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6,590 results on '"Laboratoire de Microbiologie"'

1. ISOLEMENT, IDENTIFICATION ET CARACTERISATION DE SOUCHES DE BACTERIES ACETIQUES A PARTIR DUN ALCOOL DE MANGUE FERMENTE

Author: Mariama Cire Kourouma, Malick Mbengue, Coumba Toure Kane, Laboratoire de Microbiologie Appliquee et Genie Industriel , Dakar, Senegal., and Khady Sarr
Abstract: Les bacteries acetiques sont dun tres grand interet pour lindustrie biotechnologique, maisleur application la plus importante reside dans leur capacite a oxyder lethanol en acide acetique conduisant a la production de vinaigre. Le but de cette etude etaitdisoler, de caracteriser et didentifier des souches de bacteries acetiques a partir dun alcool de mangue fermente. Les souches isolees ont fait lobjet de tests phenotypiques, et biochimiques tels que la coloration de GRAM, la recherche de la catalase et de loxydase, loxydation de lethanol en acide acetique, le pouvoir suroxydant et le metabolisme de certains glucides. Vingt-huit souches de bacteries acetiques appartenant au genre Gluconoacetobacter et Acetobacter ont ete isolees. Le test de production nous a conduits au choix des cinq souches capables de produire les quantites les plus elevees dacide acetique. Ces souches nommees respectivement VMA1, VMA5, VMA7, VMAM et VMAOont ensuite fait lobjet de caracterisation physiologique afin de determiner leursconditions optimales de croissance. Les temperatures optimales de croissance eaientcomprises entre 27Â° et 40Â°C et les pH optimum entre 5,5 et 7. Les resultats du test de la resistance a lethanol ont montre que toutes les cinq souches etaientcapables de pousser a 10% dethanol (v/v) et les souches VMA1 et VMA5 etaientcapables de resister a 25% dethanol (v/v). Ces resultats pourraient potentiellement constituer une avancee majeure pour lindustrie du vinaigre.
Published: 2021
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2. Epigenetics and pathogenesis of type 2 diabetes

Author: Aoulia Dekaken, Adel Gouri, Laboratoire de Microbiologie, Chu Dorban, Annaba, Algérie, Mohamed Bouchareb, Laboratoire de Biochimie Médicale, Chu Ibn Rochd, Annaba, Algérie., Laboratoire de Microbiologie, Eph Ibn Zohr, Guelma, Algérie., Ahmed Aimen Bentorki, Régis Guieu, Mohamed Chefrour, and Sadek Benharkat
Subjects: Pathogenesis, business.industry, Medicine, General Medicine, Type 2 diabetes, Epigenetics, business, Bioinformatics, medicine.disease
Abstract: Le diabète a atteint des proportions épidémiques dans le monde entier. Des éléments de preuves suggèrent qu’il y a une interaction complexe entre les gènes et l'environnement pouvant ainsi jouer un rôle majeur dans la pathogénie multifactorielle de cette maladie et ses complications évoquant ainsi, un résultat de l'implication des facteurs épigénétiques. De récentes études montrent que les facteurs épigénétiques, y compris la méthylation de l'ADN et les modifications de l’histone, peuvent affecter la sensibilité ainsi que l’évolution des complications du diabète de type 2. Toutefois, nos connaissances sur les mécanismes moléculaires reliés aux facteurs environnementaux et le diabète de type 2 restent limitées.
Published: 2015
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3. Changes in enzymes regulating isocitrate breakdown in neurospora crassa

Author: Laboratoire de Microbiologie et Fermentations, Institut de Botanique g??n??rale de l'Universit??, Gen??ve; Department of Botany, University of Michigan, Ann Arbor, Mich., USA, Laboratoire de Microbiologie et Fermentations, Institut de Botanique g??n??rale de l'Universit??, Gen??ve, Ann Arbor, Kobr, Milos J., Turian, Gilbert, Zimmerman, Emma J., Laboratoire de Microbiologie et Fermentations, Institut de Botanique g??n??rale de l'Universit??, Gen??ve; Department of Botany, University of Michigan, Ann Arbor, Mich., USA, Laboratoire de Microbiologie et Fermentations, Institut de Botanique g??n??rale de l'Universit??, Gen??ve, Ann Arbor, Kobr, Milos J., Turian, Gilbert, and Zimmerman, Emma J.
Abstract: 1. Crude homogenates from Neurospora crassa grown on varions concentrations of sucrose and acetate were assayed for enzymes regulating isocitrate breakdown.
Published: 2006

4. Emissions de protoxyde d'azote dans les agrosystèmes. Quantification, analyse du déterminisme et modélisation. Programme ECLAT, Evolution du climat et de l'atmosphère. AGRIGES: Agriculture, forêt, biomasse et gaz à effet de serre. Compte rendu de projet 1995-96

Author: Germon, J.C., Renault, P., Cellier, Pierre, Lensi, Robert, Hénault, Catherine, Unité de Science du Sol, ., Laboratoire de Microbiologie des Sols, ., Agence de l'Environnement pour la Maîtrise de l'Energie, ., Institut francilien recherche, innovation et société (IFRIS), Ministère de l'Education nationale, de l’Enseignement supérieur et de la Recherche (M.E.N.E.S.R.)-Institut National de la Recherche Agronomique (INRA)-École des hautes études en sciences sociales (EHESS)-OST-Université Paris-Est Marne-la-Vallée (UPEM)-ESIEE Paris-Centre National de la Recherche Scientifique (CNRS), Unité de Science du Sol, Institut National de la Recherche Agronomique (INRA), Unité de recherches en bioclimatologie, and Ministère de l'Environnement
Subjects: [SDV]Life Sciences [q-bio]
Abstract: * INRA, Unité de Science du Sol, Domaine St Paul, Site Agroparc, 84914 Avignon cedex 9 Diffusion du document : INRA, Unité de Science du Sol, Domaine St Paul, Site Agroparc, 84914 Avignon cedex 9; National audience
Published: 1996

5. Identification and characterization of a locus involved in bacteriocin biosynthesis in the lactic acid bacterium Streptococcus thermophilus

Author: UCL - SST/ISV - Institut des sciences de la vie, ENITA Bordeaux - Laboratoire de Microbiologie et de Biochimie Appliquée (LMBA), Fontaine, Laetitia, Grossiord, Benoît, Delcour, Jean, Hols, Pascal, One-day meeting Signal transduction and regulation processes in bacteria, UCL - SST/ISV - Institut des sciences de la vie, ENITA Bordeaux - Laboratoire de Microbiologie et de Biochimie Appliquée (LMBA), Fontaine, Laetitia, Grossiord, Benoît, Delcour, Jean, Hols, Pascal, and One-day meeting Signal transduction and regulation processes in bacteria
Abstract: Streptococcus thermophilus is one of the main economically important lactic acid bacteria used in the dairy industry. Increasing knowledge of its metabolic properties and physiology is a prerequisite for the improvement of its industrial properties. Determination of the entire genome sequence of S. thermophilus LMG18311 was used in this study to investigate the presence of two-component systems (TCSs) and their respective functions. Attention was especially focussed on TCSs possibly involved in the regulation of the production of antimicrobial compounds such as bacteriocins. Among the ten TCSs identified, two of them showed homology with TCSs related to bacteriocin biosynthesis loci. The aim of the present study was to characterize one of the gene clusters containing a TCS showing strong homology with the previously identified blp gene cluster (bacteriocin like peptide) of Streptococcus pneumoniae. Such a gene cluster was also present in the two related S. thermophilus strains, LMD9 and CNRZ1066, for which the full genome sequence is also available. However, some differences were present when comparing the organization of the blp gene clusters of the three strains. That allowed us to look for a functional cluster and to characterize the antimicrobial activity related to those dedicated gene clusters. The comparison of those gene clusters together with the identification of the bacteriocin encoding genes will be presented.
Published: 2004

6. Identification and characterization of a locus involved in bacteriocin biosynthesis in the lactic acid bacterium Streptococcus thermophilus

Author: UCL - SST/ISV - Institut des sciences de la vie, ENITA Bordeaux - Laboratoire de Microbiologie et de Biochimie Appliquée (LMBA), Fontaine, Laetitia, Grossiord, Benoît, Delcour, Jean, Hols, Pascal, Belgian Society for Microbiology: Biofilms, Microbial Ecology and their Role in Nature and Disease., UCL - SST/ISV - Institut des sciences de la vie, ENITA Bordeaux - Laboratoire de Microbiologie et de Biochimie Appliquée (LMBA), Fontaine, Laetitia, Grossiord, Benoît, Delcour, Jean, Hols, Pascal, and Belgian Society for Microbiology: Biofilms, Microbial Ecology and their Role in Nature and Disease.
Abstract: Streptococcus thermophilus is one of the main economically important lactic acid bacteria used in the dairy industry. Increasing knowledge of its metabolic properties and physiology is a prerequisite for the improvement of its industrial properties. Determination of the entire genome sequence of S. thermophilus LMG18311 was used in this study to investigate the presence of two-component systems (TCSs) and their respective functions. Attention was especially focussed on TCSs possibly involved in the regulation of the production of antimicrobial compounds such as bacteriocins. Among the ten TCSs identified, two of them showed homology with TCSs related to bacteriocin biosynthesis loci. The aim of the present study was to characterize one of the gene clusters containing a TCS showing strong homology with the previously identified blp gene cluster (bacteriocin like peptide) of Streptococcus pneumoniae. Such a gene cluster was also present in the two related S. thermophilus strains, LMD9 and CNRZ1066, for which the full genome sequence is also available. However, some differences were present when comparing the organization of the blp gene clusters of the three strains. That allowed us to look for a functional cluster and to characterize the antimicrobial activity related to those dedicated gene clusters. The comparison of those gene clusters together with the identification of the bacteriocin encoding genes will be presented.
Published: 2002

7. Pêche et pisciculture dans le bassin de la Senne, depuis le moyen-âge

Author: Atelier international sur la modélisation rétrospective de la qualité de l’eau des rivières (17-18 septembre 1992: Bruxelles, Laboratoire de microbiologie des milieux aquatiques, ULB), Billen, Claire, Atelier international sur la modélisation rétrospective de la qualité de l’eau des rivières (17-18 septembre 1992: Bruxelles, Laboratoire de microbiologie des milieux aquatiques, ULB), and Billen, Claire
Abstract: info:eu-repo/semantics/nonPublished
Published: 1992

8. Alfalfa nodulation in the absence of rhizobium

Author: Barker, G., Truchet, G., Camut, Sylvie, de Billy, Françoise, Laboratoire de Microbiologie, ., Laboratoire de Biologie moléculaire des relations plantes-microorganismes, Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA), Institut National de la Recherche Agronomique (INRA), and ProdInra, Migration
Subjects: [SDV] Life Sciences [q-bio], MORPHOGENESE, BIOTECHNOLOGIE, [SDV]Life Sciences [q-bio], ALFALFA, BIOLOGIE MOLECULAIRE
Published: 1989

9. Evidence of Leu-Val-Leu Hydrolysis by Clostridium butyricum

Author: Khelifa, Nasser, Perez, Felix, Courtieu, Jacques, and Rimbault, Alain
Published: 1999
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10. Characterization of a small tRNA-binding protein that interacts with the archaeal proteasome complex

Author: Gaëlle Hogrel, Laura Marino‐Puertas, Sébastien Laurent, Ziad Ibrahim, Jacques Covès, Eric Girard, Frank Gabel, Daphna Fenel, Marie‐Claire Daugeron, Béatrice Clouet‐d'Orval, Tamara Basta, Didier Flament, Bruno Franzetti, University of St Andrews. School of Biology, Institut de biologie structurale (IBS - UMR 5075), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Grenoble Alpes (UGA), Laboratoire de microbiologie des environnements extrêmophiles (LM2E), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS), Institut de Biologie Intégrative de la Cellule (I2BC), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Laboratoire de microbiologie et génétique moléculaires - UMR5100 (LMGM), Centre de Biologie Intégrative (CBI), Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Grenoble Instruct-ERIC Centre, ANR-10-INBS-0005,FRISBI,Infrastructure Française pour la Biologie Structurale Intégrée(2010), ANR-10-LABX-0049,GRAL,Grenoble Alliance for Integrated Structural Cell Biology(2010), ANR-18-CE11-0018,PROTE-IN,Réseau d'interaction du proteasome archéen: vers la démonstration d'un lien entre la fonction du protéasome et le contrôle qualité des ARNs(2018), and ANR-16-CE12-0016,CASPAR,Rôle Physiologique des Ribonucléases de type ß-CASP dans le Métabolisme des ARN chez les Archées(2016)
Subjects: Proteomics, Proteasome Endopeptidase Complex, [SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Structural Biology [q-bio.BM], ribosome-associated quality control, QH301 Biology, Archaeal Proteins, NDAS, QH426 Genetics, Crystallography, X-Ray, Microbiology, Archaea, protein-protein interaction, QH301, proteasome, RNA, Transfer, OB-fold, tRNA binding, Carrier Proteins, QH426, Molecular Biology
Abstract: Authors acknowledge financial support from the French Agence Nationale de la Recherche (grant [ANR-18-CE11-0018-01] to B.F. and [ANR-16-CE12-0016-01] to B.C.O). This work used the platforms of the Grenoble Instruct-ERIC Centre (ISBG: UMS3518 CNRS-CEA-UGA-EMBL) with support from FRISBI (ANR-10-INBS-05-02) and GRAL, a project of the University Grenoble Alpes graduate school (Ecoles Universitaires de Recherche) CBH-EUR-GS (ANR-17-EURE-0003) within the Grenoble Partnership for Structural Biology. The IBS Electron Microscope facility is supported by the Auvergne Rhône-Alpes Region, the Fonds Feder, the Fondation pour la Recherche Médicale and GIS-IBiSA. The proteasome system allows the elimination of functional or structurally impaired proteins. This includes the degradation of nascent peptides. In Archaea, how the proteasome complex interacts with the translational machinery remains to be described. Here, we characterised a small orphan protein, Q9UZY3 (Uniprot ID) conserved in Thermococcales. The protein was identified in native pull-down experiments using the proteasome regulatory complex (PAN) as bait. X-ray crystallography and SAXS experiments revealed that the protein is monomeric and adopts a β-barrel core structure with an Oligonucleotide/oligosaccharide-Binding (OB) fold, typically found in translation elongation factors. Mobility shift experiment showed that Q9UZY3 displays tRNA binding properties. Pull-downs, co-immunoprecipitation and ITC studies revealed that Q9UZY3 interacts in vitro with PAN. Native pull-downs and proteomic analysis using different versions of Q9UZY3 showed that the protein interacts with the assembled PAN-20S proteasome machinery in Pyrococcus abyssi cellular extracts. The protein was therefore named Pbp11, for Proteasome Binding Protein of 11 kDa. Interestingly, the interaction network of Pbp11 also includes ribosomal proteins, tRNA processing enzymes and exosome subunits dependent on Pbp11's N-terminal domain that was found to be essential for tRNA binding. Together these data suggest that Pbp11 participates in an interface between the proteasome and the translational machinery. Publisher PDF
Published: 2022
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11. Intracellular Positioning Systems Limit the Entropic Eviction of Secondary Replicons Toward the Nucleoid Edges in Bacterial Cells

