinguishable because of the ambiguities they introduce during the alignment of the sequencing reads. We addre...
Article
As in eukaryotes, bacterial genomes are not randomly folded. Bacterial genetic information is generally carried on a circular chromosome with a single origin of replication from which two replication forks proceed bidirectionally toward the opposite terminus region. Here, we investigate the higher-order architecture of the Escherichia coli genome,...
Chapter
This methods article described a protocol aiming at mapping E. coli Topoisomerase IV (Topo IV) binding and cleavage activity sites on the genome. The approach is readily applicable to any Type II topoisomerase on a broad variety of gram-positive and gram-negative bacterial species. Conventional ChIP-seq of flag tagged Topo IV subunits and a novel m...
Chapter
Sister chromatid cohesion is a transient state during replication in bacteria. It has been recently demonstrated that the extent of contact between cohesive sisters during the cell cycle is dependent on topoisomerase IV activity, suggesting that topological links hold sister chromatids together. In the present protocol, we describe a simple method...
Chapter
The study of the bacterial cell cycle at the single cell level can not only give insights on the fitness of the bacterial population but also reveal heterogeneous behavior. Typically, the DNA replication, the cell division, and the nucleoid conformation are appropriate representatives of the bacterial cell cycle. Because bacteria rapidly adapt thei...
Article
Full-text available
Aberrant DNA replication is a major source of the mutations and chromosomal rearrangements associated with pathological disorders. In bacteria, several different DNA lesions are repaired by homologous recombination, a process that involves sister chromatid pairing. Previous work in Escherichia coli has demonstrated that sister chromatid interaction...
Data
Segregated sister foci come back together upon MMC treatment. Representative timelapse video of wild type sister foci dynamics in response to 10μg/ml MMC. Cells were dropped on an agarose pad containing 10μg/ml MMC. One picture was taken every 3min for 2h.
Data
Segregated sister foci do not merge back together in a recN mutant. Representative timelapse video of sister foci in a recN mutant, in response to MMC treatment. One picture was taken every 3min for 2h.
Data
Nucleoid merging and foci regression are concomitant events. Representative timelapse video of sister foci and brother nucleoids coming together in response to 10μg/ml MMC treatment.
Data
Microfluidic movie of wild type cells. Representative timelapse video of a microfluidic experiment in a WT strain. Fresh medium was perfused for 20 min prior to a 10 min MMC perfusion. Cells were then washed with clean minimum medium A and imaging was carried on for 3 hours.
Data
Supplementary Figures, Supplementary Tables, and Supplementary Methods and Supplementary References
Data
Microfluidic movie of recN mutants. Representative timelapse video of a microfluidic experiment in a recN mutant strain. Fresh medium was perfused for 20 min prior to a 10 min MMC perfusion. Cells were washed with clean minimum medium A and imaging was carried on for 3 hours. One image was acquired every 3 min.
Book
This volume presents state-of-the-art protocols for key experiments that have revolutionized our understanding of the bacterial nucleoid. This book is divided into five parts: Part I introduces molecular genetic methods to study bacterial nucleoids; Part II highlights the study of bacterial nucleoid with whole genome analysis method; Part III discu...
Conference Paper
The central goal of the Biology and Physics of the Bacterial Chromosome Conference is to construct an integrated model of chromosome structure and function in the context of the living bacterial cell. This goal can only be realized through a multi-disciplinary approach and close collaboration. In the recent years, collaborations between biologists...
Article
Full-text available
Catenation links between sister chromatids are formed progressively during DNA replication and are involved in the establishment of sister chromatid cohesion. Topo IV is a bacterial type II topoisomerase involved in the removal of catenation links both behind replication forks and after replication during the final separation of sister chromosomes....
Data
A) Genome browser magnifications illustrating common non specific signal observed over rRNA operon, IS sequences in the NorflIP and ChIP-seq experiments. ParE-Flag NorflIP is represented in purple, MatP-Flag ChIP-seq is represented in blue, Mock IP with a strain that did not contained Flag tagged proteins is represented in black. Genomic localizati...
