A5049448831- Bacterial Genetics and Biotechnology
- DNA Repair Mechanisms
- Bacteriophages and microbial interactions
- RNA and protein synthesis mechanisms
- RNA modifications and cancer
- Political and Social Issues
- Social Sciences and Governance
- Genomics and Phylogenetic Studies
- CRISPR and Genetic Engineering
- Enzyme Production and Characterization
- RNA Research and Splicing
- DNA and Nucleic Acid Chemistry
- Immune Response and Inflammation
- Microbial Natural Products and Biosynthesis
- Economic Theory and Policy
- Enzyme Structure and Function
- Microbial Metabolic Engineering and Bioproduction
- Biofuel production and bioconversion
- Immunotherapy and Immune Responses
- Biochemical and Molecular Research
- Glycosylation and Glycoproteins Research
- Cancer therapeutics and mechanisms
- Viral gastroenteritis research and epidemiology
- Carcinogens and Genotoxicity Assessment
- Fungal and yeast genetics research
Microbiologie de l’alimentation au service de la santé
2013-2024
AgroParisTech
2011-2023
Université Paris-Saclay
2016-2023
Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement
2021-2023
Institut National de la Recherche Agronomique
2007-2012
Interdisciplinarité en Santé Publique Interventions et Instruments de mesure complexes – Région Est
2011
Université Paris Cité
2009
Centre National de la Recherche Scientifique
1998-2009
Institut de Biochimie et Biophysique Moléculaire et Cellulaire
2009
Département Génétique Animale
2005-2008
Outside In Acquisition and analysis of large data sets promises to move us toward a greater understanding the mechanisms by which biological systems are dynamically regulated respond external cues. Now, two papers explore responses bacterium changing nutritional conditions (see Perspective Chalancon et al. ). Nicolas (p. 1103 ) measured transcriptional regulation for more than 100 different conditions. Greater amounts antisense RNA were generated expected appeared be produced alternative...
Adaptation of cells to environmental changes requires dynamic interactions between metabolic and regulatory networks, but studies typically address only one or a few layers regulation. For nutritional shifts two preferred carbon sources Bacillus subtilis, we combined statistical model-based data analyses transcript, protein, metabolite abundances promoter activities. malate was rapid primarily controlled posttranscriptionally compared with the slow, mainly transcriptionally adaptation...
We have investigated in vivo the role of carboxy-terminal domain Bacillus subtilis Single-Stranded DNA Binding protein (SSBCter) as a recruitment platform at active chromosomal forks for many proteins genome maintenance machineries. probed this SSBCter interactome using GFP fusions and by Tap-tag biochemical analysis. It includes least 12 proteins. The was previously shown to include PriA, RecG, RecQ extended study addition DnaE, SbcC, RarA, RecJ, RecO, XseA, Ung, YpbB, YrrC. Targeting YpbB...
The enzymatic activity of yeast gene product Deg1 was identified using both disrupted strain and cloned recombinant protein expressed in <i>Escherichia coli</i>. results show that the <i>DEG1</i>-disrupted lacks synthase for formation pseudouridines Ψ<sub>38</sub>and Ψ<sub>39</sub> tRNA whereas other activities, specific Ψ at positions 13, 27, 28, 32, 34, 35, 36, 55 tRNA, remain unaffected. Also, His<sub>6</sub>-tagged Deg1p <i>E. coli</i> as well a fusion with A display only toward...
Interactions between dendritic cells and Mycobacterium tuberculosis, the aetiological agent of tuberculosis in humans, are thought to be central anti-mycobacterial immunity. We have previously shown that M. binds human monocyte-derived mostly through C-type lectin DC-SIGN (dendritic-cell-specific intercellular molecule-3-grabbing non-integrin)/CD209, we suggested may discriminate mycobacterial species recognition mannose-capping residues on lipoglycan lipoarabinomannan bacterial envelope....
In prokaryotes, transcription results from the activity of a 400 kDa RNA polymerase (RNAP) protein complex composed at least five subunits (2α, β, β', ω). To ensure adequate responses to changing environmental cues, RNAP is tightly controlled by means interacting regulatory proteins. Here, we report affinity-purification Bacillus subtilis complexes cells in different growth states and stress conditions, quantitative assessment mass spectrometry dynamic changes composition complex. The...
Abstract Genome-scale engineering enables rational removal of dispensable genes in chassis genomes. Deviating from this approach, we applied greedy accumulation deletions large regions the Bacillus subtilis genome, yielding a library 298 strains with genomes reduced up to 1.48 Mb size. High-throughput physiological phenotyping these confirmed that genome reduction is associated substantial loss cell fitness and synthetic-sick interactions. Transcriptome analysis indicated &lt;15%...
Enterococcus faecalis is an opportunistic pathogen that has emerged as a major cause of nosocomial infections worldwide. Many clinical strains are indeed resistant to last resort antibiotics and there consequently reawakening interest in exploiting virulent phages combat them. However, little still known about phage receptors resistance mechanisms enterococci. We made use prophageless derivative the well-known strain E. V583 isolate belonging Picovirinae subfamily P68 genus we named Idefix....