Author: Dauverd -Girault, Julie, Planchenault, Charlène, Pons, Marine, Schiavon, Caroline, Siguier, Patricia, Rech, Jérôme, Guynet, Catherine, Dauverd-Girault, Julie, Cury, Jean, Rocha, Eduardo, Junier, Ivan, Cornet, François, Espéli, Olivier, espeli, olivier, Appel à projets générique - Génèse et maintenance des chromosomes secondaire bactériens - - MAGISBAC2014 - ANR-14-CE10-0007 - Appel à projets générique - VALID, Centre interdisciplinaire de recherche en biologie (CIRB), Labex MemoLife, École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Collège de France (CdF (institution))-Ecole Superieure de Physique et de Chimie Industrielles de la Ville de Paris (ESPCI Paris), Université Paris sciences et lettres (PSL)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de microbiologie et génétique moléculaires - UMR5100 (LMGM), Centre de Biologie Intégrative (CBI), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Génomique évolutive des Microbes / Microbial Evolutionary Genomics, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Biologie Computationnelle et Mathématique (TIMC-IMAG-BCM), Techniques de l'Ingénierie Médicale et de la Complexité - Informatique, Mathématiques et Applications Grenoble - UMR 5525 (TIMC-IMAG), VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP ), Université Grenoble Alpes (UGA)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP ), Université Grenoble Alpes (UGA), Institut Jean Roger, This work as funded by ANR ANR-14-CE10-0007-01 to OE, FC and ER by the CNRS PICS initiative to OE and IJ and by the Foundation ARC (PJA 20171206119) to OE, ANR-14-CE10-0007,MAGISBAC,Génèse et maintenance des chromosomes secondaire bactériens(2014), Ecole Superieure de Physique et de Chimie Industrielles de la Ville de Paris (ESPCI Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Collège de France (CdF (institution))-Ecole Superieure de Physique et de Chimie Industrielles de la Ville de Paris (ESPCI Paris), Université Paris sciences et lettres (PSL)-Collège de France (CdF (institution))-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de microbiologie et génétique moléculaires (LMGM), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Centre de Biologie Intégrative (CBI), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Université Paris sciences et lettres (PSL), Génétique des Interactions macromoléculaires, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Génomique et Évolution des Microorganismes (TIMC-GEM ), Techniques de l'Ingénierie Médicale et de la Complexité - Informatique, Mathématiques et Applications, Grenoble - UMR 5525 (TIMC ), IMAG-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP ), Université Grenoble Alpes (UGA)-IMAG-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP ), École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-École normale supérieure - Paris (ENS Paris), Biologie Computationnelle et Modélisation (TIMC-BCM ), Translational Innovation in Medicine and Complexity / Recherche Translationnelle et Innovation en Médecine et Complexité - UMR 5525 (TIMC ), Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), and Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)
Subjects: [SDV.BC.BC]Life Sciences [q-bio]/Cellular Biology/Subcellular Processes [q-bio.SC], [SDV.BBM.BM] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, chemistry.chemical_compound, 0302 clinical medicine, Plasmid, Structural Biology, Chromosome Segregation, chromosome, Replicon, 0303 health sciences, Chromosomes, Bacterial, partition, segregation, Cell biology, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, MESH: DNA, Circular, polymer unmixing, DNA, Circular, Intracellular, Plasmids, DNA, Bacterial, MESH: Chromosomes, Bacterial, signal transduction and intracellular signaling Keywords: plasmid, MESH: Biological Transport, MESH: Chromosome Segregation, MESH: Replicon, [SDV.BC]Life Sciences [q-bio]/Cellular Biology, Bacterial genome size, Biology, MESH: Enterobacteriaceae, 03 medical and health sciences, Enterobacteriaceae, trafficking, MESH: Plasmids, plasmid, [SDV.BBM] Life Sciences [q-bio]/Biochemistry, Molecular Biology, [SDV.BC.BC] Life Sciences [q-bio]/Cellular Biology/Subcellular Processes [q-bio.SC], Nucleoid, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, [SDV.BC] Life Sciences [q-bio]/Cellular Biology, Molecular Biology, 030304 developmental biology, spatiotemporal organization, Chromosome, Biological Transport, [SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, biochemical phenomena, metabolism, and nutrition, MESH: DNA, Bacterial, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Section/Category: Sorting, chemistry, Cytoplasm, bacteria, [SDV.MP.BAC] Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, 030217 neurology & neurosurgery, DNA
Abstract: International audience; 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 16 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 bacterial physiology, including to the nucleoid dynamics, to limit detrimental costs leading to their counter-selection. We show that large DNA circles, whether from a natural plasmid or excised from the chromosome tend to localize in a dynamic manner in a zone separating the nucleoid from the cytoplasm at the edge of the nucleoid.This localization is in good agreement with in silico simulations of DNA circles in the nucleoid volume. Subcellular positioning systems counteract this tendency, allowing replicons to enter the nucleoid space. In enterobacteria, these systems are found in replicons above 25 kb, defining the limit with small randomly segregated plasmids. Larger replicons carry at least one of the three described family of systems, ParAB, ParRM and StbA. Replicons above 180 kb all carry a ParAB system, suggesting this system is specifically required in the cases of large replicons. Simulations demonstrated that replicon size profoundly affects localization, compaction and dynamics of DNA circles in the nucleoid volume. The present work suggests that presence of partition systems on the larger plasmids or chromids is not only due to selection for accurate segregation but also to counteract their unmixing with the chromosome and consequent exclusion from the nucleoid.
Published: 2020
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12. (Bio)chemical Strategies To Modulate Amyloid-β Self-Assembly

Author: Pierre Genevaux, Sara Ayala, Peter Faller, Christelle Hureau, Laboratoire de chimie de coordination (LCC), Institut de Chimie de Toulouse (ICT), Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de microbiologie et génétique moléculaires - UMR5100 (LMGM), Centre de Biologie Intégrative (CBI), Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Institut de Chimie de Strasbourg, Université de Strasbourg (UNISTRA)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), European Project: 638712,H2020,ERC-2014-STG,aLzINK(2015), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Institut de Chimie de Toulouse (ICT-FR 2599), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de microbiologie et génétique moléculaires (LMGM), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), and Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC)
Subjects: Physiology, Cognitive Neuroscience, Kinetics, Nanofibers, Plaque, Amyloid, Peptides and proteins, Cleavage (embryo), Fibril, Protein Aggregation, Pathological, Biochemistry, Aggregation, 03 medical and health sciences, 0302 clinical medicine, Alzheimer Disease, Amyloid precursor protein, [CHIM]Chemical Sciences, Animals, Humans, Molecule, [CHIM.COOR]Chemical Sciences/Coordination chemistry, Binding selectivity, 030304 developmental biology, 0303 health sciences, Amyloid beta-Peptides, biology, Chemistry, Cell Biology, General Medicine, 3. Good health, Metals, Covalent bond, Oligomers, biology.protein, Biophysics, Chemical chaperone, 030217 neurology & neurosurgery
Abstract: International audience; Amyloid plaques are one of the two hallmarks of Alzheimer’s disease (AD). They consist mainly of fibrils made of self-assembled amyloid-β (Aβ) peptides. Aβ is produced in healthy brains from proteolytic cleavage of the amyloid precursor protein. Aβ aggregates, in particular smaller, soluble aggregates, are toxic to cells. Hence, modulating the self-assembly of Aβ became a very active field of research, with the aim to reduce the amount of the toxic aggregates of Aβ or to block their toxic action. A great variety of molecules, chemical and biological, are able to modify the aggregation of Aβ. Here we give an overview of the different mechanistic ways to modulate Aβ aggregation and on which step in the self-assembly molecules can interfere. We discuss the aggregation modulators according to different important parameters, including the type of interaction (weak interaction, coordination or covalent bonds), the importance of kinetics and thermodynamics, the size of the modulating molecules, and binding specificity.
Published: 2019
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13. Three ParA Dimers Cooperatively Assemble on Type Ia Partition Promoters

Author: François Boudsocq, Jean-Yves Bouet, Sophie Barbe, Maya Salhi, Laboratoire de microbiologie et génétique moléculaires (LMGM), Centre de Biologie Intégrative (CBI), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Toulouse Biotechnology Institute (TBI), Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), ANR-10-BLAN-0102,DynPDE,Dynamique et EDP(2010), Laboratoire de microbiologie et génétique moléculaires - UMR5100 (LMGM), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), and Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)
Subjects: DNA, Bacterial, Operon, Stereochemistry, Inverted repeat, [SDV]Life Sciences [q-bio], Centromere, DNA Primase, Computational biology, QH426-470, Molecular Dynamics Simulation, Random hexamer, Article, bacterial DNA segregation, 03 medical and health sciences, chemistry.chemical_compound, Plasmid, Protein Domains, Escherichia coli, Genetics, plasmid F, [SDV.BBM.BC]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biochemistry [q-bio.BM], Promoter Regions, Genetic, Genetics (clinical), ParA, 030304 developmental biology, 0303 health sciences, winged-HTH, Binding Sites, Chemistry, Escherichia coli Proteins, 030302 biochemistry & molecular biology, Promoter, Gene Expression Regulation, Bacterial, Chromosomes, Bacterial, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, DNA binding site, partition promoter organization, Protein Multimerization, DNA, Plasmids
Abstract: Accurate DNA segregation is essential for faithful inheritance of genetic material. In bacteria, this process is mainly ensured by a partition system (Par) composed of two proteins, ParA and ParB, and a centromere site. The auto-regulation of Par operon expression is important for efficient partitioning, and is primarily mediated by ParA for type Ia plasmid partition systems. For the plasmid F, four ParAF monomers were proposed to bind to four repeated sequences in the promoter region. By contrast, using quantitative surface plasmon resonance, we showed that three ParAF dimers bind to this region. We uncovered that one perfect inverted repeat (IR) motif, consisting of two hexamer sequences spaced by 28-bp, constitutes the primary ParAF DNA binding site. A similar but degenerated motif overlaps the former. ParAF binding to these motifs is well supported by biochemical and modeling analyses. In addition, molecular dynamics simulations predict that the winged-HTH domain displays high flexibility, which may favor the cooperative ParA binding to the promoter region. We propose that three ParAF dimers bind cooperatively to overlapping motifs thus covering the promoter region. A similar organization is found on both closely related and distant plasmid partition systems, suggesting that such promoter organization for auto-regulated Par operons is widespread and may have evolved from a common ancestor.
Published: 2021
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14. The essential role of mRNA degradation in understanding and engineering E. coli metabolism

Author: Laurence Girbal, Charlotte Roux, Delphine Ropers, Muriel Cocaign-Bousquet, Thibault A. Etienne, Agamemnon J. Carpousis, Eliane Hajnsdorf, Toulouse Biotechnology Institute (TBI), Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut de biologie physico-chimique (IBPC (FR_550)), Centre National de la Recherche Scientifique (CNRS), Modeling, simulation, measurement, and control of bacterial regulatory networks (IBIS), Laboratoire Adaptation et pathogénie des micro-organismes [Grenoble] (LAPM), Centre National de la Recherche Scientifique (CNRS)-Université Joseph Fourier - Grenoble 1 (UJF)-Centre National de la Recherche Scientifique (CNRS)-Université Joseph Fourier - Grenoble 1 (UJF)-Inria Grenoble - Rhône-Alpes, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Institut Jean Roget, Laboratoire de microbiologie et génétique moléculaires (LMGM), Centre de Biologie Intégrative (CBI), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), This work was supported by the French National Research Agency [ANR-18-CE43-0010]., ANR-18-CE43-0010,RIB-ECO,Ingénierie du cycle de vie des ARN pour une approche économique de l'énergétique microbienne: application à la bioconversion des sources de carbone dérivées de la biomasse(2018), CNRS UMR8261, Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Université Joseph Fourier - Grenoble 1 (UJF)-Centre National de la Recherche Scientifique (CNRS)-Université Joseph Fourier - Grenoble 1 (UJF)-Centre National de la Recherche Scientifique (CNRS)-Inria Grenoble - Rhône-Alpes, Analyse, ingénierie et contrôle des micro-organismes (MICROCOSME), Inria Grenoble - Rhône-Alpes, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Université Grenoble Alpes (UGA), Laboratoire de microbiologie et génétique moléculaires - UMR5100 (LMGM), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), and Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Systems biology, RNA Stability, [SDV]Life Sciences [q-bio], Bioengineering, Biology, Applied Microbiology and Biotechnology, Metabolic engineering, 03 medical and health sciences, Transcription (biology), Gene expression, Transcriptional regulation, Protein biosynthesis, Escherichia coli, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, 2. Zero hunger, 0303 health sciences, Messenger RNA, Heterologous protein production, 030302 biochemistry & molecular biology, Translation (biology), Cell biology, Microbe engineering, Metabolism, Metabolic Engineering, mRNA degradation, Metabolic Networks and Pathways, Biotechnology
Abstract: International audience; Metabolic engineering strategies are crucial for the development of bacterial cell factories with improved performance. Until now, optimal metabolic networks have been designed based on systems biology approaches integrating large-scale data on the steady-state concentrations of mRNA, protein and metabolites, sometimes with dynamic data on fluxes, but rarely with any information on mRNA degradation. In this review, we compile growing evidence that mRNA degradation is a key regulatory level in E. coli that metabolic engineering strategies should take into account. We first discuss how mRNA degradation interacts with transcription and translation, two other gene expression processes, to balance transcription regulation and remove poorly translated mRNAs. The many reciprocal interactions between mRNA degradation and metabolism are also highlighted: metabolic activity can be controlled by changes in mRNA degradation and in return, the activity of the mRNA degradation machinery is controlled by metabolic factors. The mathematical models of the crosstalk between mRNA degradation dynamics and other cellular processes are presented and discussed with a view towards novel mRNA degradation-based metabolic engineering strategies. We show finally that mRNAdegradation-based strategies have already successfully been applied to improve heterologous protein synthesis. Overall, this review underlines how important mRNA degradation is in regulating E. coli metabolism and identifies mRNA degradation as a key target for innovative metabolic engineering strategies in biotechnology.
Published: 2021
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15. Phylogenetic Diversity of Lhr Proteins and Biochemical Activities of the Thermococcales aLhr2 DNA/RNA Helicase

Author: Manon Batista, Sébastien Laurent, Béatrice Clouet-d’Orval, Didier Flament, Gwennaele Fichant, Petra Langendijk-Genevaux, Ziad Abdel-Razzak, Yves Quentin, Mirna Hajj, Hala Chamieh, Régine Capeyrou, Marie Bouvier, Laboratoire de microbiologie et génétique moléculaires (LMGM), Centre de Biologie Intégrative (CBI), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Unité de biologie moléculaire, cellulaire et du développement (MCD), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Centre de Biologie Intégrative (CBI), Laboratoire de microbiologie des environnements extrêmophiles (LM2E), Centre National de la Recherche Scientifique (CNRS)-Université de Brest (UBO)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), and Lebanese University [Beirut] (LU)
Subjects: DNA repair, archaea, Archaeal Proteins, SF2 helicases, Biochemistry, Microbiology, Article, aLhr2 helicases, 03 medical and health sciences, chemistry.chemical_compound, Annealing activity, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Molecular Biology, Phylogeny, 030304 developmental biology, Adenosine Triphosphatases, RNA metabolism, 0303 health sciences, biology, Sequence Homology, Amino Acid, 030302 biochemistry & molecular biology, DNA Helicases, RNA, Helicase, DNA, biology.organism_classification, RNA Helicase A, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], QR1-502, Thermococcales, chemistry, biology.protein, Sulfolobales, RNA Helicases
Abstract: International audience; Helicase proteins are known to use the energy of ATP to unwind nucleic acids and to remodel protein-nucleic acid complexes. They are involved in almost every aspect of DNA and RNA metabolisms and participate in numerous repair mechanisms that maintain cellular integrity. The archaeal Lhr-type proteins are SF2 helicases that are mostly uncharacterized. They have been proposed to be DNA helicases that act in DNA recombination and repair processes in Sulfolobales and Methanothermobacter. In Thermococcales, a protein annotated as an Lhr2 protein was found in the network of proteins involved in RNA metabolism. To investigate this, we performed in-depth phylogenomic analyses to report the classification and taxonomic distribution of Lhr-type proteins in Archaea, and to better understand their relationship with bacterial Lhr. Furthermore, with the goal of envisioning the role(s) of aLhr2 in Thermococcales cells, we deciphered the enzymatic activities of aLhr2 from Thermococcus barophilus (Tbar). We showed that Tbar-aLhr2 is a DNA/RNA helicase with a significant annealing activity that is involved in processes dependent on DNA and RNA transactions.
Published: 2021
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16. Ribosomal RNA degradation induced by the bacterial RNA polymerase inhibitor rifampicin

Author: Lina Hamouche, Agamemnon J. Carpousis, Leonora Poljak, Laboratoire de microbiologie et génétique moléculaires (LMGM), Centre de Biologie Intégrative (CBI), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Toulouse Biotechnology Institute (TBI), Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), ANR-16-CE12-0014,IB-mRND,Biologie integrative de la dégradation des ARN messagers(2016), Laboratoire de microbiologie et génétique moléculaires - UMR5100 (LMGM), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), and Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)
Subjects: ribosomal RNA degradation, RNase E, RNase P, RNase R, rifampicin, Article, 03 medical and health sciences, Transcription (biology), Protein biosynthesis, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Molecular Biology, Polymerase, 030304 developmental biology, PNPase, 0303 health sciences, Messenger RNA, biology, 030306 microbiology, Chemistry, Ribosomal RNA, Molecular biology, cell size, mRNA degradation, biology.protein, RNA extraction
Abstract: Rifampicin, a broad-spectrum antibiotic, inhibits bacterial RNA polymerase. Here we show that rifampicin treatment of Escherichia coli results in a 50% decrease in cell size due to a terminal cell division. This decrease is a consequence of inhibition of transcription as evidenced by an isogenic rifampicin-resistant strain. There is also a 50% decrease in total RNA due mostly to a 90% decrease in 23S and 16S rRNA levels. Control experiments showed this decrease is not an artifact of our RNA purification protocol and therefore due to degradation in vivo. Since chromosome replication continues after rifampicin treatment, ribonucleotides from rRNA degradation could be recycled for DNA synthesis. Rifampicin-induced rRNA degradation occurs under different growth conditions and in different strain backgrounds. However, rRNA degradation is never complete thus permitting the re-initiation of growth after removal of rifampicin. The orderly shutdown of growth under conditions where the induction of stress genes is blocked by rifampicin is noteworthy. Inhibition of protein synthesis by chloramphenicol resulted in a partial decrease in 23S and 16S rRNA levels whereas kasugamycin treatment had no effect. Analysis of temperature-sensitive mutant strains implicate RNase E, PNPase and RNase R in rifampicin-induced rRNA degradation. We cannot distinguish between a direct role for RNase E in rRNA degradation versus an indirect role involving a slowdown of mRNA degradation. Since mRNA and rRNA appear to be degraded by the same ribonucleases, competition by rRNA is likely to result in slower mRNA degradation rates in the presence of rifampicin than under normal growth conditions.
Published: 2021
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17. RNase R is associated in a functional complex with the RhpA DEAD-box RNA helicase in Helicobacter pylori