Data
Measure of the distance between two adjacent Topo IV cleavage sites in the dif region (A) and the region containing oriC and SNAP2 (B). For this analysis the 571 Topo IV cleavage sites observed in the 3 experiments were pooled. C) Distribution of the Topo IV cleavages inside genes and intergenic regions. The gene sizes were normalized to 1. D) RSAT...
Data
Flow cytometry analysis of the synchronization experiment. Samples were fixed in ethanol at different time points: after 1h30 at 40°C (G1), 20 min after downshift to 30°C (S20), 40 min after downshift to 30°C (S40), 60 min after downshift to 30°C (G2) and in stationary phase. (PDF)
Data
A) Measure of the colony formation unit (CFU) of the WT, nalR, ParC-Flag, ParC-Flag nalR and ParE-Flag nalR strains. Culture were grown until OD 0.2 and treated for 40 minutes with norfloxacin 2μM and plated on LB plates. B) Measure of the growth rate of the nalR, ParC-Flag nalR and ParE-Flag nalR strains. C) Southern blot analysis of Topo IV media...
Data
Genome browser magnifications illustrating common non-specific signal observed over rRNA operons, tRNA and IS sequences. ParE-Flag ChIP-seq is represented in red, MatP-Flag ChIP-seq is represented in blue, Mock IP with a strain that did not contain Flag tagged proteins is represented in black. Genes, ribosomal operons and tRNA are represented below...
Data
A) Analysis of the Topo IV nonspecific binding. Normalized enrichment (Average number of reads in a 1kb sliding window divided by the total amount of reads) of each flag immuno-precipitation experiment was plotted as a function of the genomic position. Left panel a 100 kb region near oriC (positions 4.26 to 4.36 Mb) is represented. Right panel a 10...
Data
A) Distribution of ParE-Flag 1 ChIP-seq enrichment in the region overlapping or not a H-NS binding site. B) Box plot of the distribution of GC% in the regions depleted for Topo IV (IP/input <0.6) or enriched for Topo IV (IP/input >1.2) or enriched for H-NS. C) Distribution of the GC% in 172 validated Topo IV cleavage sites as function of NorflIP IP...
Data
A) Analysis of the robustness of the Topo IV-XerC-dif complex in the presence of increasing amounts of XerD protein. EMSA were performed with prebound Topo IV and XerC on dif and subsequent addition of XerD for 10 minutes before loading on the gel. B) Analysis of Topo IV binding to negatively supercoiled plasmid by EMSA on agarose gel. Topo IV from...
Data
A) Southern Blot analysis of Topo IV cleavage in the nalR strain at dif and an ectopic dif site located at 1.3Mb on the genomic map. B) Southern Blot analysis of Topo IV cleavage on a plasmid (pFC25) carrying the dif region (10 kb around dif) + or–dif (PDF)
Data
Sheet 1) Validated ChIP-seq sites. Sheet 2) NorflIP sites observed in the ParC-Flag 1 NorflIP, ParE-Flag NorflIP and ParC-Flag 2 NorflIP. Sheet 3) Common NorflIP sites for the different experiments. Sheet 4) Manually Validated Topo IV cleavages. (XLSX)
Data
A) Snapshots of the ChIP-seq and NorflIP experiments at the position 1.85 and 1.92 Mb. Topo IV binding to position 1.85 Mb was only revealed by the ChIP-seq experiment in the presence of formaldehyde. Topo IV cleavage at position 1.92 Mb was only revealed by the NorflIP experiment. NorflIP peaks present a characteristic shape illustrated on the 1.9...
Data
A) Box plot of the distribution of distance between TopoIV cleavages and the closest highly expressed transcription unit (T.U.). For this analysis the 571 Topo IV cleavage sites observed in the 3 experiments were pooled. T.U. expression was determined by RNAseq. An arbitrary threshold was set to 500 reads, it corresponds to the 10% of the T.U. the...
Data
Model to test the correlation between TopoIV binding and the progression of replication. To test if ParC and ParE ChIP-seq biases were related to chromosome replication we constructed in silico models The result of this null model is that in all cases (overlapping or non-overlapping rounds) the observed mean occupancy should follow the dosage. Henc...
