François-Xavier Barre

François-Xavier Barre
French National Centre for Scientific Research | CNRS · Institute for Integrative Biology of the Cell

PhD

About

148
Publications
10,173
Reads
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4,126
Citations
Additional affiliations
January 2002 - December 2004
Université Toulouse III - Paul Sabatier
Position
  • Principal Investigator
January 2005 - January 2015
French National Centre for Scientific Research
Position
  • Principal Investigator
January 1999 - December 2001
University of Oxford

Publications

Publications (148)
Article
Full-text available
Vibrio cholerae harbours a primary chromosome derived from the monochromosomal ancestor of the Vibrionales (ChrI) and a secondary chromosome derived from a megaplasmid (ChrII). The coordinated segregation of the replication terminus of both chromosomes (TerI and TerII) determines when and where cell division occurs. ChrI encodes a homologue of Esch...
Article
Full-text available
Replication is initiated bidirectionally in the three domains of life by the assembly of two replication forks at an origin of replication. This is made possible by the recruitment of two replicative helicases to a nucleoprotein platform built at the origin of replication with the initiator protein. The reason why replication is initiated bidirecti...
Preprint
The cellular arrangement and segregation choreography of the genetic material is involved in the timing of assembly and cellular positioning of the cell division apparatus in bacteria. Key to this mode of regulation is the positioning of sister copies of the replication terminus zone (ter) of the chromosomes at the end of the replication cycle. The...
Article
Full-text available
Vibrio cholerae, the causative agent of cholera epidemics, is a rod-shaped bacterium with a highly polarized cellular organization. It can survive harmful growth conditions by entering a non-proliferating spheroplast state, which involves loss of the cell envelope and polarity. How polarized rod organization cells are formed when the spheroplasts e...
Article
Full-text available
Introduction DNA damage repair (DDR) is an essential process for living organisms and contributes to genome maintenance and evolution. DDR involves different pathways including Homologous recombination (HR), Nucleotide Excision Repair (NER) and Base excision repair (BER) for example. The activity of each pathway is revealed with particular drug ind...
Article
Full-text available
The chromosome dimer resolution machinery of bacteria is generally composed of two tyrosine recombinases, XerC and XerD. They resolve chromosome dimers by adding a crossover between sister copies of a specific site, dif. The reaction depends on a cell division protein, FtsK, which activates XerD by protein-protein interactions. The toxin-linked cry...
Article
Full-text available
Partition systems are widespread among bacterial chromosomes. They are composed of two effectors, ParA and ParB, and cis acting sites, parS, located close to the replication origin of the chromosome (oriC). ParABS participate in chromosome segregation, at least in part because they serve to properly position sister copies of oriC. A fourth element,...
Article
Full-text available
About 10% of bacteria have a multi-chromosome genome with a primary replicon of bacterial origin, called the chromosome, and other replicons of plasmid origin, the chromids. Studies on multi-chromosome bacteria revealed potential points of coordination between the replication/segregation of chromids and the progression of the cell cycle. For exampl...
Preprint
Full-text available
Many mobile elements take advantage of the highly-conserved chromosome dimer resolution system of bacteria, Xer. They participate in the transmission of antibiotic resistance and pathogenicity determinants. In particular, the toxin-linked cryptic satellite phage (TLCΦ) plays an essential role in the continuous emergence of new toxigenic clones of t...
Article
Full-text available
Vibrio cholerae , the agent of the deadly human disease cholera, propagates as a curved rod-shaped bacterium in warm waters. It is sensitive to cold, but persists in cold waters under the form of viable but non-dividing coccoidal shaped cells. Additionally, V. cholerae is able to form non-proliferating spherical cells in response to cell wall damag...
Article
Full-text available
Sister chromatid interactions are a key step to ensure the successful segregation of sister chromatids after replication. Our knowledge about this phenomenon is mostly based on microscopy approaches, which have some constraints such as resolution limit and the impossibility of studying several genomic positions at the same time. Here, we present a...
Preprint
A general survival strategy of many life forms faced with harmful growth conditions is to enter into a non-proliferating state until conditions suitable for growth are restored. In bacteria, this survival strategy is associated with antimicrobial tolerance, chronic infections and environmental dispersion. In particular, the agent of the deadly huma...
Article
Sister-chromatid cohesion describes the orderly association of newly replicated DNA molecules behind replication forks. It plays an essential role in the maintenance and faithful transmission of genetic information. Cohesion is created by DNA topological links and proteinaceous bridges, whose formation and deposition could be potentially affected b...
Preprint
Sister-chromatid cohesion describes the orderly association of newly-replicated DNA molecules behind replication forks. It plays an essential role in the maintenance and the faithful transmission of genetic information. It is created by DNA topological links and proteinaceous bridges, whose formation and deposition could be potentially affected by...