Author: Etienne Kornobis, Valérie Briolat, Maxime Bouilloux-Lafont, Cecília M. Arraiano, Bertrand Raynal, Eloïse Galtier, Mariette Matondo, Yves Quentin, Thibaut Douché, Alejandro Tejada-Arranz, Hilde De Reuse, Rute G. Matos, Pathogenèse de Helicobacter / Helicobacter Pathogenesis, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP), Université de Paris (UP), Instituto de Tecnologia Química e Biológica António Xavier (ITQB), Universidade Nova de Lisboa = NOVA University Lisbon (NOVA), Laboratoire de microbiologie et génétique moléculaires (LMGM), Centre de Biologie Intégrative (CBI), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Pôle Biomics (C2RT), Centre de Ressources et de Recherche Technologique - Center for Technological Resources and Research (C2RT), Institut Pasteur [Paris]-Institut Pasteur [Paris], Hub Bioinformatique et Biostatistique - Bioinformatics and Biostatistics HUB, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Plateforme de Protéomique / Proteomics platform, Spectrométrie de Masse pour la Biologie – Mass Spectrometry for Biology (UTechS MSBio), Institut Pasteur [Paris]-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Institut Pasteur [Paris]-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Biophysique Moléculaire (plateforme) - Molecular Biophysics (platform), European Union's Horizon 2020 research and innovation program under the Marie Sklodowska-Curie [665807], Institut Carnot Pasteur Microbes & Santé, Fondation pour la Recherche Médicale [DBF20161136767 to H.D.R.], Pasteur-Weizmann Consortium of ‘The Roles of Noncoding RNAs in Regulation of Microbial Life Styles and Virulence’ to HDR, work at ITQB NOVA was financially supported by: Project UIDB/04612/2020 and UIDP/04612/2020 (Microbiologia Molecular, Estrutural e Celular) funded by FEDER funds through COMPETE2020 – Programa Operacional Competitividade e Internacionalização (POCI) and by national funds through FCT – Fundação para a Ciência e a Tecnologia, project PTDC/BIA-BQM/28479/2017 to R.G.M. R.G.M. was also financed by an FCT contract [CEECIND/02065/2017]. Funding for open access charge: Institut Pasteur., European Project: 665807,H2020,H2020-MSCA-COFUND-2014,PASTEURDOC(2015), Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), Université Paris Cité (UPCité), Laboratoire de microbiologie et génétique moléculaires - UMR5100 (LMGM), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Institut Pasteur [Paris] (IP)-Institut Pasteur [Paris] (IP), Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Institut Pasteur [Paris] (IP)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Institut Pasteur [Paris] (IP)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), and Laboratoire de Microbiologie et de Génétique Moléculaires (LMGM) , Centre de Biologie Intégrative (CBI), Université de Toulouse, UMR CNRS 5100, 31062 TOULOUSE Cedex 9, France.
Subjects: DEAD box, AcademicSubjects/SCI00010, [SDV]Life Sciences [q-bio], Amino Acid Motifs, RNase R, DEAD-box RNA Helicases, 03 medical and health sciences, 5S ribosomal RNA, Exoribonuclease, Genetics, RNA, Double-Stranded, 030304 developmental biology, Regulation of gene expression, 0303 health sciences, Helicobacter pylori, biology, Nucleic Acid Enzymes, 030302 biochemistry & molecular biology, RNA, Ribosomal, 5S, Helicase, RNA, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], RNA Helicase A, Molecular biology, Exoribonucleases, biology.protein, Epsilonproteobacteria
Abstract: Ribonucleases are central players in post-transcriptional regulation, a major level of gene expression regulation in all cells. Here, we characterized the 3′-5′ exoribonuclease RNase R from the bacterial pathogen Helicobacter pylori. The ‘prototypical’ Escherichia coli RNase R displays both exoribonuclease and helicase activities, but whether this latter RNA unwinding function is a general feature of bacterial RNase R had not been addressed. We observed that H. pylori HpRNase R protein does not carry the domains responsible for helicase activity and accordingly the purified protein is unable to degrade in vitro RNA molecules with secondary structures. The lack of RNase R helicase domains is widespread among the Campylobacterota, which include Helicobacter and Campylobacter genera, and this loss occurred gradually during their evolution. An in vivo interaction between HpRNase R and RhpA, the sole DEAD-box RNA helicase of H. pylori was discovered. Purified RhpA facilitates the degradation of double stranded RNA by HpRNase R, showing that this complex is functional. HpRNase R has a minor role in 5S rRNA maturation and few targets in H. pylori, all included in the RhpA regulon. We concluded that during evolution, HpRNase R has co-opted the RhpA helicase to compensate for its lack of helicase activity.
Published: 2021
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18. Lipoprotein DolP supports proper folding of BamA in the bacterial outer membrane promoting fitness upon envelope stress

Author: Cyril Moulin, Yiying Yang, Violette Morales, Jérôme Rech, Gladys Munoz, Cécile Albenne, David Ranava, Raffaele Ieva, David Bikard, Lun Cui, Julien Marcoux, Anne Caumont-Sarcos, Catherine Turlan, François Rousset, Luis Orenday-Tapia, Carine Froment, Laboratoire de microbiologie et génétique moléculaires - UMR5100 (LMGM), Centre de Biologie Intégrative (CBI), Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Biologie de Synthèse - Synthetic biology, Institut Pasteur [Paris] (IP), Institut de pharmacologie et de biologie structurale (IPBS), Further financial support was provided by: the Fondation pour la Recherche Médicale to DR, the Chinese Scholarship Council as part of a joint international PhD program with Toulouse University Paul Sabatier to YY, the French Ministry of Higher Education and Research to LO-T, the Ecole Normale Supérieure to FR, the European Research Council (Europe Union’s Horizon 2020 research and innovation program, grant agreement No 677823), the French governmental Investissement d'Avenir program and the Laboratoire d’Excellence ‘Integrative Biology of Emerging Infectious Diseases’ (ANR-10-LABX-62-IBEID) to DB, the Centre National de la Recherche Scientifique and the ATIP-Avenir program to RI., ANR-10-LABX-0062,IBEID,Integrative Biology of Emerging Infectious Diseases(2010), European Project: 677823,H2020,ERC-2015-STG,CRISPAIR(2016), Laboratoire de microbiologie et génétique moléculaires (LMGM), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Institut Pasteur [Paris], Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), and Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées
Subjects: Protein Folding, Cell division, QH301-705.5, Lipoproteins, Science, General Biochemistry, Genetics and Molecular Biology, 03 medical and health sciences, chemistry.chemical_compound, 0302 clinical medicine, Bama, Escherichia coli, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Biology (General), 030304 developmental biology, Envelope (waves), 0303 health sciences, Microbiology and Infectious Disease, BAM, General Immunology and Microbiology, Chemistry, Outer membrane biogenesis, General Neuroscience, Escherichia coli Proteins, E. coli, Envelope stress, General Medicine, DolP, bacterial infections and mycoses, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, YraP, Cell biology, Folding (chemistry), Bacterial Outer Membrane, bacteria, Medicine, Peptidoglycan, Genetic Fitness, Bacterial outer membrane, OMPs, 030217 neurology & neurosurgery, Biogenesis, Lipoprotein, Research Article, Bacterial Outer Membrane Proteins
Abstract: In Proteobacteria, integral outer membrane proteins (OMPs) are crucial for the maintenance of the envelope permeability barrier to some antibiotics and detergents. In Enterobacteria, envelope stress caused by unfolded OMPs activates the sigmaE (σE) transcriptional response. σE upregulates OMP biogenesis factors, including the β-barrel assembly machinery (BAM) that catalyses OMP folding. Here we report that DolP (formerly YraP), a σE-upregulated and poorly understood outer membrane lipoprotein, is crucial for fitness in cells that undergo envelope stress. We demonstrate that DolP interacts with the BAM complex by associating with outer membrane-assembled BamA. We provide evidence that DolP is important for proper folding of BamA that overaccumulates in the outer membrane, thus supporting OMP biogenesis and envelope integrity. Notably, mid-cell recruitment of DolP had been linked to regulation of septal peptidoglycan remodelling by an unknown mechanism. We now reveal that, during envelope stress, DolP loses its association with the mid-cell, thereby suggesting a mechanistic link between envelope stress caused by impaired OMP biogenesis and the regulation of a late step of cell division.
Published: 2021
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19. ClpXP-mediated Degradation of the TAC Antitoxin is Neutralized by the SecB-like Chaperone in Mycobacterium tuberculosis

Author: Pierre Genevaux, Anne-Marie Cirinesi, Patricia Bordes, Ambre Sala, Jyotsna Nagpal, Pauline Texier, David A. Dougan, Xibing Xu, Moise Mansour, Laboratoire de microbiologie et génétique moléculaires - UMR5100 (LMGM), Centre de Biologie Intégrative (CBI), Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Environnement, Ville, Société (EVS), École normale supérieure de Lyon (ENS de Lyon)-École des Mines de Saint-Étienne (Mines Saint-Étienne MSE), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Université Lumière - Lyon 2 (UL2)-Université Jean Moulin - Lyon 3 (UJML), Université de Lyon-Université de Lyon-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université Jean Monnet - Saint-Étienne (UJM)-École Nationale des Travaux Publics de l'État (ENTPE)-École nationale supérieure d'architecture de Lyon (ENSAL)-Centre National de la Recherche Scientifique (CNRS), Centre de recherche en pharmacologie - santé (CRPS), Centre National de la Recherche Scientifique (CNRS), ANR-19-CE12-0026,M-TOX,Etude de la toxine RNase du système TAC chez Mycobacterium tuberculosis(2019), Laboratoire de microbiologie et génétique moléculaires (LMGM), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Environnement Ville Société (EVS), École normale supérieure - Lyon (ENS Lyon)-École des Mines de Saint-Étienne (Mines Saint-Étienne MSE), Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA)-Université Jean Monnet [Saint-Étienne] (UJM)-École Nationale des Travaux Publics de l'État (ENTPE)-École nationale supérieure d'architecture de Lyon (ENSAL)-Centre National de la Recherche Scientifique (CNRS), Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-École nationale supérieure d'architecture de Lyon (ENSAL)-École des Mines de Saint-Étienne (Mines Saint-Étienne MSE), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-École Nationale des Travaux Publics de l'État (ENTPE)-Université Jean Monnet [Saint-Étienne] (UJM)-Université Jean Moulin - Lyon 3 (UJML), and Université de Lyon-Université Lumière - Lyon 2 (UL2)-École normale supérieure - Lyon (ENS Lyon)
Subjects: Proteases, medicine.medical_treatment, [SDV]Life Sciences [q-bio], Genetic Vectors, Gene Expression, Bacterial genome size, complex mixtures, Microbiology, Mycobacterium tuberculosis, 03 medical and health sciences, 0302 clinical medicine, Bacterial Proteins, Structural Biology, medicine, Escherichia coli, Protein Isoforms, Cloning, Molecular, Molecular Biology, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, 0303 health sciences, Protease, biology, Chemistry, Escherichia coli Proteins, Toxin-Antitoxin Systems, Endopeptidase Clp, Gene Expression Regulation, Bacterial, biology.organism_classification, Recombinant Proteins, 3. Good health, Chaperone (protein), Proteolysis, biology.protein, Chaperone binding, ATPases Associated with Diverse Cellular Activities, Degron, Antitoxin, 030217 neurology & neurosurgery, Genome, Bacterial, Molecular Chaperones
Abstract: Bacterial toxin-antitoxin (TA) systems are composed of a deleterious toxin and its antagonistic antitoxin. They are widespread in bacterial genomes and mobile genetic elements, and their functions remain largely unknown. Some TA systems, known as TAC modules, include a cognate SecB-like chaperone that assists the antitoxin in toxin inhibition. Here, we have investigated the involvement of proteases in the activation cycle of the TAC system of the human pathogen Mycobacterium tuberculosis. We show that the deletion of endogenous AAA+ proteases significantly bypasses the need for a dedicated chaperone and identify the mycobacterial ClpXP1P2 complex as the main protease involved in TAC antitoxin degradation. In addition, we show that the ClpXP1P2 degron is located at the extreme C-terminal end of the chaperone addiction (ChAD) region of the antitoxin, demonstrating that ChAD functions as a hub for both chaperone binding and recognition by proteases.
Published: 2021
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20. High Frequency of Enterocytozoon bieneusi Genotype WL12 Occurrence among Immunocompromised Patients with Intestinal Microsporidiosis

Author: Ghaya Cherif, A. Kallel, Mariem Messaoud, Slaheddine Belhadj, Najla Fakhfekh, Helmi Mardassi, Mayssa Gnaien, Sana Jemel, Sonia Marouen, Sadri Znaidi, Kalthoum Kallel, Mohamed Amine Skhairia, Yasmine Rebai, Salma Abbes, Hôpital La Rabta [Tunis], Laboratoire de Microbiologie Moléculaire, Vaccinologie et Développement Biotechnologique (LR11IPT01), Institut Pasteur de Tunis, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP), Université de Tunis El Manar (UTM), Biologie et Pathogénicité fongiques - Fungal Biology and Pathogenicity (BPF), Institut Pasteur [Paris] (IP)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), and Financial support to K.K. (Research Unit # UR17SP03) was obtained from the Tunisian Ministry of Health and the Ministry of Higher Education & Scientific Research. S.Z. is an Institut Pasteur International Network Affiliate Program Fellow. S.Z. was supported by grants/funds from the Laboratoire de Microbiologie Moléculaire, Vaccinologie et Développement Biotechnologique (LR16IPT01, Institut Pasteur de Tunis, Tunis-Belvédère, Tunisia), the Unité Biologie & Pathogénicité Fongiques (Institut Pasteur, Paris, France), the Institut Pasteur de Tunis Programmes Collaboratifs Internes (Grants # PCI22 and PCI32), the Ministry of Higher Education and Scientific Research (Young Investigator Grant Award # 19PEJC06-02) and the Institut Pasteur Division of International Affairs, Paris, France (Institut Pasteur International Network Affiliate Program Fellowship).
Subjects: Microbiology (medical), Encephalitozoon spp, Enterocytozoon bieneusi, Opportunistic infection, [SDV]Life Sciences [q-bio], Plant Science, Microsporidiosis, Article, emerging infectious diseases, 03 medical and health sciences, fluids and secretions, Genotype, molecular diagnosis, parasitic diseases, medicine, Genotyping, lcsh:QH301-705.5, Ecology, Evolution, Behavior and Systematics, Immunodeficiency, 030304 developmental biology, 0303 health sciences, biology, Molecular epidemiology, 030306 microbiology, Transmission (medicine), fungi, virus diseases, HIV, biology.organism_classification, medicine.disease, genotype WL12, Virology, lcsh:Biology (General), immunocompromised patients
Abstract: Microsporidiosis is an emerging opportunistic infection causing severe digestive disorders in immunocompromised patients. The aim of this study was to investigate the prevalence of intestinal microsporidia carriage among immunocompromised patients hospitalized at a major hospital complex in the Tunis capital area, Tunisia (North Africa), and perform molecular epidemiology and population structure analyses of Enterocytozoon bieneusi, which is an emerging fungal pathogen. We screened 250 stool samples for the presence of intestinal microsporidia from 171 patients, including 81 organ transplant recipients, 73 Human Immunodeficiency Virus (HIV)-positive patients, and 17 patients with unspecified immunodeficiency. Using a nested PCR-based diagnostic approach for the detection of E. bieneusi and Encephalitozoon spp., we identified 18 microsporidia-positive patients out of 171 (10.5%), among which 17 were infected with E. bieneusi. Microsporidia-positive cases displayed chronic diarrhea (17 out of 18), which was associated more with HIV rather than with immunosuppression other than HIV (12 out of 73 versus 6 out of 98, respectively, p = 0.02) and correlated with extended hospital stays compared to microsporidia-negative cases (60 versus 19 days on average, respectively, p = 0.001). Strikingly, internal transcribed spacer (ITS)-based genotyping of E. bieneusi strains revealed high-frequency occurrence of ITS sequences that were identical (n = 10) or similar (with one single polymorphic site, n = 3) to rare genotype WL12. Minimum-spanning tree analyses segregated the 17 E. bieneusi infection cases into four distinct genotypic clusters and confirmed the high prevalence of genotype WL12 in our patient population. Phylogenetic analyses allowed the mapping of all 17 E. bieneusi strains to zoonotic group 1 (subgroups 1a and 1b/1c), indicating loose host specificity and raising public health concern. Our study suggests a probable common source of E. bieneusi genotype WL12 transmission and prompts the implementation of a wider epidemiological investigation.
Published: 2021
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21. Super-resolved live-cell imaging using Random Illumination Microscopy