Article
The link between chromosome structure and function is a challenging open question because chromosomes in vivo are highly dynamic and arduous to manipulate. Here, we examine several promising approaches to tackle this question specifically in bacteria, by integrating knowledge from different sources. Toward this end, we first provide a brief overvie...
Article
Responsable : Olivier Espeli Recherche Notre laboratoire s’interesse a l’analyse de l’evolution de la structure et de l’expression des chromosomes en reponse a des stimuli ou des stress dont l’origine est le cytoplasme ou l’environnement. Nous utilisons une combinaison de methodes de genetique, genomique et biologie cellulaire pour decrire ces chan...
Article
Processes favoring the exceptional resistance to genotoxic stress of Deinococcus radiodurans are not yet completely characterized. It was postulated that its nucleoid and chromosome(s) organization could participate in the DNA double strand break repair process. Here, we investigated the organization of chromosome 1 by localization of three chromos...
Article
The mechanisms driving bacterial chromosome segregation remain poorly characterized. While a number of factors influencing chromosome segregation have been described in recent years, none of them appeared to play an essential role in the process comparable to the eukaryotic centromere / spindle complex. The research community involved in bacterial...
Article
The E. coli chromosome is condensed into insulated regions termed macrodomains (MDs), which are essential for genomic packaging. How chromosomal MDs are specifically organized and compacted is unknown. Here, we report studies revealing the molecular basis for Terminus-containing (Ter) chromosome condensation by the Ter-specific factor MatP. MatP co...
Article
Bacterial genomes are organized by a plethora of chromatin proteins and physical mechanisms. This organization appears to be hierarchical with DNA folding events at the nm scale influencing higher levels of chromosome organization. Besides acting in shaping the genome these factors also play important regulatory roles in numerous DNA transactions....
Data
Tolerance to Large Inversions within a Replichore Nucleoid and cell analyses of strains carrying intrareplichore inversions between NSright and Ori MD (strain Intra O-NSright2), between NSright and Right MD in a strain deleted for TerH and TerI (strain Intra R-NSright3 ΔTerHI), and between NSleft and Left MD (Intra L-NSleft1). Nucleoid and cell ana...
Data
Physiology of the R127-LC13-BO-NSR transposed strain. (A) Cells were grown until OD 0.2 in LB, fixed and DNA stained with DAPI as described before (Esnault et al., 2007). Percentage of cells in each size category according to their number of nucleoids in the wild type strain (left) and the transposed LC13-R127-BONSR strain (right). Coloured horizon...
Data
Imbalance of Replication Arms Nucleoid and cell analyses of strains carrying chromosomes with various levels of imbalance. These inverted configurations were obtained upon interreplichore inversions. For each strain, the genetic map of the chromosome in the inverted configuration is shown. The level of imbalance is indicated above the map, the colo...
Data
Coefficient diffusion of chromosomal markers. (DOCX)
Data
PCR reactions to control the transposition reaction generating strain LC13-R127-BO-NSR. (A) Schematic map of att sites in strain LC13-R127 before and after transposition. To control the result of the transposition reaction, 5 pairs of primers flanking the att sites were used (black arrows). Pairs 1 and 2 amplify respectively the attB and attR sites...
Data
parS tags used in this study. (DOCX)
Data
Long range interactions measured by excisive recombination. (DOC)
Article
Full-text available
The organization of the Escherichia coli chromosome into a ring composed of four macrodomains and two less-structured regions influences the segregation of sister chromatids and the mobility of chromosomal DNA. The structuring of the terminus region (Ter) into a macrodomain relies on the interaction of the protein MatP with a 13-bp target called ma...
Article
Full-text available
Dividing cells have mechanisms to ensure that their genomes are faithfully segregated into daughter cells. In bacteria, the description of these mechanisms has been considerably improved in the recent years. This review focuses on the different aspects of bacterial chromosome segregation that can be understood thanks to the studies performed with m...
