A5036642325- Bacterial Genetics and Biotechnology
- Bacteriophages and microbial interactions
- Genomics and Phylogenetic Studies
- RNA and protein synthesis mechanisms
- Microbial Community Ecology and Physiology
- Enzyme Structure and Function
- DNA and Nucleic Acid Chemistry
- DNA Repair Mechanisms
- Antibiotic Resistance in Bacteria
- Cancer therapeutics and mechanisms
- Glycosylation and Glycoproteins Research
- Protein Structure and Dynamics
- Machine Learning in Bioinformatics
- Protist diversity and phylogeny
- Molecular Biology Techniques and Applications
- Escherichia coli research studies
- Legume Nitrogen Fixing Symbiosis
- Genomics and Chromatin Dynamics
- Probiotics and Fermented Foods
- Virology and Viral Diseases
- Polysaccharides and Plant Cell Walls
- Fungal and yeast genetics research
- Amino Acid Enzymes and Metabolism
- Mitochondrial Function and Pathology
- Plant Reproductive Biology
Centre National de la Recherche Scientifique
2014-2024
Institut de Biologie Intégrative de la Cellule
2015-2024
Université Paris-Saclay
2013-2024
CEA Paris-Saclay
2014-2024
Commissariat à l'Énergie Atomique et aux Énergies Alternatives
2014-2024
Université Paris-Sud
2007-2020
Expression Génétique Microbienne
2010-2014
Université Paris Cité
2008
Biology of Extremophiles Laboratory
2007
Institut de Biologie Physico-Chimique
1994-2003
The study of the conservation gene order or synteny constitutes a powerful methodology to assess orthology genomic regions and predict functional relationships between genes. exponential growth microbial databases is expected improve predictions significantly. Paradoxically, this data plethora, without information on organisms relatedness, could impair performance analysis programs. In work, I present SyntTax, web service designed take full advantage large amount archaeal bacterial genomes...
Background The Escherichia coli heterodimeric HU protein is a small DNA-bending associated with the bacterial nucleoid. It can introduce negative supercoils into closed circular DNA in presence of topoisomerase I. Cells lacking grow very poorly and display many phenotypes. Methodology/Principal Findings We analyzed transcription profile every gene absence one or both subunits. This genome-wide silico transcriptomic approach, performed parallel vivo genetic experimentation, defined regulon....
Cells from the three domains of life produce extracellular membrane vesicles (MVs), suggesting that MV production is a fundamental aspect cellular physiology. We have recently shown MVs produced by hyperthermophilic archaeon Thermococcus kodakaraensis can be used as vehicles to transfer exogenous recombinant plasmid DNA cell cell. Here, we show nautilus, which harbours plasmids, pTN1, pTN2 and pTN3, produces MVs, some them selectively incorporate pTN1 pTN3. Interestingly, pTN3 represents...
The 2 465 177 bp genome of Sulfolobus islandicus LAL14/1, host the model rudivirus SIRV2, was sequenced. Exhaustive comparative genomic analysis S. LAL14/1 and nine other completely sequenced strains isolated from Iceland, Russia USA revealed a highly syntenic common core approximately Mb long hyperplastic region containing most strain-specific genes. In latter is enriched in insertion sequences, CRISPR (clustered regularly interspaced short palindromic repeats), glycosyl transferase genes,...
Yeast Qri7 and human OSGEPL are members of the orthologous Kae1(OSGEP)/YgjD protein family, last class universally conserved proteins without assigned function. Phylogenetic analyses indicate that eukaryotic Qri7(OSGEPL) originated from bacterial YgjD proteins. We have recently shown archaeal Kae1 is a DNA-binding exhibits apurinic endonuclease activity in vitro . show here Qri7/OSGEPL localize mitochondria involved mitochondrial genome maintenance two model organisms, Saccharomyces...
B. subtilis grows more rapidly using the amino sugar glucosamine as carbon source, than with N-acetylglucosamine. Genes for transport and metabolism of N-acetylglucosamine (nagP nagAB) are found in all sequenced Bacilli (except Anoxybacillus flavithermus). In there is an additional operon (gamAP) encoding second copies genes catabolism glucosamine. We have developed a method to make multiple deletion mutations employing excisable spectinomycin resistance cassette. Using this we analysed...