Author: Tong Li, Anne Sentenac, Magali Suzanne, Grégoire Michaux, Mathieu Pinot, Claire Estibal, Marc Allain, Thomas Mangeat, Awoke Negash, Simon Labouesse, Renaud Poincloux, Sylvie Tournier, Christian Rouvière, Sophie Allart, Anaïs Bouissou, Debora Keller, Xia Bo Wang, Emmanuel Martin, Sylvain Cantaloube, Elodie Vega, Jérôme Idier, Aude Guénolé, Valentin Debarnot, Roland Le Borgne, Centre de Biologie Intégrative (CBI), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Institut FRESNEL (FRESNEL), Centre National de la Recherche Scientifique (CNRS)-École Centrale de Marseille (ECM)-Aix Marseille Université (AMU), Coherent Optical Microscopy and X-rays (COMiX), Centre National de la Recherche Scientifique (CNRS)-École Centrale de Marseille (ECM)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)-École Centrale de Marseille (ECM)-Aix Marseille Université (AMU), Laboratoire de Biologie Cellulaire et Moléculaire du Contrôle de la Prolifération (LBCMCP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Centre de Biologie Intégrative (CBI), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Institut de pharmacologie et de biologie structurale (IPBS), Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Laboratoire de microbiologie et génétique moléculaires (LMGM), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Centre de Physiopathologie Toulouse Purpan (CPTP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Institut de Génétique et Développement de Rennes (IGDR), Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique )-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES), Laboratoire des Sciences du Numérique de Nantes (LS2N), IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Université de Nantes - UFR des Sciences et des Techniques (UN UFR ST), Université de Nantes (UN)-Université de Nantes (UN)-École Centrale de Nantes (ECN)-Centre National de la Recherche Scientifique (CNRS), SEMO (SEMO), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Aix Marseille Université (AMU)-École Centrale de Marseille (ECM)-Centre National de la Recherche Scientifique (CNRS), Aix Marseille Université (AMU)-École Centrale de Marseille (ECM)-Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU)-École Centrale de Marseille (ECM)-Centre National de la Recherche Scientifique (CNRS), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Centre de Biologie Intégrative (CBI), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de microbiologie et génétique moléculaires - UMR5100 (LMGM), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Université de Rennes (UR)-Centre National de la Recherche Scientifique (CNRS)-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique ), Université de Nantes - UFR des Sciences et des Techniques (UN UFR ST), Université de Nantes (UN)-Université de Nantes (UN)-École Centrale de Nantes (ECN)-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Centre de Biologie Intégrative (CBI), and Idier, Jérôme
Subjects: Cultural Studies, Spatial correlation, History, Brightness, Materials science, [SPI.OPTI] Engineering Sciences [physics]/Optics / Photonic, Literature and Literary Theory, Science, [SDV]Life Sciences [q-bio], Structured illumination microscopy, super-resolution, QD415-436, Iterative reconstruction, variance, Biochemistry, 01 natural sciences, computational imaging, 010309 optics, 03 medical and health sciences, Speckle pattern, Optics, Live cell imaging, 0103 physical sciences, Microscopy, Fluorescence microscope, [SDV.BBM] Life Sciences [q-bio]/Biochemistry, Molecular Biology, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, [SPI.SIGNAL] Engineering Sciences [physics]/Signal and Image processing, 030304 developmental biology, Physics, 0303 health sciences, Scattering, business.industry, Resolution (electron density), live imaging, Sample (graphics), Superresolution, aberration, microscopy, [SPI.OPTI]Engineering Sciences [physics]/Optics / Photonic, fluorescence, speckle, business, [SPI.SIGNAL]Engineering Sciences [physics]/Signal and Image processing, TP248.13-248.65, Biotechnology
Abstract: Summary: Current super-resolution microscopy (SRM) methods suffer from an intrinsic complexity that might curtail their routine use in cell biology. We describe here random illumination microscopy (RIM) for live-cell imaging at super-resolutions matching that of 3D structured illumination microscopy, in a robust fashion. Based on speckled illumination and statistical image reconstruction, easy to implement and user-friendly, RIM is unaffected by optical aberrations on the excitation side, linear to brightness, and compatible with multicolor live-cell imaging over extended periods of time. We illustrate the potential of RIM on diverse biological applications, from the mobility of proliferating cell nuclear antigen (PCNA) in U2OS cells and kinetochore dynamics in mitotic S. pombe cells to the 3D motion of myosin minifilaments deep inside Drosophila tissues. RIM's inherent simplicity and extended biological applicability, particularly for imaging at increased depths, could help make SRM accessible to biology laboratories. Motivation: Super-resolution optical microscopy (SRM) has been instrumental to rapid progress in cell biology. Many SRM variants are now available with different compromises between phototoxicity, spatiotemporal resolutions, and sensitivity to aberrations. Yet, established SRM techniques, even implemented as expensive turn-key systems, require expert know-how at the instrumentation or image reconstruction levels to operate at the best of their capabilities. The present challenge is to develop a simple, easy to use, and low-cost SRM technique that would combine artifact-free super-resolution, robustness to aberration, low toxicity, and good temporal resolution for routine functional imaging of live cells within normal or pathological tissues.
Published: 2021
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22. MeJA Elicitation of Chicory Hairy Roots Promotes Efficient Increase of 3,5-diCQA Accumulation, a Potent Antioxidant and Antibacterial Molecule

Author: Nathalie Jullian, Harmony Alves Dos Alves Dos Santos, Jennifer Samaillie, Jean-Louis Hilbert, Sevser Sahpaz, Sylvie Chevalier, Ali Tahrioui, David Gagneul, Audrey Etienne, Caroline Rambaud, Céline Rivière, Christel Neut, Guillaume Bernard, Transfrontalière BioEcoAgro (Transfrontalière BioEcoAgro), Université d'Artois (UA)-Université de Liège-Université de Picardie Jules Verne (UPJV)-Université du Littoral Côte d'Opale (ULCO)-Université de Lille-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institute for Translational Research in Inflammation - U 1286 (INFINITE (Ex-Liric)), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Lille-Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille), Laboratoire de Microbiologie Signaux et Microenvironnement (LMSM), Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-Normandie Université (NU), University of LilleRegion Hauts-de-FranceFEDER funds of the Region Hauts-de-FranceFederative Research Structure SFR CondorcetAlibiotech grant, Transfrontalière BioEcoAgro - UMR 1158 (BioEcoAgro), Université d'Artois (UA)-Université de Liège-Université de Picardie Jules Verne (UPJV)-Université du Littoral Côte d'Opale (ULCO)-Université de Lille-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-JUNIA (JUNIA), Université catholique de Lille (UCL)-Université catholique de Lille (UCL), CHU Lille, INRA, ISA, Inserm, Univ. Artois, Univ. Littoral Côte d’Opale, Université de Lille, Institut Charles Viollette (ICV) - ULR 7394 [ICV], Institut Charles Viollette (ICV) - ULR 7394, Institut de Recherche Translationnelle sur l'Inflammation (INFINITE) - U1286, Institut Charles Viollette (ICV) - EA 7394 [ICV], Transfrontalière BioEcoAgro - UMR 1158 [BioEcoAgro], Laboratoire de Microbiologie du Froid – Signaux et Micro-Environnement [LMDF-SME], and Prévot-Liger, Perrine
Subjects: 0106 biological sciences, 0301 basic medicine, Microbiology (medical), [SDV]Life Sciences [q-bio], Secondary metabolite, medicine.disease_cause, 01 natural sciences, Biochemistry, Microbiology, 5-dicaffeoylquinic acid 3, Article, 03 medical and health sciences, chemistry.chemical_compound, Pyocyanin, Cichorium, medicine, Pharmacology (medical), Food science, General Pharmacology, Toxicology and Pharmaceutics, 3,5-dicaffeoylquinic acid 3,4,5-tricaffeoylquinic acid, Methyl jasmonate, Pyoverdine, biology, Cichorium intybus, Pseudomonas aeruginosa, pyoverdine, lcsh:RM1-950, 5-tricaffeoylquinic acid, 4, 3, hairy roots, Biofilm, 15. Life on land, biology.organism_classification, [SDV] Life Sciences [q-bio], lcsh:Therapeutics. Pharmacology, 030104 developmental biology, Infectious Diseases, chemistry, Antibacterial activity, 010606 plant biology & botany, medicine.drug
Abstract: Cichorium intybus L. (Asteraceae) is an important industrial crop, as well as a medicinal plant which produces some bioactive compounds implicated in various biological effects with potential applications in human health. Particularly, roots produce hydroxycinnamic acids like 5-caffeoyquinic acid and 3,5-dicaffeoylquinic acid (di-CQA). The present investigation relates to the use of methyl jasmonate for enhancing phenolic compounds accumulation and production in hairy root cultures of C. intybus. Elicitated hairy root growth rate increased 13.3 times compared with the initial inoculum in a period of 14 days and di-CQA production represented about 12% of DW. The elicitation has also promoted the production of tricaffeoylquinic acid never described in the chicory roots and identified as 3,4,5-tricaffeoyquinic acid by means of nuclear magnetic resonance. Our study confirmed the strong anti-oxidant effect of di-CQA. Our results also confirmed globally a selectivity of action of di-CQA against Gram-positive bacteria, in particular against some strains of Staphylococcus and Streptococcus. However, a non-negligible antibacterial activity of di-CQA against Pseudomonas aeruginosa was also underlined (MIC = 0.156 mg.mL&minus, 1 against some P. aeruginosa strains). The influence of di-CQA has been explored to evaluate its impact on the physiology of P. aeruginosa. Di-CQA showed no effect on the biofilm formation and the production of extracellular pyocyanin. However, it demonstrated an effect on virulence through the production of pyoverdine with a dose-dependent manner by more than 7-fold when treated at a concentration of 128 &micro, g&middot, mL&minus, 1, thus suggesting a link between di-CQA and iron sequestration. This study shows that elicitated hairy root cultures of chicory can be developed for the production of di-CQA, a secondary metabolite with high antibacterial potential.
Published: 2020
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23. Staphylococcus capitis isolated from bloodstream infections: a nationwide 3-month survey in 38 neonatal intensive care units