Article
Full-text available
In Escherichia coli, the essential motor protein Rho promotes transcription termination in a tightly controlled manner that is not fully understood. Here, we show that the general post-transcriptional regulatory protein Hfq associates with Rho to regulate Rho function. The Hfq:Rho complex can be further stabilized by RNA bridging both factors in a...
Article
Full-text available
La grande taille des chromosomes comparée à la dimension des cellules impose une compaction des molécules d'ADN. Ainsi, le facteur de compaction du génome de cellules eucaryotes est de l'ordre de 10 5 et celui de cellules procaryotes de l'ordre de 10 3 [1]. Cette compaction doit néanmoins permettre le bon déroulement des processus méta-boliques ass...
Article
The organization of the Escherichia coli chromosome into insulated macrodomains influences the segregation of sister chromatids and the mobility of chromosomal DNA. Here, we report that organization of the Terminus region (Ter) into a macrodomain relies on the presence of a 13 bp motif called matS repeated 23 times in the 800-kb-long domain. matS s...
Article
The organization of the Escherichia coli chromosome has been defined genetically as consisting of four insulated macrodomains and two less constrained regions. Here we have examined the movement of chromosomal loci by tracking fluorescent markers in time-lapse microscopy during a complete cell cycle. Analysing the positioning, the segregation patte...
Article
Full-text available
Chromosome organizations of related bacterial genera are well conserved despite a very long divergence period. We have assessed the forces limiting bacterial genome plasticity in Escherichia coli by measuring the respective effect of altering different parameters, including DNA replication, compositional skew of replichores, coordination of gene ex...
Data
Full-text available
Phenotypic Analysis of Strains Carrying a Chromosome with an Intrareplichore Inversion between the Right and Ter MDs (A–D) show cells from strain Intra R-T1 in the inverted configuration; and (E) shows colonies of strain Intra R-T2. (A) Microscopic phase contrast image of fixed cells. (B) Microscopic fluorescence image of fixed cells expressing gfp...
Data
Full-text available
Intrareplichore Inversion between the Right and Ter MDs The genetic map of the chromosome in the inverted configuration is shown for strain Intra R-T4 carrying intrareplichore inversion between Ter and Right MDs. The MDs (Ori in green, Right in red, Left in blue, and Ter in cyan), the ten Ter sites (from A to J), oriC, migS, and dif are indicated....
Data
Full-text available
Intrareplichore Inversions between the Right and Ori MDs (A) The genetic map of chromosome in the inverted configuration is shown for strain Intra O-R6 ΔTerHI. (B) The genetic map of chromosome in the inverted configuration is shown for strain Intra O-R7 ΔTerHI. (C) The genetic map of chromosome in the inverted configuration is shown for strain Int...
Article
Recent advances in fluorescent microscopy have revealed the non-random organization of chromosomes in bacterial cells. In Escherichia coli, segments included in two large regions show similar localization patterns allowing the definition of two macrodomains centered, respectively, on the centromere-like site migS (the Ori domain) and the replicatio...
Article
The biochemical steps by which bacterial topoisomerases alter the topology of DNA are well known. However, it has been a more vexing task to establish physiological roles and sites of action of the different topoisomerases within the context of the bacterial cell cycle. This difficulty can be attributed in part to the redundancy among the activitie...
Article
Full-text available
FtsK and topoisomerase (Topo) IV are both involved in chromosome segregation in Escherichia coli. The former protein resides at the septal ring and is required for resolution of chromosome dimers. The latter protein is the chromosomal decatenase. We have demonstrated recently that Topo IV activity is concentrated at the septal proximal regions of t...
Article
SetB was identified as a high-copy suppressor of the partition defect of a mutation in parC, encoding one of the subunits of topoisomerase IV. Deletion of this integral inner membrane protein causes a delay in chromosome segregation, whereas its overproduction causes nucleoid disintegration and stretching, leading to a cell division defect. setB de...
Article
We isolated a mutant allele of dnaX, encoding the tau and gamma subunits of the DNA polymerase III holoenzyme, that causes extreme cell filamentation but does not affect either cell growth or DNA replication. This phenotype results from a defect in daughter chromosome decatenation during rapid growth. In these cells, ParC, one subunit of topoisomer...