Article
Full-text available
Significance Cholera toxin, the principal virulence factor of Vibrio cholerae , is encoded in the genome of an integrative mobile element exploiting Xer (IMEX), CTXΦ. Nontoxigenic strains generally lack a suitable CTXΦ attachment site. In addition, CTXΦ integration is intrinsically irreversible. Nevertheless, new epidemic clones carrying potentiall...
Article
Full-text available
Bacterial chromosomes harbour a unique origin of bidirectional replication, oriC. They are almost always circular, with replication terminating in a region diametrically opposite to oriC, the terminus. The oriC-terminus organisation is reflected by the orientation of the genes and by the disposition of DNA-binding protein motifs implicated in the c...
Article
Many organisms have established symbiotic relationships with acquired mobile genetic elements (MGEs) integrated in their genomes (1). MGEs spread among genomes within and across microbial species through horizontal gene transfer and, once integrated into host chromosome, are disseminated vertically to the progeny, causing rapid evolution of drug re...
Article
Full-text available
It was recently reported that the recBC mutants of Escherichia coli, deficient for DNA double-strand break (DSB) repair, have a decreased copy number of their terminus region. We previously showed that this deficit resulted from DNA loss after post-replicative breakage of one of the two sister-chromosome termini at cell division. A viable cell and...
Data
Percentages of cells with zero, one or two foci in different mutants. (PDF)
Data
Time-lapse microscopy of recB cells. Cells were mounted on an M9 glucose agarose pad and incubated at 30°C on the microscope stage. Images were captured every 10 min. The dif/terC region of chromosome is visualized as a green fluorescent focus by binding of GFP-ParBpMT1 protein to ydeV::parSpMT1. All frames are labelled. The double white arrows ind...
Data
Percentage of cells with zero, one or two foci, ratio of initial events and of inherited events are independent of strain background (see Materials and methods). (PDF)
Data
Marker frequency analyses. (A) wild-type, (B) recA, (C) recA recB and (D) recA recD mutants. See legend of S1 Fig. (PDF)
Data
Marker frequency analyses. (A) matP, (B) matP recB, (C) matP ftsKΔCTer and (D) matP ftsKΔCTer recB mutants. See legend of S1 Fig. (PDF)
Data
Time-lapse microscopy of recB yddW:: parSpMT1 cells with a circular chromosome. The cell at the top produced a focus-less cell at each division (frames 18, 39, 50) and a cell below produced focus-less cells (frame 49 and 56). (AVI)
Data
Oligonucleotides used in this study. (PDF)
Data
Marker frequency analyses. (A) wild-type. (B) recB mutant. Normalized replication profiles of exponentially growing cells are shown. Sequence read frequencies are normalized to the total number of reads and then the normalized reads (y-axis) are plotted against the chromosome coordinates in kb (x-axis). The approximate position of replication termi...
Data
Marker frequency of wild-type and recB mutants with a linear chromosome. See legend of S1 Fig. (PDF)
Data
Model for the loss of terminal DNA in the recB mutant with a linear chromosome. In a first step, during replication progression one replication fork is accidentally broken. On the left part of the figure the left fork is broken, and on the right part of the figure the right fork is broken. The other replication fork progresses to the end of the chr...
Data
Time-lapse microscopy of recA cells showing an example of heritable focus loss with cell elongation. The cell on the left elongates (frames 19 to 28) before producing a focus-less cell frame 31, and elongates again (frames 32 to 49) before producing a second focus-less cell frame 50. A cell on the top elongates from frame 30 to the end of the video...
Data
Time-lapse microscopy of recB yddW:: parSpMT1 cells with a linear chromosome. A focus-less cell was produced frame 6 and divided (frames 14, 20, 23, 29). After producing a focus-less cell, the focus-containing cell returned to normal growth. (AVI)
Data
Marker frequency analyses. (A) ruvAB, (B) ruvAB recB, (C) sbcB sbcD, and (D) recA sbcB sbcD mutants. See legend of S1 Fig. (PDF)
Data
Time-lapse microscopy of recA cells, showing an example of heritable focus loss with a return to normal growth after two generations. Heritable focus loss rarely occurred for more than 2 or 3 generations in the recA mutant. (AVI)
Data
Time-lapse microscopy of recA recD cells. Most focus loss in the recA recD mutant was transmitted at each generation as in the recB or the recA recB mutants, but alternative behaviours were more frequent that in recB and recA recB mutants, accounting for a slightly lower percentage of heritable events. Two examples are shown here. The cell at the t...