Author: Sylvie Joron, Stéphane Marret, Fabrice Lapeyre, Jérôme Larche, Jacqueline Grando, David Leyssene, Jean Nakhleh, Clarisse Dupin, Tania Foucan, Stéphanie Bordes-Couecou, Géraldine Abadie, Franck Labbe, Marie Kempf, Manuel Petitfrere, Audrey Robine, Marie Decalonne, Chantal Chaplain, Philippe Jouvencel, Florent Goube, Benjamin Cotte, Laurent Villeneuve, Adeline Lacazette, Raoul Baron, Jean-Marc Jellimann, Anne-Sophie Trentesaux, Nathalie Chautemps, Laurent Mereghetti, Olivier Dauwalder, Nicolas Fortineau, Christine Roques Ceschin, Rafik Ben Ammar, Sandra Bourdon, Alain Gravet, Audrey Glanard, Olivier Belmonte, Jacques Gilquin, Arnaud Florentin, Souad Slimani, Annick Lefebvre, Jérôme Guinard, Edith Malpote, Céline Chatelet, Isabelle Bauvin, Alain Lozniewski, Anaëlle Muggeo, Geneviève Héry-Arnaud, Stéphane Le Vu, Isabelle Ligi, Anne Le Pourhiennec, Christian Cattoen, Olivier Join-Lambert, Bruno Pozetto, Carole De Chillaz, Amine Siali, Pascale Martres, Michel Drancourt, Claire Lesteven, Sandra C. dos Santos, Nadège Bourgeois-Nicolaos, Aude Davy, Claude Olive, Rémi Gimenes, Laure Gibert, Raymond Ruimy, Virginie Morange, Antoine Bouissou, Julien Mourdie, Emmanuelle Bille, Marie-Noëlle Noulard, Vincent Cattoir, Martine Delorme, Dominique Trivier, Luc Desfrere, Hugues Patural, Patrick Barthelemy, Nadia Idri, Florence Lemann, Franck-Olivier Mallaval, Sophie Ketterer-Martinon, Christian Vandenbussche, Pierre Frange, Sylvie Ledru, Mouna Khecharem, Pierre Lureau, Sophie Boyer, Philippe Berthelot, Salma Ben Hadj Yahia, Clément Legeay, Emilie Benabid, Guillaume Menard, Marion Levast-Raffin, Céline Coroller-Bec, Claire Huart, Maryvonne Demasure, Pascal Bolot, Yasmina Berrouane, Hélène Cormier, Pascale Minery, Pascale Penn, Peggy Larroude, Evelyne Werner, Géraldine Gascoin, Virginie Forget, Nathalie van der Mee-Marquet, Stéphanie Soive, Karine Gambarotto, Vanina Ambrogi, Aurore Claudinon, Serge Klosowski, Brigitte Riviere, Véronique Merle, Laura Menvielle, Véronique Faraut-Derouin, Saïd Aberrane, Alain Beuchee, Nolwenn Le Sache, Hôpital Bretonneau, CHU Trousseau [Tours], Centre Hospitalier Régional Universitaire de Tours (CHRU Tours), Centre hospitalier Félix-Guyon [Saint-Denis, La Réunion], Centre Hospitalier René Dubos [Pontoise], Centre Hospitalier Intercommunal de Créteil (CHIC), Centre Hospitalier Régional Universitaire de Brest (CHRU Brest), Hôpital de la Conception [CHU - APHM] (LA CONCEPTION), Centre hospitalier de Pau, Centre Hospitalier Universitaire de La Réunion (CHU La Réunion), AP-HP - Hôpital Antoine Béclère [Clamart], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Centre Hospitalier de Calais, Centre Hospitalier Universitaire de Nice (CHU Nice), Centre Hospitalier Universitaire de Saint-Etienne [CHU Saint-Etienne] (CHU ST-E), CHU Pontchaillou [Rennes], Institut Necker Enfants-Malades (INEM - UM 111 (UMR 8253 / U1151)), Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Centre Hospitalier de Saint-Denis [Ile-de-France], Centre Hospitalier de la Côte Basque (CHCB), Groupe Hospitalier du Havre, Hôpital Charles Nicolle [Rouen], CHU Rouen, Normandie Université (NU)-Normandie Université (NU), Centre hospitalier [Valenciennes, Nord], Centre Hospitalier Universitaire [Rennes], GHT de l'Artois, Centre Hospitalier Victor Dupouy, Centre Hospitalier Métropole Savoie [Chambéry], Centre Hospitalier Universitaire d'Angers (CHU Angers), PRES Université Nantes Angers Le Mans (UNAM), Centre Hospitalier Le Mans (CH Le Mans), Clinique du Val d'Ouest, CHU Necker - Enfants Malades [AP-HP], Hospices Civils de Lyon (HCL), Centre hospitalier Saint-Brieuc, Centre Hospitalier Georges Renon [Niort] (CH Georges Renon Niort), Centre Hospitalier Régional d'Orléans (CHRO), Hôpital Louis Mourier - AP-HP [Colombes], Microbes évolution phylogénie et infections (MEPHI), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), CHU de Saint-Brieuc, Interactions Gènes-Risques environnementaux et Effets sur la Santé (INGRES), Université de Lorraine (UL), Unité de Recherche Environnement Physique de la plante Horticole (EPHOR), Université d'Angers (UA)-AGROCAMPUS OUEST, AP-HP Hôpital Bicêtre (Le Kremlin-Bicêtre), CHU Pointe-à-Pitre/Abymes [Guadeloupe], Groupe de Recherche sur l'Adaptation Microbienne (GRAM 2.0), Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU)-Université de Rouen Normandie (UNIROUEN), Normandie Université (NU), Hôpital Hôtel-Dieu [Paris], Hôpital Delafontaine, Centre Hospitalier de Mulhouse, site du Hasenrain (Mulhouse), Laboratoire Universitaire de Biodiversité et Ecologie Microbienne (LUBEM), Université de Brest (UBO), Service de réanimation néonatale [CHRU Nancy], Centre Hospitalier Régional Universitaire de Nancy (CHRU Nancy), Pathogénie des infections systémiques (UMR_S 570), Centre Régional de PharmacoVigilance Nord-Pas-de-Calais [CHU Lille] (CRPV), Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille)-Faculté de Médecine Henri Warembourg - Université de Lille, Centre de Recherche en Cancérologie Nantes-Angers (CRCNA), PRES Université Nantes Angers Le Mans (UNAM)-PRES Université Nantes Angers Le Mans (UNAM)-Hôtel-Dieu de Nantes-Institut National de la Santé et de la Recherche Médicale (INSERM)-Hôpital Laennec-Centre National de la Recherche Scientifique (CNRS)-Faculté de Médecine d'Angers-Centre hospitalier universitaire de Nantes (CHU Nantes), CHU de la Martinique [Fort de France], Groupe Hospitalier du Havre Hôpital Jacques Monod (MONTIVILLIERS) (GHH), Polyclinique Médipôle Saint-Roch [Cabestany], Centre Hospitalier Universitaire de Reims (CHU Reims), CHU Caen, Normandie Université (NU)-Tumorothèque de Caen Basse-Normandie (TCBN), Université d'Auvergne - Clermont-Ferrand I (UdA), Aix-Marseille Université - École de médecine (AMU SMPM MED), Aix-Marseille Université - Faculté des sciences médicales et paramédicales (AMU SMPM), Aix Marseille Université (AMU)-Aix Marseille Université (AMU), Service de microbiologie [CHU Nancy], Service psychiatrique de l'enfant et de l'adolescent [CHU Hôpital Robert Debré], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpital Robert Debré, Service de bactériologie-virologie [Tours], Centre Hospitalier Régional Universitaire de Tours (CHRU Tours)-Hôpital Bretonneau, Infectiologie et Santé Publique (UMR ISP), Université de Tours (UT)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Registre EPIMAD, Normandie Université (NU)-Normandie Université (NU)-CHU Amiens-Picardie-Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille), Pathogénie des Staphylocoques – Staphylococcal Pathogenesis (StaPath), Centre International de Recherche en Infectiologie (CIRI), École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Groupe Hospitalier Artois-Ternois Centre Hospitalier d’Arras, Système Nerveux Autonome - Epidémiologie, Physiologie, Ingénierie, Santé (SNA - EPIS), Centre Hospitalier Universitaire de Saint-Etienne [CHU Saint-Etienne] (CHU ST-E)-Université Jean Monnet - Saint-Étienne (UJM), ELSAN Polyclinique Majorelle, Centre Hospitalier Intercommunal Castres-Mazamet (CHIC-CM), Centre Hospitalier Universitaire de Toulouse (CHU Toulouse), Centre Hospitalier Universitaire de Martinique [Fort-de-France, Martinique], Centre Hospitalier de Lens, Institut de Veille Sanitaire (INVS), Hôpital Trousseau, Jonchère, Laurent, Centre Hospitalier Universitaire de Saint-Etienne (CHU de Saint-Etienne), Le CHCB, Centre Hospitalier de la Côte Basque, Centre International de Recherche en Infectiologie - UMR (CIRI), École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Système Nerveux Autonome - Epidémiologie, Physiologie, Ingénierie, Santé (SNA-EPIS), Université Jean Monnet - Saint-Étienne (UJM)-Centre Hospitalier Universitaire de Saint-Etienne, CHU Saint-Etienne, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-Normandie Université (NU)-Université de Caen Normandie (UNICAEN), Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille)-Université Lille 2 - Faculté de Médecine, Université de Tours-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille)-CHU Rouen, Normandie Université (NU)-Normandie Université (NU)-CHU Amiens-Picardie, Centre Hospitalier Régional Universitaire de Tours (CHRU TOURS), Institut National de la Santé et de la Recherche Médicale (INSERM)-École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), Université Jean Monnet [Saint-Étienne] (UJM)-Centre Hospitalier Universitaire de Saint-Etienne, CHU Toulouse [Toulouse], Centre Hospitalier Universitaire Félix-Guyon [Saint-Denis, La Réunion, France], Centre Hospitalier Universitaire de Toulouse, Department of Microbiology Brest, Department of Microbiology, Brest, CHU CLAMART, Centre Hospitalier Universitaire de Nice (CHU de Nice), Centre Hospitalier Côte Basque, Bayonne, CHU Le Havre, Laboratory of microbiology and infection control, Assistance publique-Hôpitaux de Paris, Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Centre Hospitalier Universitaire Charles Nicolle, Partenaires INRAE, CHU de la Réunion, Saint-Denis, France., CHU Lens, CHU Argenteuil, Centre Hospitalier Métropole Savoie-Site de Chambéry, La Clinique du Val d'Ouest, Hôpitaux Est Hôpital Louis Pradel - Hospices Civils de Lyon, Centre Hospitalier Régional d'Orléans (CHR), Hopital Louis Mourier - AP-HP [Colombes], Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU), Service de virologie, Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-CHU Pontchaillou [Rennes], Hôpital Antoine Béclère, Assistance Publique - Hôpitaux de Paris (AP-HP), Service de Bactériologie-Virologie, Hôpital Bretonneau-Centre Hospitalier Régional Universitaire de Tours (CHRU Tours), Centre d'infectiologie Necker-Pasteur [CHU Necker], Service de chirurgie infantile, CHU Felix Guyon, Saint Denis de La Réunion, Hôtel-Dieu, Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôtel-Dieu, Unité d'Hygiène Hospitalière, hospices civils de Lyon, Hôpital du Hasenrain, Mulhouse, CHU Valenciennes, Université Henri Poincaré - Nancy 1 (UHP), Hôpital de Bayonne [Bayonne], CHU Kremlin-Bicétre, Anofel Cryptosporidium National Network, Polyclinique de St Roch, CHU Pau, Unité de prévention et de lutte contre les infections nosocomiales [CHU Angers], PRES Université Nantes Angers Le Mans (UNAM)-PRES Université Nantes Angers Le Mans (UNAM), Division of Neonatology, La Conception Hospital, Assistance Publique-Hôpitaux de Marseille and Faculté de Médecine, Université de la Méditerranée - Aix-Marseille 2, Laboratoire de Microbiologie clinique et environnementale [Pointe-à-Pitre, Guadeloupe, France], Centre Hospitalier Universitaire de Rennes (CHU Rennes), Hôpital privé de l'Estuaire [Le Havre], Pathogénie des Staphylocoques – Staphylococcal Pathogenesis, Hôpital d'Arras, CHU Le MAns, Polyclinique Majorelle, Laboratoire de Microbiologie, Centre Hospitalier Intercommunal Castres-Mazamet, Laboratoire de bactériologie, Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-AP-HP - Hôpital Bichat - Claude Bernard [Paris]-Université Paris Diderot - Paris 7 (UPD7), Laboratoire de Recherche Opérationnelle et Mathématiques de la Décision - LAROMAD (Alger, Algérie), Centre Hospitalier d’Arras, Unité de Méthodologie en Recherche Clinique, Université Claude Bernard Lyon 1 (UCBL), and Université de Lyon-Université de Lyon-Hospices Civils de Lyon (HCL)
Subjects: Male, 0301 basic medicine, Pediatrics, Clone (cell biology), NRCS-A clone, 030501 epidemiology, Staphylococcus capitis, Medical microbiology, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Drug Resistance, Multiple, Bacterial, Medicine, [SDV.MP.VIR] Life Sciences [q-bio]/Microbiology and Parasitology/Virology, [SDV.MHEP.ME] Life Sciences [q-bio]/Human health and pathology/Emerging diseases, [SDV.MHEP.ME]Life Sciences [q-bio]/Human health and pathology/Emerging diseases, biology, Brief Report, Gestational age, General Medicine, Staphylococcal Infections, Anti-Bacterial Agents, 3. Good health, [SDV.MHEP.CSC] Life Sciences [q-bio]/Human health and pathology/Cardiology and cardiovascular system, Nationwide active surveillance, Infectious Diseases, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, [SDV.MHEP.MI] Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Vancomycin, Female, France, 0305 other medical science, Infant, Premature, [SDV.MP.PAR] Life Sciences [q-bio]/Microbiology and Parasitology/Parasitology, medicine.drug, Microbiology (medical), medicine.medical_specialty, Bloodstream catheter-related infection, Birth weight, Preterm babies, 030106 microbiology, Late onset, 03 medical and health sciences, [SDV.MHEP.CSC]Life Sciences [q-bio]/Human health and pathology/Cardiology and cardiovascular system, Intensive Care Units, Neonatal, Sepsis, Intensive care, Humans, [SDV.MP.PAR]Life Sciences [q-bio]/Microbiology and Parasitology/Parasitology, business.industry, Neonatal Intensive Care Unit (NICU), Infant, Newborn, Neonates, biology.organism_classification, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Catheter-Related Infections, [SDV.MP.BAC] Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, business
Abstract: To increase the knowledge about S. capitis in the neonatal setting, we conducted a nationwide 3-month survey in 38 neonatal intensive care units (NICUs) covering 56.6% of French NICU beds. We demonstrated 14.2% of S. capitis BSI (S.capBSI) among nosocomial BSIs. S.capBSI incidence rate was 0.59 per 1000 patient-days. A total of 55.0% of the S.capBSIs were late onset catheter-related BSIs. The S. capitis strains infected preterm babies (median gestational age 26 weeks, median birth weight 855 g). They were resistant to methicillin and aminoglycosides and belonged to the NRCS-A clone. Evolution was favorable in all but one case, following vancomycin treatment.
Published: 2020
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24. The absence of SigX results in impaired carbon metabolism and membrane fluidity in Pseudomonas aeruginosa

Author: Ali Tahrioui, Maud Flechard, Sylvie Chevalier, Cecil Onyedikachi Azuama, Eric Déziel, Gwendoline Gicquel, Cécile Duclairoir-Poc, Rachel Duchesne, Manuella Catel-Ferreira, Emeline Bouffartigues, Thomas Clamens, Marie-Christine Groleau, Damien Tortuel, Coralie Lagy, Ségolène Depayras, Marc G. J. Feuilloley, Hermann J. Heipieper, Pierre Cornelis, Olivier Maillot, Olivier Lesouhaitier, Julie Hardouin, Jonchère, Laurent, Interactions cellulaires et moléculaires (ICM), Université de Rennes (UR)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Microbiologie Signaux et Microenvironnement (LMSM), Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-Normandie Université (NU), Laboratoire de Microbiologie du Froid – Signaux et Micro-Environnement (LMDF-SME), Microbiologie de l'Eau (MDE), Ecologie et biologie des interactions (EBI), Université de Poitiers-Centre National de la Recherche Scientifique (CNRS)-Université de Poitiers-Centre National de la Recherche Scientifique (CNRS), Polymères Biopolymères Surfaces (PBS), Normandie Université (NU)-Normandie Université (NU)-Institut national des sciences appliquées Rouen Normandie (INSA Rouen Normandie), Institut National des Sciences Appliquées (INSA)-Normandie Université (NU)-Institut National des Sciences Appliquées (INSA)-Institut Normand de Chimie Moléculaire Médicinale et Macromoléculaire (INC3M), Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU)-École Nationale Supérieure d'Ingénieurs de Caen (ENSICAEN), Normandie Université (NU)-Université Le Havre Normandie (ULH), Normandie Université (NU)-Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-Institut national des sciences appliquées Rouen Normandie (INSA Rouen Normandie), Institut National des Sciences Appliquées (INSA)-Normandie Université (NU)-Institut National des Sciences Appliquées (INSA)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Université de Caen Normandie (UNICAEN), Normandie Université (NU)-École Nationale Supérieure d'Ingénieurs de Caen (ENSICAEN), Normandie Université (NU)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Helmholtz Zentrum für Umweltforschung = Helmholtz Centre for Environmental Research (UFZ), Institut Armand Frappier (INRS-IAF), Institut National de la Recherche Scientifique [Québec] (INRS)-Réseau International des Instituts Pasteur (RIIP), Laboratory of Microbial Interactions, Université de Brussel, Vriendenkring VUB, Microbiology, Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Centre National de la Recherche Scientifique (CNRS), Institut national des sciences appliquées Rouen Normandie (INSA Rouen Normandie), Institut National des Sciences Appliquées (INSA)-Normandie Université (NU)-Institut National des Sciences Appliquées (INSA)-Normandie Université (NU)-Institut de Chimie du CNRS (INC)-Institut Normand de Chimie Moléculaire Médicinale et Macromoléculaire (INC3M), Institut de Chimie du CNRS (INC)-École Nationale Supérieure d'Ingénieurs de Caen (ENSICAEN), Institut National des Sciences Appliquées (INSA)-Normandie Université (NU)-Institut National des Sciences Appliquées (INSA)-Université Le Havre Normandie (ULH), Normandie Université (NU)-Centre National de la Recherche Scientifique (CNRS)-Université de Caen Normandie (UNICAEN), and Normandie Université (NU)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Catabolite Repression, 0301 basic medicine, Proteome, Membrane Fluidity, Mutant, Catabolite repression, lcsh:Medicine, Sigma Factor, [SDV.TOX.TCA]Life Sciences [q-bio]/Toxicology/Toxicology and food chain, [SDV.BC.IC] Life Sciences [q-bio]/Cellular Biology/Cell Behavior [q-bio.CB], Article, Cell wall, 03 medical and health sciences, chemistry.chemical_compound, Bacterial Proteins, Lysogeny broth, [SDV.BC.IC]Life Sciences [q-bio]/Cellular Biology/Cell Behavior [q-bio.CB], Membrane fluidity, lcsh:Science, ComputingMilieux_MISCELLANEOUS, Regulation of gene expression, Multidisciplinary, Chemistry, Gene Expression Profiling, lcsh:R, Biological Transport, Gene Expression Regulation, Bacterial, Metabolism, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Phenotype, Carbon, Cell biology, 030104 developmental biology, [SDV.TOX.TCA] Life Sciences [q-bio]/Toxicology/Toxicology and food chain, general, Pseudomonas aeruginosa, lcsh:Q, [SDV.MP.BAC] Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Energy Metabolism
Abstract: In Pseudomonas aeruginosa, SigX is an extra-cytoplasmic function σ factor that belongs to the cell wall stress response network. In previous studies, we made the puzzling observation that sigX mutant growth was severely affected in rich lysogeny broth (LB) but not in minimal medium. Here, through comparative transcriptomic and proteomic analysis, we show that the absence of SigX results in dysregulation of genes, whose products are mainly involved in transport, carbon and energy metabolisms. Production of most of these genes is controlled by carbon catabolite repression (CCR), a key regulatory system than ensures preferential carbon source uptake and utilization, substrate prioritization and metabolism. The strong CCR response elicited in LB was lowered in a sigX mutant, suggesting altered nutrient uptake. Since the absence of SigX affects membrane composition and fluidity, we suspected membrane changes to cause such phenotype. The detergent polysorbate 80 (PS80) can moderately destabilize the envelope resulting in non-specific increased nutrient intake. Remarkably, growth, membrane fluidity and expression of dysregulated genes in the sigX mutant strain were restored in LB supplemented with PS80. Altogether, these data suggest that SigX is indirectly involved in CCR regulation, possibly via its effects on membrane integrity and fluidity.
Published: 2018
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25. Emerging fields in chaperone proteins: A French workshop