Many different modified nucleotides are found in naturally occurring tRNA, especially the anticodon region. Their importance for efficiency of translational process begins to be well documented. Here we have analyzed vivo effect deleting genes coding yeast tRNA-modifying enzymes, namely Pus1p, Pus3p, Pus4p, or Trm4p, on termination readthrough and +1 frameshift events. To this end, transformed each deletion strains with a lacZ-luc dual-reporter vector harboring selected programmed recoding...
Summary DNA polymerases of the X family have been implicated in a variety repair processes eukaryotes. Here we show that Deinococcus radiodurans , highly radioresistant bacterium able to mend hundreds radiation‐induced double‐stranded breaks, expresses polymerase belonging family. This novel bacterial polymerase, named PolX Dr was identified as product Deinococcal DR0467 gene. The purified protein possesses activity is stimulated by MnCl 2 property polymerases. Antibodies raised against...
Non-homologous end joining is a ligation process repairing DNA double strand breaks in eukaryotes and many prokaryotes. The ring structured eukaryotic Ku binds ends recruits other factors which can access through the threading of inward DNA, making this protein key ingredient for scaffolding NHEJ machinery. However, ability seems unevenly conserved among bacterial Ku. As differ mainly by their C-terminus, we evaluate role region loading abilities Bacillus subtilis stimulation ligase LigD. We...
Adherent-invasive Escherichia coli (AIEC) strains are frequently recovered from stools of patients with dysbiotic microbiota. They have remarkable properties adherence to the intestinal epithelium, and survive better than other E . in macrophages. The best studied these AIEC is probably strain LF82, which was isolated a Crohn’s disease patient. This contains five complete prophages, not been until now. We undertook their analysis, both vitro inside macrophages, show that all them form...
Yeast Pus1p catalyzes the formation of pseudouridine (ψ) at specific sites several tRNAs, but its function is not essential for cell viability. We show here that becomes when another tRNA:pseudouridine synthase, Pus4p, or minor tRNA glutamine are mutated. Strikingly, this mutant tRNA, which carries a mismatch in TψC arm, displays nuclear export defect. Furthermore, least one wild-type species defective absence Pus1p. Our data, thus, modifications formed by other aspects biogenesis...
Summary To evaluate the importance of RecA in DNA double‐strand break (DSB) repair, we examined effect low and high concentrations such as 2500 100 000 molecules per cell expressed from inducible P spac promoter Deinococcus radiodurans absence or presence IPTG respectively. We showed that at concentration, has a negligible on survival after γ‐irradiation when bacteria were immediately plated TGY agar whereas it significantly decreased to Δ ddrA cells while overexpression can partially...
Deinococcus radiodurans is an extraordinarily radioresistant bacterium that able to repair hundreds of radiation-induced double-stranded DNA breaks. One the players in this pathway X family polymerase (PolX(Dr)). Deletion PolX(Dr) has been shown decrease rate breaks and increase cell sensitivity gamma-rays. A 3'-->5' exonuclease activity stops cutting close loops also demonstrated. The present crystal structure solved at 2.46-A resolution reveals a novel extended conformation stark contrast...
Non homologous end-joining (NHEJ) is a double strand break (DSB) repair pathway which does not require any template and can ligate two DNA ends together. The basic bacterial NHEJ machinery involves partners: the Ku protein, end binding protein for DSB recognition multifunctional LigD composed ligase, nuclease polymerase domain, processing ligation of broken ends. In silico analyses performed in 38 sequenced genomes Streptomyces species revealed existence large panel NHEJ-like genes. Indeed,...
Bulk microbiome, as well virome-enriched shotgun sequencing only reveals the double-stranded DNA (dsDNA) content of a given sample, unless specific treatments are applied. However, genomes viruses often consist circular single-stranded (ssDNA) molecule. Pre-treatment and amplification using multiple displacement (MDA) method enables conversion ssDNA to dsDNA, but this process can lead over-representation these genomes. A more recent alternative permits bypass step, library adapters ligated...
Bacteriophages are remarkable for the wide diversity of proteins they encode to perform DNA replication and homologous recombination. Looking back at these ancestral forms life may help understanding how similar work in more sophisticated organisms. For instance, Sak4 family is composed archaeal RadB protein, a Rad51 paralog. We have previously shown that allowed single-strand annealing vivo, but only weakly compared phage λ Redβ highlighting putatively requires partners be efficient. Here,...
ABSTRACT Streptomyces are renowned for their prolific production of specialized metabolites with applications in medicine and agriculture. These multicellular bacteria present a sophisticated developmental cycle, play key role soil ecology. Little is known about -phage interactions the impact phages on physiology. In this study, we investigated conditions governing expression ‘Samy’, prophage found ambofaciens ATCC 23877. This siphoprophage produced simultaneously activation other mobile...