Data
Time-lapse microscopy of recB ydeV:: parSpMT1 cells with a linear chromosome. Focus-less cells are produced from different parental cells (frame 10, 34, and 37). After producing a focus-less cell, the focus-containing cells returned to normal growth, and focus-less cells did not divide. (AVI)
Article
Full-text available
Marker frequency analysis of the Escherichia coli recB mutant chromosome has revealed a deficit of DNA in a specific zone of the terminus, centred on the dif/TerC region. Using fluorescence microscopy of a marked chromosomal site, we show that the dif region is lost after replication completion, at the time of cell division, in one daughter cell on...
Data
Marker frequency analysis of exponential phase cells. Original normalized profiles are shown except for the bottom panel where ratio of Fts ATPase and wild-type data is shown. (TIF)
Data
Marker frequency analysis of exponential phase cells. (TIF)
Data
Time lapse microscopy of recB cells. Cells were mounted on M9 glucose agarose pad and incubated at 30°C on stage of the microscope. Images were captured every 10 min. dif/TerC region of chromosome is visualized as green fluorescence focus by binding of GFP-ParBpMT1 protein to ydeV::parSpMT1. All frames are labelled. The double white arrows indicate...
Data
Time lapse microscopy of dif cells. In contrast to recB cells, where only one daughter cell loses focus, in some dif cells both daughter cells lose focus due to breakage of unresolved chromosome dimers during cell division (Frame 26). Importantly, there was a considerable delay in cell division observed before the loss of focus in dif cells (Frame...
Data
Marker frequency analysis of exponential phase cells. Original normalized profiles are shown. Lower left panel shows the magnified terminus region of ΔLC3-R111 mutant. In ΔLC3-R111 the two replication forks are expected to merge at equal distance from the origin in both directions, between TerA and TerB. However, the MFA shows an excess of reads in...
Data
Marker frequency analysis of exponential phase cells. Original normalized profiles are shown. Lower left panel shows the magnified terminus region of InvT2. (TIF)
Data
Time lapse microscopy of tus recB cells. (AVI)
Data
Time lapse microscopy of ftsKΔCTer recB cells. In addition to the recB phenotype (Frame 16, 26 etc.), where only one daughter cell loses focus, in ftsKΔCTer recB cells, occasionally, both daughter cells lose focus due to breakage of DNA in unresolved chromosome dimers during cell division (Frame 31). (AVI)
Data
Marker frequency analysis of exponential phase cells. Original normalized profiles are shown except for the top left panel which shows ratio of parEts recB and wild-type, and top right panel which shows the ratio of recB containing the indicated plasmids. (TIF)
Data
Marker frequency analysis of exponential phase cells. Original normalized profiles are shown except for the lowest right panel where ratio of cephalexin-treated recB and wild-type cells is shown. (TIF)
Data
Time lapse microscopy of ftsKΔCTer recB cells. In this example we show that in addition to recB phenotype (Frame 5, 15 and 24), where one daughter cell loses focus at the time of cell division, in ftsKΔCTer recB cells, foci could also sometimes disappear randomly during the cell cycle (Frame 32). This unusual loss is indicated by a yellow cross. (A...
Data
Marker frequency analysis of exponential phase cells. Original normalized profiles are shown except for the top middle panel where ratio of recC and wild-type data is shown. (TIF)
Data
Marker frequency analysis of exponential phase cells. (TIF)
Data
Marker frequency analysis of exponential phase cells. (TIF)
Data
Percentage of cells with zero, one or two foci in mutant strains. (PDF)
Data
Time lapse microscopy of ftsKΔCTer recB cells. In this example we show that some ftsKΔCTer recB cells lose focus and die due to other problems, which may arise because of the inhibition of FtsK translocation and need of RecB for repair. (AVI)
Article
Full-text available
Bacteria display a highly flexible cell cycle in which cell division can be temporally disconnected from the replication/segregation cycle of their genome. The accuracy of genetic transmission is enforced by restricting the assembly of the cell division apparatus to the low DNA-density zones that develop between the regularly spaced nucleoids origi...
Chapter
We present a method through which one may monitor the relative binding affinity of a given protein to DNA motifs on the scale of a whole genome. Briefly, the protein of interest is incubated with fragmented genomic DNA and then affixed to a column. Washes with buffers containing low salt concentrations will remove nonbound DNA fragments, while step...
Article
Full-text available
Recently, we described a method for multiplex genome editing by natural transformation (MuGENT). Mutant constructs for MuGENT require large arms of homology (>2000 bp) surrounding each genome edit, which necessitates laborious in vitro DNA splicing. In Vibrio cholerae, we uncover that this requirement is due to cytoplasmic ssDNA exonucleases, which...