Author: Reynald Gillet, Elisabetta Mileo, Patricia Bordes, Chantal Iobbi-Nivol, Marie-Thérèse Giudici-Orticoni, Alessandro Barducci, Marie-Pierre Castanié-Cornet, Cyrille Garnier, Brigitte Gontero, Pierre Goloubinoff, Pierre Genevaux, Françoise Ochsenbein, Olivier Genest, Marianne Ilbert, Gilbert Richarme, Bioénergétique et Ingénierie des Protéines (BIP ), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Centre de Biochimie Structurale [Montpellier] (CBS), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Institut National de la Santé et de la Recherche Médicale (INSERM), Laboratoire de microbiologie et génétique moléculaires (LMGM), Centre de Biologie Intégrative (CBI), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Mécanismes moléculaires dans les démences neurodégénératives (MMDN), Université de Montpellier (UM)-Université Montpellier 2 - Sciences et Techniques (UM2)-Institut National de la Santé et de la Recherche Médicale (INSERM)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES), Institut de Génétique et Développement de Rennes (IGDR), Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique )-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES), Université de Lausanne (UNIL), Institut de Biologie Intégrative de la Cellule (I2BC), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Chimie et de Biochimie Pharmacologiques et Toxicologiques (LCBPT - UMR 8601), Université Paris Descartes - Paris 5 (UPD5)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), BIP laboratory, Agence Nationale de la Recherche [ANR-16-CE11-0002-01], Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de microbiologie et génétique moléculaires - UMR5100 (LMGM), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM), Université de Rennes (UR), Université de Rennes (UR)-Centre National de la Recherche Scientifique (CNRS)-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique ), Université de Lausanne = University of Lausanne (UNIL), ANR-16-CE11-0002,ChaperomEnvBact,Exploration du chaperome des bactéries environnementales : découverte de nouveaux chaperons(2016), Laboratoire de Bioénergétique et Ingénierie des Protéines, Centre National de la Recherche Scientifique (CNRS), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Université Montpellier 2 - Sciences et Techniques (UM2)-École pratique des hautes études (EPHE)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Centre National de la Recherche Scientifique (CNRS)-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique ), Université Paris-Sud - Paris 11 (UP11)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université Paris-Saclay, and Université Paris Descartes - Paris 5 (UPD5)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0301 basic medicine, [SDV.GEN]Life Sciences [q-bio]/Genetics, Engineering, Plasticity, biology, business.industry, Folding/misfolding, education, Library science, General Medicine, Biochemistry, GroEL, [SDV.BBM.BC]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biomolecules [q-bio.BM], Aggregation, 03 medical and health sciences, 030104 developmental biology, Chaperone proteins, Chaperone (protein), Hsp33, Multifunctionality, biology.protein, Structural dynamics, Protein folding, [SDV.BBM.BC]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biochemistry [q-bio.BM], business
Abstract: International audience; The "Bioenergetique et Ingenierie des Proteines (BIP)" laboratory, CNRS (France), organized its first French workshop on molecular chaperone proteins and protein folding in November 2017. The goal of this workshop was to gather scientists working in France on chaperone proteins and protein folding. This initiative was a great success with excellent talks and fruitful discussions. The highlights were on the description of unexpected functions and post-translational regulation of known molecular chaperones (such as Hsp90, Hsp33, SecB, GroEL) and on state-of-the-art methods to tackle questions related to this theme, including Cryo-electron microscopy, Nuclear Magnetic Resonance (NMR), Electron Paramagnetic Resonance (EPR), simulation and modeling. We expect to organize a second workshop in two years that will include more scientists working in France in the chaperone field.
Published: 2018
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26. Protein polarization driven by nucleoid exclusion of DnaK(HSP70)–substrate complexes

Author: Collet, Clémence, Thomassin, Jenny-Lee, Francetic, Olivera, Genevaux, Pierre, Tran Van Nhieu, Guy, Centre interdisciplinaire de recherche en biologie (CIRB), Labex MemoLife, École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Collège de France (CdF (institution))-Ecole Superieure de Physique et de Chimie Industrielles de la Ville de Paris (ESPCI Paris), Université Paris sciences et lettres (PSL)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Université Paris sciences et lettres (PSL), Biochimie des Interactions Macromoléculaires / Biochemistry of Macromolecular Interactions, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de microbiologie et génétique moléculaires - UMR5100 (LMGM), Centre de Biologie Intégrative (CBI), Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), This work was funded by the Inserm, the CNRS and the Collège de France, as well as grants from the Labex Memolife 'Microlife' and the PSL Idex 'Shigaforce'. C.C. is the recipient of an MERT grant attributed by the Université Paris-Diderot, Ecole Doctorale: B3MI. J.L.T. is the recipient of an NSERC postdoctoral fellowship., École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Ecole Superieure de Physique et de Chimie Industrielles de la Ville de Paris (ESPCI Paris), Université Paris sciences et lettres (PSL)-Collège de France (CdF (institution))-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Collège de France (CdF (institution))-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM), Université Paris sciences et lettres (PSL)-Collège de France (CdF (institution)), Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Laboratoire de microbiologie et génétique moléculaires (LMGM), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), and BENEDIC, Bénédicte
Subjects: Protein Folding, MESH: Antigens, Bacterial/metabolism, Intravital Microscopy, MESH: Protein Folding, [SDV]Life Sciences [q-bio], Science, MESH: Antigens, Bacterial/genetics, MESH: Escherichia coli Proteins, MESH: Host Microbial Interactions, Article, MESH: Recombinant Proteins, Protein Aggregates, MESH: Intravital Microscopy, [SDV.BBM] Life Sciences [q-bio]/Biochemistry, Molecular Biology, Escherichia coli, MESH: Protein Binding, HSP70 Heat-Shock Proteins, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, lcsh:Science, MESH: HSP70 Heat-Shock Proteins, Antigens, Bacterial, Host Microbial Interactions, MESH: Escherichia coli, Escherichia coli Proteins, MESH: Cell Division/physiology, Recombinant Proteins, MESH: Protein Aggregates, [SDV] Life Sciences [q-bio], MESH: Mutagenesis, Site-Directed, Mutagenesis, Site-Directed, bacteria, lcsh:Q, Cell Division, Protein Binding
Abstract: Many bacterial proteins require specific subcellular localization for function. How Escherichia coli proteins localize at one pole, however, is still not understood. Here, we show that the DnaK (HSP70) chaperone controls unipolar localization of the Shigella IpaC type III secretion substrate. While preventing the formation of lethal IpaC aggregates, DnaK promoted the incorporation of IpaC into large and dynamic complexes (LDCs) restricted at the bacterial pole through nucleoid occlusion. Unlike stable polymers and aggregates, LDCs show dynamic behavior indicating that nucleoid occlusion also applies to complexes formed through transient interactions. Fluorescence recovery after photobleaching analysis shows DnaK-IpaC exchanges between opposite poles and DnaKJE-mediated incorporation of immature substrates in LDCs. These findings reveal a key role for LDCs as reservoirs of functional DnaK-substrates that can be rapidly mobilized for secretion triggered upon bacterial contact with host cells., Many bacterial proteins exhibit spatially defined localization important for function. Here the authors show that the polar localization of Shigella IpaC type III secretion substrate is mediated by its interaction with the DnaK chaperone and occlusion by the bacterial nucleoid.
Published: 2018
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27. On the Ubiquity of Magnetic Reconnection Inside Flux Transfer Event‐Like Structures at the Earth's Magnetopause

Author: Michael O. Chandler, Elena Grigorenko, S. M. Petrinec, Hiroshi Hasegawa, Charlie J. Farrugia, Victoria N. Coffey, W. R. Paterson, C. Schiff, John C. Dorelli, Thomas E. Moore, Marit Øieroset, S. Fadanelli, K. J. Trattner, Sergio Toledo-Redondo, Jonathan Eastwood, S. A. Fuselier, T. D. Phan, C. J. Pollock, J. A. Sauvaud, Benoit Lavraud, Yoshitaka Saito, Q. Lenouvel, C. Jacquey, Philippe Garnier, James L. Burch, D. J. Gershman, R. Kieokaew, N. Fargette, D. L. A. Avanov, S. E. Smith, Vincent Génot, Emmanuel Penou, Barbara L. Giles, Science and Technology Facilities Council (STFC), Institut de recherche en astrophysique et planétologie (IRAP), Institut national des sciences de l'Univers (INSU - CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Observatoire Midi-Pyrénées (OMP), Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Centre National de la Recherche Scientifique (CNRS), Space Sciences Laboratory [Berkeley] (SSL), University of California [Berkeley], University of California-University of California, Centre de physique moléculaire optique et hertzienne (CPMOH), Centre National de la Recherche Scientifique (CNRS)-Université Sciences et Technologies - Bordeaux 1, Space Science Division [San Antonio], Southwest Research Institute [San Antonio] (SwRI), Lockheed Martin Advanced Technology Center (ATC), Institute of Space and Astronautical Science (ISAS), Japan Aerospace Exploration Agency [Sagamihara] (JAXA), Laboratoire de microbiologie et génétique moléculaires (LMGM), Centre de Biologie Intégrative (CBI), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), NASA Goddard Space Flight Center (GSFC), Laboratoire de Parasitologie-Mycologie, Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpital Henri Mondor-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12), NASA Headquarters, Space Research Institute of the Russian Academy of Sciences (IKI), Russian Academy of Sciences [Moscow] (RAS), Hokkaido University [Sapporo, Japan], Centre d'Immunologie de Marseille - Luminy (CIML), Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU), Joint Global Change Research Institute, Pacific Northwest National Laboratory (PNNL)-University of Maryland [College Park], University of Maryland System-University of Maryland System, Université de Toulouse (UT)-Université de Toulouse (UT)-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire Midi-Pyrénées (OMP), Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Centre National de la Recherche Scientifique (CNRS), University of California [Berkeley] (UC Berkeley), University of California (UC)-University of California (UC), Université Sciences et Technologies - Bordeaux 1 (UB)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de microbiologie et génétique moléculaires - UMR5100 (LMGM), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire Midi-Pyrénées (OMP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Centre National de la Recherche Scientifique (CNRS), Université Sciences et Technologies - Bordeaux 1-Centre National de la Recherche Scientifique (CNRS), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), and Génot, Vincent
Subjects: Physics, 010504 meteorology & atmospheric sciences, [SDU.ASTR.EP]Sciences of the Universe [physics]/Astrophysics [astro-ph]/Earth and Planetary Astrophysics [astro-ph.EP], [SDU.ASTR.EP] Sciences of the Universe [physics]/Astrophysics [astro-ph]/Earth and Planetary Astrophysics [astro-ph.EP], Magnetic reconnection, Geophysics, 01 natural sciences, Physics::Space Physics, 0103 physical sciences, Meteorology & Atmospheric Sciences, General Earth and Planetary Sciences, Magnetopause, Flux transfer event, 010303 astronomy & astrophysics, ComputingMilieux_MISCELLANEOUS, Earth (classical element), 0105 earth and related environmental sciences
Abstract: Flux transfer events (FTEs) are transient phenomena frequently observed at the Earth's magnetopause. Their usual interpretation is a flux rope moving away from the reconnection region. However, the Magnetospheric Multiscale Mission revealed that magnetic reconnection sometimes occurs inside these structures, questioning their flux rope configuration. Here we investigate 229 FTE‐type structures and find reconnection signatures inside 19% of them. We analyze their large‐scale magnetic topology using electron heat flux and find that it is significantly different across the FTE reconnecting current sheets, demonstrating that they are constituted of two magnetically disconnected structures. We also find that the interplanetary magnetic field (IMF) associated with reconnecting FTEs presents a strong By component. We discuss several formation mechanisms to explain these observations. In particular, the maximum magnetic shear model predicts that for large IMF By, two spatially distinct X lines coexist at the magnetopause. They can generate separate magnetic flux tubes that may become interlaced.
Published: 2020
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28. RNA processing machineries in Archaea: the 5'-3' exoribonuclease aRNase J of the β-CASP family is engaged specifically with the helicase ASH-Ski2 and the 3'-5' exoribonucleolytic RNA exosome machinery

Author: Manon Batista, Violette Morales, Sébastien Laurent, Didier Flament, Yann Moalic, Mohamed Jebbar, Petra Langendijk-Genevaux, Marie Bouvier, Clarisse Etienne, Duy Khanh Phung, Béatrice Clouet-d’Orval, Sophie Liuu, Gwennaele Fichant, Laboratoire de microbiologie et génétique moléculaires (LMGM), Centre de Biologie Intégrative (CBI), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de microbiologie des environnements extrêmophiles (LM2E), Centre National de la Recherche Scientifique (CNRS)-Université de Brest (UBO)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), MICrobiologie de l'ALImentation au Service de la Santé (MICALIS), AgroParisTech-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Plateforme d'Analyse Protéomique de Paris Sud Ouest (PAPPSO), CNRSUniversity Paul SabatierUniversity of Western BritanyIfremerUniversity of ToulouseIdex-emergence program (to B.C.O.)French Ministère de l’Enseignement Supérieur et de la Recherche PhD Fellowship (to D.K.P and C.E.), and ANR-16-CE12-0016,CASPAR,Rôle Physiologique des Ribonucléases de type ß-CASP dans le Métabolisme des ARN chez les Archées(2016)
Subjects: Pyrococcus abyssi, Exosome complex, RNase P, AcademicSubjects/SCI00010, RNA, Archaeal, Euryarchaeota, Ribosome, 03 medical and health sciences, Exoribonuclease, Protein Interaction Mapping, Genetics, RNA and RNA-protein complexes, [SDV.BBM.BC]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biochemistry [q-bio.BM], RNA Processing, Post-Transcriptional, 030304 developmental biology, 0303 health sciences, biology, Exosome Multienzyme Ribonuclease Complex, 030302 biochemistry & molecular biology, RNA, Helicase, RNA Helicase A, Cell biology, Thermococcus, Exoribonucleases, biology.protein, RNA Helicases
Abstract: We are indebted to L. Correia of the Paris Sud Ouest PAPPSO proteomics core facility (http://papso.inra.fr) which is supported by INRA (http://www.inra.fr), the Ile-de-France regional council (https://www.iledefrance.fr/education-recherche), IBiSA (https://www.ibisa.net) and CNRS (http://www.cnrs.fr) for LC/MS analyses and to L. Correia. We thank Y. Quentin for its expertise in taxonomic identification of archaeal Csl4 and Rrp41 members, L.Plassart and J. Caumes for technical help and P. Vitali and M. Kwapisz for helpful discussions.; International audience; A network of RNA helicases, endoribonucleases and exoribonucleases regulates the quantity and quality of cellular RNAs. To date, mechanistic studies focussed on bacterial and eukaryal systems due to the challenge of identifying the main drivers of RNA decay and processing in Archaea. Here, our data support that aRNase J, a 5'-3' exoribonuclease of the β-CASP family conserved in Euryarchaeota, engages specifically with a Ski2-like helicase and the RNA exosome to potentially exert control over RNA surveillance, at the vicinity of the ribosome. Proteomic landscapes and direct protein-protein interaction analyses, strengthened by comprehensive phylogenomic studies demonstrated that aRNase J interplay with ASH-Ski2 and a cap exosome subunit. Finally, Thermococcus barophilus whole-cell extract fractionation experiments provide evidences that an aRNase J/ASH-Ski2 complex might exist in vivo and hint at an association of aRNase J with the ribosome that is emphasised in absence of ASH-Ski2. Whilst aRNase J homologues are found among bacteria, the RNA exosome and the Ski2-like RNA helicase have eukaryotic homologues, underlining the mosaic aspect of archaeal RNA machines. Altogether, these results suggest a fundamental role of β-CASP RNase/helicase complex in archaeal RNA metabolism.
Published: 2020
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29. The ex planta signal activity of a Medicago ribosomal uL2 protein suggests a moonlighting role in controlling secondary rhizobial infection