Escherichia coli and Salmonella can use chitin-derived oligosaccharides as carbon nitrogen sources. Chitosugars traverse the outer membrane through a dedicated chitoporin, ChiP, are transported across cytoplasmic by chitobiose transporter (ChbBCA). Previous work revealed that synthesis of requires transcription chbBCARFG operon. A sequence from chbBC portion transcript was shown to act decoy target for regulatory small RNA, ChiX, normally blocks chiP expression. ChiX is destabilized degraded...
Abstract Summary: Absynte (Archaeal and Bacterial Synteny Explorer) is a web-based service designed to display local syntenies in completely sequenced prokaryotic chromosomes. The genomic contexts are determined with multiple center star clustering topology on the basis of user-provided protein sequence all (or set of) chromosomes from publicly available archaeal bacterial genomes. results consist dynamic web page where consistent color-coding permits rapid visual evaluation relative...
Thermococcus nautili, strain 30-1 T (formerly reported as nautilus), was isolated from a hydrothermal chimney sample collected the East Pacific Rise at depth of 2633 m on ‘La chainette PP57’ area. Cells were motile, irregular cocci with polar tuft flagella (0.8–1.5 µm) and divided by constriction. The micro-organism grew optimally 87.5 °C (range 55–95 °C), pH 7 4–9) 2 % NaCl 1–4 %). Doubling time 64 min in Zillig’s broth medium under optimal conditions. Growth strictly anaerobic. It...
The mechanisms underpinning the replication of genomic DNA have recently been challenged in
The binding of regulatory proteins to their specific DNA targets determines the accurate expression neighboring genes. in silico prediction new sites completely sequenced genomes is a key aspect deeper understanding gene networks. Several algorithms have been described discriminate against false-positives targets; however none them has implemented so far assist detection at genomic scale. FITBAR (Fast Investigation Tool for Bacterial and Archaeal Regulons) web service designed identify...
In Bacillus subtilis separate sets of genes are implicated in the transport and metabolism amino sugars, glucosamine N-acetylglucosamine. The for use N-acetylglucosamine (nagAB nagP) found most firmicutes controlled by a GntR family repressor NagR (YvoA). (gamAP) repressed another GamR (YbgA). gamR-gamAP synton is only B. few very close relatives. Although phylogenetically, there no cross regulation between their operons. GlcN6P prevents all binding to its targets. binds specifically targets...
Apolipoprotein N-acyltransferase (Lnt) is an essential membrane-bound enzyme that catalyzes the third and last step in post-translational modification of bacterial lipoproteins. In order to identify residues implicated substrate recognition and/or binding we screened for non-functional variants Lnt obtained by error-prone polymerase chain reaction a complementation assay using lnt depletion strain. Mutations included amino acid substitutions active site located on flexible loops catalytic...
Abstract DNA gyrase is a type II topoisomerase with the unique capacity to introduce negative supercoiling in DNA. In bacteria, has an essential role homeostatic regulation of supercoiling. While ubiquitous was previously reported have patchy distribution Archaea but its emergent function and evolutionary history this domain life remains elusive. study, we used phylogenomic approaches up-to date sequence dataset establish global archaea-specific phylogenies gyrases. The most parsimonious...
Homologs of the dimeric HU protein Escherichia coli can be found in every prokaryotic organism that has been analyzed. In this work, we demonstrate Serratia marcescens synthesizes two distinct subunits, like E. and Salmonella typhimurium, suggesting heterodimeric could a common feature enteric bacteria. A phylogenetic analysis HU-type proteins (HU IHF) is presented, scheme for origin hup genes onset heterodimericity suggested.
Summary Soupene et al . [ J. Bacteriol. (2003) 185 5611–5626] made the unexpected observation that presence of a mutation, in gene for N ‐acetylglucosamine repressor, nagC , increased growth rate Escherichia coli MG1655 on galactose, an unrelated sugar. We have found NagC, binds to single, high‐affinity site overlapping promoter galP (galactose permease) and expression is repressed by combination GalR GalS. In addition previously identified galOE operator, other gal operators further...
Mycoplasmas are the smallest known microorganisms, with drastically reduced genome sizes. One of essential biochemical pathways lost in mycoplasmas is methylation-mediated DNA repair (MMR), which responsible for correction base substitutions, insertions, and deletions both bacteria higher organisms. We found that histone-like protein encoded by himA/hup_2 gene Mycoplasma gallisepticum (mgHU) recognizes typical MMR substrates, contrast to homologues from other species. The recognition...