Preprint
Full-text available
Recently, we described a method for multiplex genome editing by natural transformation (MuGENT). Mutant constructs for MuGENT require large arms of homology (>2000 bp) surrounding each genome edit, which necessitates laborious in vitro DNA splicing. In Vibrio cholerae, we uncover that this requirement is due to cytoplasmic ssDNA exonucleases, which...
Article
Full-text available
Homologous recombination between the circular chromosomes of bacteria can generate chromosome dimers. They are resolved by a recombination event at a specific site in the replication terminus of chromosomes, dif, by dedicated tyrosine recombinases. The reaction is under the control of a cell division protein, FtsK, which assembles into active DNA p...
Data
List of bacterial strains used in this study. (DOCX)
Data
Comparison of dif-cassette excision and recA-dependency in E. coli (Ec) and V. cholerae (Vc) with similar number of generations. Mean of at least 3 independent experiments. Error bars represent standard deviations. (A) Influence of homologous recombination on the rate of dif-cassette excision in E. coli and V. cholerae cells grown in LB for 8 h and...
Data
Rate of dif-cassette excision (A) and recA-dependency (B) of dif-cassette excision measured over 8 h in fast (LB) and slow (M9) growing E. coli cells. Mean of at least 3 independent experiments. Error bars represent standard deviations. *: p <0.05 (with unpaired two-tailed t-test for (A) and with Welch’s correction for (B)). (TIF)
Data
(A) Consensus images of the cell shape (left panel) and SPOR domain (right panel) of E. coli cells grown in M9. (B) Cell shape (left panels) and SPOR domain (right panels) image choreographies of individual cells. (TIFF)
Data
Time-lapse images of ydeV (ter) and oriC (ori) loci in E. coli cells grown in M9-Rich (A) or M9 (B) in the presence of 10 μg/ml cephalexin. NR: first frame in the time-lapse analysis in which new ori loci split. In the bottom right corner of each frame is indicated the time in minutes from the beginning of the time-lapse experiment. (TIF)
Data
List of plasmids used in this study. (DOCX)
Data
Time-lapse of ydeV (green) and oriC (red) loci localisation in E. coli cells. One frame was taken every 2 minutes. Cells were grown in M9-Rich. 10 μg/ml cephalexin was added to the agarose slide. (AVI)
Data
Time-lapse of ydeV (green) and oriC (red) loci localisation in E. coli cells. One frame was taken every 4 minutes. Cells were grown in M9. 10 μg/ml cephalexin was added to the agarose slide. (AVI)
Data
(A) Overnight recA- and recA+ E. coli (Ec) and V. cholerae (Vc) cell cultures were diluted in fresh media and grown to an identical OD in the exponential phase. Colony forming units (CFU) of the cultures were determined by spreading serial dilutions on plates. In the graphs are shown the ratio of the CFU in recA- over recA+ strains in Ec and Vc cel...
Data
Rate of dif-cassette excision and recA-dependency in E. coli (Ec) and V. cholerae (Vc). Mean of at least 3 independent experiments. Error bars represent standard deviations. (A) Influence of homologous recombination on the rate of dif-cassette excision in E. coli cells grown in M9-Rich medium for 16 h. **: p<0.01 (Unpaired two-tailed t test). (B) r...
Data
(A) Time-lapse images of an E. coli cell grown in M9. The red arrow indicates the detection of constriction. (B) Mean pixel intensity along the cell length. Profile numbers correspond to the cell frame numbers of panel A. Profiles in which constriction could not be detected are shown in black. The profile in which constriction was first detected is...
Data
Examples of individual cell cycles of E. coli matP- cells growing in M9-Rich medium. In the left panels, representation of the manually detected ydeV spots and constriction sites. Green spots represent ydeV loci (fluorescent traces in right panels) and Black spots the constriction mark (bright field traces in central panels). For the fluorescent tr...
Data
Examples of individual cell cycles of E. coli ftsKATP- cells growing in M9-Rich medium. In the left panels, representation of the manually detected ydeV spots and constriction sites. Green spots represent ydeV loci (fluorescent traces in right panels) and Black spots the constriction mark (bright field traces in central panels). Y-axis: 0, old cell...
Article
Full-text available
Bacterial cell division is a highly regulated process, which involves the formation of a complex apparatus, the divisome, by over a dozen proteins. In the few model bacteria in which the division process was detailed, divisome assembly occurs in two distinct steps: a few proteins, including the FtsZ tubulin-like protein, form a membrane associated...
Article
Cell division must be coordinated with chromosome replication and segregation to ensure the faithful transmission of genetic information during proliferation. In most bacteria, assembly of the division apparatus, the divisome, starts with the polymerization of a tubulin homologue, FtsZ, into a ring-like structure at mid-cell, the Z-ring1. It typica...