Author: Sorroche, Fernando, Morales, Violette, Mouffok, Saïda, Pichereaux, Carole, Garnerone, A. Marie, Zou, Lan, Soni, Badrish, Carpéné, Marie-Anne, Gargaros, Audrey, Maillet, Fabienne, Burlet-Schiltz, Odile, Poinsot, Verena, Polard, Patrice, Gough, Clare, Batut, Jacques, Erist, Montpellier, Autoregulation de l'infection dans la symbiose rhizobium-legumineuses - - AOI2015 - ANR-15-CE20-0004 - AAPG2015 - VALID, BLANC - Signalisation par l'AMP cyclique et contrôle de l'infection chez Sinorhizobium meliloti, le symbiote de Medicago - - RhizocAMP2010 - ANR-10-BLAN-1719 - BLANC - VALID, Towards a Unified theory of biotic Interactions: the roLe of environmental - - TULIP2010 - ANR-10-LABX-0041 - LABX - VALID, Infrastructure Française de Protéomique - - ProFI2010 - ANR-10-INBS-0008 - INBS - VALID, Laboratoire des Interactions Plantes Microbes Environnement (LIPME), Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Laboratoire de microbiologie et génétique moléculaires - UMR5100 (LMGM), Centre de Biologie Intégrative (CBI), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Fédération de Recherche Agrobiosciences, Interactions et Biodiversité (FR AIB), Institut de pharmacologie et de biologie structurale (IPBS), Institut des Maladies Métaboliques et Cardiovasculaires (I2MC), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM), Post-doctoral AGREENSKILLS fellowship, CSC PhD scholarship, INRA SPE post-doctoral fellowship, French Ministere de l'Enseignement superieur et de la Recherche, Agri Sud Ouest Innovation, European Union (EU), Toulouse Metropole, Region Occitanie, ANR-15-CE20-0004,AOI,Autoregulation de l'infection dans la symbiose rhizobium-legumineuses(2015), ANR-10-BLAN-1719,RhizocAMP,Signalisation par l'AMP cyclique et contrôle de l'infection chez Sinorhizobium meliloti, le symbiote de Medicago(2010), ANR-10-LABX-0041,TULIP,Towards a Unified theory of biotic Interactions: the roLe of environmental(2010), ANR-10-INBS-0008,ProFI,Infrastructure Française de Protéomique(2010), Laboratoire de microbiologie et génétique moléculaires (LMGM), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, and Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Toulouse III - Paul Sabatier (UT3)
Subjects: Protein Extraction, [SDV.BBM.BM] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, Biochemistry, Plant Root Nodulation, Plant Roots, Cell Signaling, Gene Expression Regulation, Plant, Medicago, Medicine and Health Sciences, Plant Immunity, Post-Translational Modification, Flowering Plants, Plant Proteins, Extraction Techniques, Coinfection, Eukaryota, food and beverages, Fabaceae, Plants, [SDV.BV.BOT]Life Sciences [q-bio]/Vegetal Biology/Botanics, Legumes, Signaling Cascades, Ethylene Signaling Cascade, Experimental Organism Systems, Medicine, [SDV.BBM.GTP] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Cellular Structures and Organelles, Root Nodules, Plant, Signal Peptides, Research Article, Signal Transduction, Ribosomal Proteins, Science, Research and Analysis Methods, Genes, Plant, [SDV.BV.BOT] Life Sciences [q-bio]/Vegetal Biology/Botanics, Model Organisms, Plant and Algal Models, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Medicago truncatula, Symbiosis, Organisms, Biology and Life Sciences, Proteins, [SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, Cell Biology, Ethylenes, biochemical phenomena, metabolism, and nutrition, Health Care, Species Interactions, Animal Studies, Ribosomes, Sinorhizobium meliloti
Abstract: We recently described a regulatory loop, which we termed autoregulation of infection (AOI), by which Sinorhizobium meliloti, a Medicago endosymbiont, downregulates the root susceptibility to secondary infection events via ethylene. AOI is initially triggered by so-far unidentified Medicago nodule signals named signal 1 and signal 1’ whose transduction in bacteroids requires the S. meliloti outer-membrane-associated NsrA receptor protein and the cognate inner-membrane-associated adenylate cyclases, CyaK and CyaD1/D2, respectively. Here, we report on advances in signal 1 identification. Signal 1 activity is widespread as we robustly detected it in Medicago nodule extracts as well as in yeast and bacteria cell extracts. Biochemical analyses indicated a peptidic nature for signal 1 and, together with proteomic analyses, a universally conserved Medicago ribosomal protein of the uL2 family was identified as a candidate signal 1. Specifically, MtRPuL2A (MtrunA17Chr7g0247311) displays a strong signal activity that requires S. meliloti NsrA and CyaK, as endogenous signal 1. We have shown that MtRPuL2A is active in signaling only in a non-ribosomal form. A Medicago truncatula mutant in the major symbiotic transcriptional regulator MtNF-YA1 lacked most signal 1 activity, suggesting that signal 1 is under developmental control. Altogether, our results point to the MtRPuL2A ribosomal protein as the candidate for signal 1. Based on the Mtnf-ya1 mutant, we suggest a link between root infectiveness and nodule development. We discuss our findings in the context of ribosomal protein moonlighting. Copyright: © 2020 Sorroche et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Published: 2020
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30. Post-replicative pairing of sister ter regions in Escherichia coli involves multiple activities of MatP

Author: Bianca Sclavi, David Holcman, Pietro Cicuta, Catherine Tardin, Estelle Crozat, Philippe Rousseau, François Cornet, Armand Lablaine, Maya Salhi, Tommaso Bertoni, Centre de Biologie Intégrative (CBI), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Laboratoire de microbiologie et génétique moléculaires (LMGM), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Centre de Biologie Intégrative (CBI), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Institut de pharmacologie et de biologie structurale (IPBS), Institut de biologie de l'ENS Paris (UMR 8197/1024) (IBENS), Département de Biologie - ENS Paris, École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Biologie Computationnelle et Quantitative = Laboratory of Computational and Quantitative Biology (LCQB), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut de Biologie Paris Seine (IBPS), Sorbonne Université (SU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Crozat, Estelle [0000-0002-0641-4373], Salhi, Maya [0000-0002-8601-3077], Rousseau, Philippe [0000-0002-6376-6527], Bertoni, Tommaso [0000-0002-4798-7733], Sclavi, Bianca [0000-0002-3883-8592], Cicuta, Pietro [0000-0002-9193-8496], Cornet, François [0000-0001-8576-7451], Apollo - University of Cambridge Repository, Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Laboratoire Jean Perrin (LJP), Institut de Biologie Paris Seine (IBPS), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de biologie et pharmacologie appliquée (LBPA), Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Ecole Normale Supérieure Paris-Saclay (ENS Paris Saclay), Cavendish Laboratory, University of Cambridge [UK] (CAM), Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Département de Biologie - ENS Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut de Biologie Paris Seine (IBPS), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Institut de biologie de l'ENS Paris (IBENS), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Département de Biologie - ENS Paris, Cornet, Francois, Laboratoire de microbiologie et génétique moléculaires - UMR5100 (LMGM), École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), and Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0301 basic medicine, Cell division, Chromosomal Proteins, Non-Histone, [SDV]Life Sciences [q-bio], General Physics and Astronomy, Cell Cycle Proteins, medicine.disease_cause, 14, chemistry.chemical_compound, 0302 clinical medicine, Chromosome condensation, lcsh:Science, Genetics, Multidisciplinary, 631/326/41, Escherichia coli Proteins, food and beverages, 631/326/88, Chromosomes, Bacterial, 631/337/641/2358, [SDV] Life Sciences [q-bio], DNA-Binding Proteins, 9, Cell Division, 631/337/641/2002, DNA Replication, Science, Locus (genetics), General Biochemistry, Genetics and Molecular Biology, Article, Bacterial genetics, 03 medical and health sciences, Tetramer, medicine, Escherichia coli, Cellular microbiology, 14/35, Bacteria, Circular bacterial chromosome, General Chemistry, Chromosome segregation, 030104 developmental biology, chemistry, Pairing, 14/63, lcsh:Q, human activities, 030217 neurology & neurosurgery, DNA
Abstract: Funder: Université Toulouse III - Paul Sabatier (University of Toulouse III Paul Sabatier); doi: https://doi.org/10.13039/501100009160, The ter region of the bacterial chromosome, where replication terminates, is the last to be segregated before cell division in Escherichia coli. Delayed segregation is controlled by the MatP protein, which binds to specific sites (matS) within ter, and interacts with other proteins such as ZapB. Here, we investigate the role of MatP by combining short-time mobility analyses of the ter locus with biochemical approaches. We find that ter mobility is similar to that of a non ter locus, except when sister ter loci are paired after replication. This effect depends on MatP, the persistence of catenanes, and ZapB. We characterise MatP/DNA complexes and conclude that MatP binds DNA as a tetramer, but bridging matS sites in a DNA-rich environment remains infrequent. We propose that tetramerisation of MatP links matS sites with ZapB and/or with non-specific DNA to promote optimal pairing of sister ter regions until cell division.
Published: 2020
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31. A divergent CheW confers plasticity to nucleoid-associated chemosensory arrays

Author: Leon Espinosa, Aurelie Barneoud, Deborah Byrne, Emilia M. F. Mauriello, Virginie Molle, Julien Herrou, Tâm Mignot, Philippe Roche, Marie-Jeanne Basse, Annick Guiseppi, Juan Jesus Vicente, Audrey Moine, Laboratoire de chimie bactérienne (LCB), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), University of Washington [Seattle], Institut de Microbiologie de la Méditerranée (IMM), Laboratoire de microbiologie et génétique moléculaires - UMR5100 (LMGM), Centre de Biologie Intégrative (CBI), Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Laboratory of Pathogen Host Interactions [Montpellier] (LPHI), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Institut Méditerranéen d'Ecologie et de Paléoécologie (IMEP), Université Paul Cézanne - Aix-Marseille 3-Université de Provence - Aix-Marseille 1-Avignon Université (AU)-Centre National de la Recherche Scientifique (CNRS), ANR-14-CE11-0023,Bacterial sensing,Perception microbiénne pendant les comportements sociaux(2014), Laboratoire de microbiologie et génétique moléculaires (LMGM), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), LPHI - Laboratory of Pathogen Host Interactions (LPHI), and Université Paul Cézanne - Aix-Marseille 3-Centre National de la Recherche Scientifique (CNRS)-Avignon Université (AU)-Université de Provence - Aix-Marseille 1
Subjects: Cancer Research, Operon, Cell motility, QH426-470, Biochemistry, 0302 clinical medicine, Protein structure, Cell Movement, Macromolecular Structure Analysis, Post-Translational Modification, Amino Acids, Phosphorylation, Genetics (clinical), chemistry.chemical_classification, Regulation of gene expression, Fluorescence microscopy, Microscopy, 0303 health sciences, Crystallography, Organic Compounds, Physics, Chemotaxis, Light Microscopy, Condensed Matter Physics, Amino acid, Cell biology, Chemistry, Phenotype, Physical Sciences, Basic Amino Acids, Signal transduction, Chemosensory clusters, Research Article, Signal Transduction, Cell Physiology, Myxococcus xanthus, Methyl-Accepting Chemotaxis Proteins, Biology, Research and Analysis Methods, 03 medical and health sciences, Bacterial Proteins, Genetics, Solid State Physics, Nucleoid, Protein structure comparison, Histidine, Molecular Biology, Cell fusion, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, 030306 microbiology, Crystal structure, Organic Chemistry, fungi, Chemical Compounds, Biology and Life Sciences, Proteins, [SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, Cell Biology, Gene Expression Regulation, Bacterial, chemistry, Frzb, bacteria, 030217 neurology & neurosurgery
Abstract: Chemosensory systems are highly organized signaling pathways that allow bacteria to adapt to environmental changes. The Frz chemosensory system from M. xanthus possesses two CheW-like proteins, FrzA (the core CheW) and FrzB. We found that FrzB does not interact with FrzE (the cognate CheA) as it lacks the amino acid region responsible for this interaction. FrzB, instead, acts upstream of FrzCD in the regulation of M. xanthus chemotaxis behaviors and activates the Frz pathway by allowing the formation and distribution of multiple chemosensory clusters on the nucleoid. These results, together, show that the lack of the CheA-interacting region in FrzB confers new functions to this small protein., Author summary Chemosensory systems are signaling complexes that are widespread in bacteria and allow the modulation of different cellular functions, such as taxis and development, in response to the environment. We show that the Myxococcus xanthus FrzB is a divergent CheW lacking the region involved in the interaction with the histidine kinase FrzE. Instead, it acts upstream of FrzCD to allow the formation of multiple distributed Frz chemosensory arrays at the nucleoid. The loss of the CheA-interacting region in FrzB might have been selected to confer plasticity to nucleoid-associated chemosensory systems. By unraveling a new accessory protein and its function, this work opens new insights into the knowledge of the regulatory potentials of bacterial chemosensory systems.
Published: 2019
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32. Increase of precuneus metabolism correlates with reduction of PTSD symptoms after EMDR therapy in military veterans: an 18F-FDG PET study during virtual reality exposure to war

Author: Florian Nicolas, Antoine Verger, Eric Guedj, Pierre-François Rousseau, Stéphanie Khalfa, Eric Malbos, C. Lançon, Laboratoire de microbiologie et génétique moléculaires (LMGM), Centre de Biologie Intégrative (CBI), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Hôpital de la Conception [CHU - APHM] (LA CONCEPTION), Nancyclotep- Experimental Imaging Platform = Plate-forme d'imagerie moléculaire, Centre Hospitalier Régional Universitaire de Nancy (CHRU Nancy)-Université de Lorraine (UL), Imagerie Adaptative Diagnostique et Interventionnelle (IADI), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Lorraine (UL), Service de Médecine Nucléaire [Nancy], Centre Hospitalier Régional Universitaire de Nancy (CHRU Nancy), Hopital d'instruction des armées Sainte-Anne [Toulon] (HIA), Service Central de Biophysique et de Médecine Nucléaire, Hôpital de la Timone [CHU - APHM] (TIMONE), Institut FRESNEL (FRESNEL), Centre National de la Recherche Scientifique (CNRS)-École Centrale de Marseille (ECM)-Aix Marseille Université (AMU), Centre Européen de Recherche en Imagerie médicale (CERIMED), Aix Marseille Université (AMU)-Assistance Publique - Hôpitaux de Marseille (APHM)-École Centrale de Marseille (ECM)-Institut Paoli-Calmettes, Fédération nationale des Centres de lutte contre le Cancer (FNCLCC)-Fédération nationale des Centres de lutte contre le Cancer (FNCLCC)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre de Biologie Intégrative (CBI), Assistance Publique - Hôpitaux de Marseille (APHM), Hôpital Sainte-Marguerite [CHU - APHM] (Hôpitaux Sud ), Institut de Neurosciences de la Timone (INT), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de microbiologie et génétique moléculaires - UMR5100 (LMGM), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Service de Médecine Nucléaire [CHRU Nancy], and Aix Marseille Université (AMU)-École Centrale de Marseille (ECM)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Adult, Eye Movement Desensitization Reprocessing, medicine.medical_treatment, Precuneus, Statistical parametric mapping, behavioral disciplines and activities, 030218 nuclear medicine & medical imaging, 18f fdg pet, Stress Disorders, Post-Traumatic, 03 medical and health sciences, 0302 clinical medicine, Fluorodeoxyglucose F18, Parietal Lobe, mental disorders, Eye movement desensitization and reprocessing, medicine, Humans, Radiology, Nuclear Medicine and imaging, ComputingMilieux_MISCELLANEOUS, Veterans, business.industry, [SCCO.NEUR]Cognitive science/Neuroscience, Virtual Reality, General Medicine, Pet imaging, Armed Conflicts, 3. Good health, Posttraumatic stress, Military Personnel, Treatment Outcome, medicine.anatomical_structure, Positron-Emission Tomography, 030220 oncology & carcinogenesis, business, METABOLIC FEATURES, After treatment, [SDV.MHEP]Life Sciences [q-bio]/Human health and pathology, Clinical psychology
Abstract: International audience; Reviewers' comments: Reviewer #1: Comments to Editor The manuscript "Increase of precuneus metabolism correlates with reduction of PTSD symptoms after EMDR therapy in military veterans: an 18F-FDG PET study during virtual reality exposure to war" by Rousseau et al deals with very actual topic: the disclosure of the neurobiology of psychotherapies. Furthermore, approaching such matter by PET activation studies, after about 30 years since the first 15O-H2O ones, using FDG might start a new season for this fascinating research field The manuscript is concise, well written and pretty clear in the aims, methods, results and discussion and in my opinion misses only a few information that will would improve its quality. I have a general comment and some minor specific remarks General comments The authors have recently published on the EJNMMI an editorial promoting functional 18F-FDG PET brain activation imaging. A similar study to the present one was published on the same Journal in 2015 (Eur J Nucl Med Mol Imaging (2015) 42:733-740) in which the very same protocol and methodology were used with the only difference that the stressing stimulus was olfactory and not visual. Since the readers of the present paper will be (firstly) nuclear medicine physicians it is opinion of this reviewer that the above paper should be quoted and the methodology implemented in both of them better "promoted" in the introduction and discussion to stimulate the colleagues to perform similar studies. It is also the opinion of this reviewer that it is a pity that the authors decided to submit such interesting and groundbreaking paper as short communication instead of full paper. Reply: Thanks to the Reviewer for his/her highly positive comments. As mentioned, we are limited by the constraints of a short communication that we indeed chose considering this work as a pilot study with the inclusion of only fifteen subjects. At the discretion of the Editor, the paper could possibly be considered for an Editorial to highlight the original points raised by the Reviewer. Nevertheless, the text has been reasonably lengthened on this revision to better include these aspects. In details, the use of 18 F-FDG brain PET imaging for activation studies has now been promoted in regard to our recent published articles (ref 5 and 7), but also the interesting recommended reference proposed by the Reviewer (ref 6), in the Introduction (p3, l19-22 Indeed, the use of 18 F-FDG brain PET imaging for activation studies has been recently proposed to investigate brain metabolic changes during stimuli tasks such as olfactory stimulations or VRE tasks Discussion (p7, l6-12): Therefore, this study highlights the exciting opportunity to use PET imaging to investigate
Published: 2019
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33. Factor IX assays in treated hemophilia B patients

Author: Claire, Pouplard, Emmanuelle, Jeanpierre, Dominique, Lasne, Véronique, Le Cam Duchez, Valérie, Eschwege, Claire, Flaujac, Hubert, Galinat, Ines, Harzallah, Valérie, Proulle, Motalib, Smahi, Frédéric, Sobas, Catherine, Ternisien, Pierre, Toulon, Sophie, Voisin, Christophe, Nougier, Annelise, Voyer, Hôpital Trousseau, Centre Hospitalier Régional Universitaire de Tours (CHRU Tours), Groupe innovation et ciblage cellulaire (GICC), EA 7501 [2018-...] (GICC EA 7501), Université de Tours (UT), Récepteurs nucléaires, maladies cardiovasculaires et diabète - U 1011 (RNMCD), Institut Pasteur de Lille, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Lille-Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille), Service d'Hématologie Cellulaire [Lille], Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille), Laboratoire de Microbiologie Clinique [AP-HP Hôpital Necker-Enfants Malades], CHU Necker - Enfants Malades [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Centre d'Investigation Clinique [CHU Rouen] (CIC Rouen), Hôpital Charles Nicolle [Rouen]-CHU Rouen, Normandie Université (NU)-Normandie Université (NU)-Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-Institut National de la Santé et de la Recherche Médicale (INSERM), Service d'Hématologie [CHRU Nancy], Centre Hospitalier Régional Universitaire de Nancy (CHRU Nancy), Centre Hospitalier de Versailles André Mignot (CHV), Hôpital de la Cavale Blanche - CHRU Brest (CHU - BREST ), Laboratoire de Microbiologie [GHR Mulhouse Sud-Alsace, Mulhouse], Groupe hospitalier de la région de Mulhouse Sud-Alsace (GHRMSA), Hémostase, Inflammation, Thrombose (HITH - U1176 Inserm - CHU Bicêtre), Université Paris-Sud - Paris 11 (UP11)-Institut National de la Santé et de la Recherche Médicale (INSERM)-AP-HP Hôpital Bicêtre (Le Kremlin-Bicêtre), CH eaubonne montmorency, Hospices Civils de Lyon (HCL), Centre hospitalier universitaire de Nantes (CHU Nantes), Hôpital Pasteur [Nice] (CHU), Service d'Hématologie [IUCT Toulouse], Université Fédérale Toulouse Midi-Pyrénées-Institut Universitaire du Cancer de Toulouse - Oncopole (IUCT Oncopole - UMR 1037), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-CHU Toulouse [Toulouse]-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-CHU Toulouse [Toulouse]-Institut National de la Santé et de la Recherche Médicale (INSERM), Service d’Hématologie [Centre Hospitalier Lyon Sud - HCL], Centre Hospitalier Lyon Sud [CHU - HCL] (CHLS), Hospices Civils de Lyon (HCL)-Hospices Civils de Lyon (HCL), Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP)-Université de Lille-Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille)-Institut National de la Santé et de la Recherche Médicale (INSERM), Université Paris-Sud - Paris 11 (UP11)-AP-HP Hôpital Bicêtre (Le Kremlin-Bicêtre)-Institut National de la Santé et de la Recherche Médicale (INSERM), CHU Toulouse [Toulouse]-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-CHU Toulouse [Toulouse]-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM), Université de Tours, Hôpital Charles Nicolle [Rouen], CHU Rouen, Normandie Université (NU)-Normandie Université (NU)-CHU Rouen, Service Hématologie - IUCT-Oncopole [CHU Toulouse], Pôle Biologie [CHU Toulouse], Centre Hospitalier Universitaire de Toulouse (CHU Toulouse)-Centre Hospitalier Universitaire de Toulouse (CHU Toulouse)-Pôle IUCT [CHU Toulouse], and Centre Hospitalier Universitaire de Toulouse (CHU Toulouse)
Subjects: 030213 general clinical medicine, medicine.medical_specialty, Gastroenterology, Hemophilia B, Factor IX, 03 medical and health sciences, Collaborative group, 0302 clinical medicine, Internal medicine, medicine, Humans, In patient, Monitoring, Physiologic, Plasma samples, medicine.diagnostic_test, [SDV.MHEP.HEM]Life Sciences [q-bio]/Human health and pathology/Hematology, General Medicine, Prognosis, 3. Good health, Hemorrhagic diseases, Coagulation, MESH: Blood Chemical Analysis/methods, Blood Coagulation Tests/methods, Monitoring, Physiologic/methods, Blood Coagulation Tests, Chronometric assays, Blood Chemical Analysis, medicine.drug, Partial thromboplastin time, Chromogenic assays
Abstract: International audience; Replacement therapy with plasma-derived or recombinant FIX (pdFIX or rFIX) concentrates is the standard of treatment in patients with hemophilia B. The method predominantly used for measuring factor IX (FIX:C) levels is the one-stage clotting assay (OSA) but this method depends on the activated partial thromboplastin time (APTT) reagent and the coagulation analyzer used, and wide variations in the measurements of FIX recovery have been reported with some factor concentrates. The French study group on the biology of hemorrhagic diseases (a collaborative group of the GFHT and MHEMO network), presents a review of the literature and proposals for the monitoring of FIX:C levels in treated hemophilia B patients. The use of OSA calibrated with a plasma reference tested against the current FIX WHO International Standard is recommended for the monitoring of patients treated with pdFIX or rFIX. Chromogenic substrate assays (CSA) are adequate for the monitoring of patients treated with Rixubis®, but data available for Benefix® are currently too limited. For extended half-life rFIX (EHL-rFIX), large discordances in the FIX:C levels measured were evidenced, depending on the method and reagents used. Great attention is therefore required for measuring FIX:C levels by OSA in patients substituted by EHL-rFIX. Commercial kits for CSA are not equivalent, and although potentially useful, they are not validated for all EHL-rFIX. Most of recent studies reported data obtained with spiked plasmas, which deserve to be confirmed on plasma samples collected in treated patients.
Published: 2019
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34. Archaeal SF1 and SF2 Helicases

Author: Ziad Abdel-Razzak, Hala Chamieh, Marie Bouvier, Manon Batista, Béatrice Clouet d'Orval, Mirna Hajj, Samar El-Hamaoui, Génétique Diversité et Ecophysiologie des Céréales (GDEC), Institut National de la Recherche Agronomique (INRA)-Université Blaise Pascal - Clermont-Ferrand 2 (UBP), Laboratoire de microbiologie et génétique moléculaires (LMGM), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Lebanese University [Beirut], Centre de Génétique Moléculaire, Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS), Laboratory of Applied Biotechnology, Institut National de la Recherche Agronomique (INRA)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), Centre de Biologie Intégrative (CBI), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Lebanese University [Beirut] (LU), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de microbiologie et génétique moléculaires - UMR5100 (LMGM), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), and Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)
Subjects: RNA metabolism, 0303 health sciences, [SDV]Life Sciences [q-bio], 030302 biochemistry & molecular biology, Cellular functions, Helicase, RNA, Computational biology, Biology, biology.organism_classification, DNA metabolism, 03 medical and health sciences, chemistry.chemical_compound, chemistry, biology.protein, Bacteria, DNA, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, Archaea
Abstract: Archaea, the third domain of life, are significant microorganism models in understanding fundamental aspects of molecular biology. Since the archaeal informational system shares many eukaryal features, structure–function studies using Archaea as models have largely contributed to our understanding of many eukaryotic cellular processes. Helicases of superfamilies 1 (SF1) and 2 (SF2) have been shown to be of major importance in RNA and DNA metabolism in Eukarya and in Bacteria. In Archaea, the cellular functions of these enzymes remain dispersed and only few members were characterized. In this chapter, we review our knowledge on the archaeal SF1 and SF2 helicases. We focus on phylogenomic studies that revealed archaeal helicase families and give insights into their respective biochemical and structural properties. Finally, we raise the question of the mode of actions of these helicases in archaeal DNA and RNA metabolism.
Published: 2019
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35. Cold-conserved hybrid immature embryos for efficient wheat transformation

Author: Caroline Tassy, Giacomo Bastianelli, Pierre Sourdille, Robin Michard, Pierre Barret, Marie-Claire Debote, Alain Loussert, Alain Nicolas, Manon Batista, Génétique Diversité et Ecophysiologie des Céréales (GDEC), Institut National de la Recherche Agronomique (INRA)-Université Blaise Pascal - Clermont-Ferrand 2 (UBP), Meiogenix, Dynamique de l'information génétique : bases fondamentales et cancer (DIG CANCER), Institut Curie-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), PSL Research University, Centre National de la Recherche Scientifique (CNRS), Institut Curie, ANRT CIFRE [2014/1020], Institut National de la Recherche Agronomique (INRA)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), Laboratoire de microbiologie et génétique moléculaires (LMGM), Centre de Biologie Intégrative (CBI), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Institut Curie [Paris]-Sorbonne Université (SU), Université Paris sciences et lettres (PSL), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Institut National de la Recherche Agronomique (INRA), Laboratoire de microbiologie et génétique moléculaires - UMR5100 (LMGM), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), and Institut Curie [Paris]-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0106 biological sciences, ble tendre, [SDV.BIO]Life Sciences [q-bio]/Biotechnology, Cold treatment, biolistic, Horticulture, Biology, 01 natural sciences, cold treatment, wheat, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Hybrid, 2. Zero hunger, hybrids, Chinese spring, transformation, Plant physiology, food and beverages, Embryo, traitement au froid, Transgenesis, Transformation (genetics), microprojectile bombardment, soft wheat, Callus, embryonic structures, biolistique, 010606 plant biology & botany, transgénèse végétale
Abstract: Transgenesis through biolistic of immature embryos is the most convenient way to introduce artificially new genes in bread wheat (Triticum aestivum L.). However, only a few genotypes can be efficiently transformed. To improve the transformation of wheat varieties, we stored immature seeds at room temperature or 4 degrees C during 4 or 7 days and extracted immature embryos prior to transformation. Shelling stops the embryo's growth and almost all the embryos formed a callus on selective media when stored at 4 degrees C for 4 or 7 days (respectively 87% and 99%). We also used hybrid immature embryos derived from a cross between a transformable line (Courtot) and a non-transformable line (Chinese Spring) for biolistic transformation. Hybrid embryos showed the same response to biolistic than the responsive parent. All together, these results improve significantly the biolistic protocol for wheat transformation by reducing the number of mother plants in the greenhouse, and improve the transformation of additional genotypes through hybrid transformation.
Published: 2019
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36. Detachment of the RNA degradosome from the inner membrane of Escherichia coli results in a global slowdown of mRNA degradation, proteolysis of RNase E and increased turnover of ribosome-free transcripts

Author: Marie Bouvier, Lydia Hadjeras, Agamemnon J. Carpousis, Muriel Cocaign-Bousquet, Quentin Morin‐Ogier, Isabelle Canal, Leonora Poljak, Laurence Girbal, Laboratoire de microbiologie et génétique moléculaires (LMGM), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Laboratoire d'Ingénierie des Systèmes Biologiques et des Procédés (LISBP), Centre National de la Recherche Scientifique (CNRS)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Institut National de la Recherche Agronomique (INRA), French National Research Agency (ANR) [ANR-13-BSV6-0005], Centre de Biologie Intégrative (CBI), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), ANR-13-BSV6-0005,memRNase,Localisation membranaire de la RNase E : rôle dans la maturation, la surveillance et la dégradation des ARNm(2013), Laboratoire de microbiologie et génétique moléculaires - UMR5100 (LMGM), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Institut National de la Recherche Agronomique (INRA)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), and Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)
Subjects: RNA Stability, RNase P, Biology, Microbiology, Ribosome, 03 medical and health sciences, Multienzyme Complexes, Endoribonucleases, Escherichia coli, Inner membrane, Nucleoid, RNA, Messenger, Molecular Biology, membrane, expression arn m, Research Articles, 030304 developmental biology, Polyribonucleotide Nucleotidyltransferase, 0303 health sciences, Messenger RNA, 030306 microbiology, Escherichia coli Proteins, RNA, MRNA stabilization, Gene Expression Regulation, Bacterial, Cell biology, RNA, Bacterial, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, ribosome, Proteolysis, RNA-seq, Ribosomes, RNA Helicases, Research Article
Abstract: Summary The reason for RNase E attachment to the inner membrane is largely unknown. To understand the cell biology of RNA degradation, we have characterized a strain expressing RNase E lacking the membrane attachment site (cytoplasmic RNase E). Genome‐wide data show a global slowdown in mRNA degradation. There is no correlation between mRNA stabilization and the function or cellular location of encoded proteins. The activity of cRNase E is comparable to the wild‐type enzyme in vitro, but the mutant protein is unstable in vivo. Autoregulation of cRNase E synthesis compensates for protein instability. cRNase E associates with other proteins to assemble a cytoplasmic RNA degradosome. CsrB/C sRNAs, whose stability is regulated by membrane‐associated CsrD, are stabilized. Membrane attachment of RNase E is thus necessary for CsrB/C turnover. In contrast to mRNA stability, ribosome‐free transcripts are sensitive to inactivation by cRNase E. Our results show that effects on RNA degradation are not due to the differences in the activity or level of cRNase E, or failure to assemble the RNA degradosome. We propose that membrane attachment is necessary for RNase E stability, functional interactions with membrane‐associated regulatory factors and protection of ribosome‐free transcripts from premature interactions with RNase E in the nucleoid., Attachment of RNase E to the inner membrane of E. coli is important for multiple processes including efficient degradation of mRNA, interactions with membrane‐associated regulatory factors involved in the posttranscriptional control of gene expression, and the protection of nascent transcripts in the nucleoid from degradation by RNase E. Detachment of RNase E from the inner membrane results in its proteolysis, which could be important for downregulating RNase E activity under stress conditions.
Published: 2019
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37. Validation of EN ISO method 15216 - Part 1 – Quantification of hepatitis A virus and norovirus in food matrices

Author: Joanna Ollivier, Gwenola Hardouin, P.H. in’t Veld, Sophie Butot, Alexandre Leclercq, Bertrand Lombard, S.A. Rutjes, James A. Lowther, Albert Bosch, D. Mäde, Centre for Environment, Fisheries and Aquaculture Science [Weymouth] (CEFAS), Universitat de Barcelona (UB), Nestlé Institute of Health Sciences SA [Lausanne, Switzerland], Laboratoire de Microbiologie, Environnement, Microbiologie et Phycotoxines (EMP), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Lower Saxony State Office for Consumer Protection and Food Safety, National Institute for Public Health and the Environment [Bilthoven] (RIVM), Association Française de Normalisation (AFNOR), Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Netherlands Food and Consumer Product Safety Authority (NVWA), Centre National de Référence Listeria - National Reference Center Listeria (CNRL), Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM), Biologie des Infections - Biology of Infection, Centre collaborateur de l'OMS Listeria / WHO Collaborating Centre Listeria (CC-OMS / WHO-CC), Institut Pasteur [Paris] (IP)-Organisation Mondiale de la Santé / World Health Organization Office (OMS / WHO), The validation of International Standard EN ISO 15216-1 was carried out under the framework of European Mandate No. M381 of DG SANTE and DG GROW (European Commission)., DIAKITE, andrée, Laboratoire de Microbiologie, IFREMER, Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Institut Pasteur [Paris]-Institut National de la Santé et de la Recherche Médicale (INSERM), and Institut Pasteur [Paris]-Organisation Mondiale de la Santé / World Health Organization Office (OMS / WHO)
Subjects: 0301 basic medicine, Bivalve molluscan shellfish, Standardization, [SDV]Life Sciences [q-bio], MESH: Bivalvia, medicine.disease_cause, Limit of Detection, MESH: Reverse Transcriptase Polymerase Chain Reaction, Validation, Vegetables, MESH: Animals, Risk management, MESH: Shellfish, [SDV.MP.VIR] Life Sciences [q-bio]/Microbiology and Parasitology/Virology, [SDV.MHEP] Life Sciences [q-bio]/Human health and pathology, Reverse Transcriptase Polymerase Chain Reaction, General Medicine, Bottled water, Hepatitis a virus, 3. Good health, Surfaces, MESH: Reproducibility of Results, [SDV] Life Sciences [q-bio], [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, MESH: Fruit, MESH: Norovirus, 030106 microbiology, MESH: Limit of Detection, Biology, Microbiology, 03 medical and health sciences, Environmental health, MESH: Hepatitis A virus, Soft fruit, medicine, MESH: European Union, Food microbiology, Animals, Humans, European Union, MESH: Food Microbiology, [SDV.MP] Life Sciences [q-bio]/Microbiology and Parasitology, Shellfish, MESH: Humans, business.industry, International standard, Norovirus, Reproducibility of Results, Virology, MESH: Vegetables, Bivalvia, Real-time RT-PCR, [SDV.AEN] Life Sciences [q-bio]/Food and Nutrition, Fruit, Food Microbiology, Hepatitis A virus, business, [SDV.AEN]Life Sciences [q-bio]/Food and Nutrition, [SDV.MHEP]Life Sciences [q-bio]/Human health and pathology, Food Science
Abstract: International audience; Hepatitis A virus (HAV) and norovirus are important agents of food-borne human viral illness, with common vehicles including bivalve molluscan shellfish, soft fruit and various vegetables. Outbreaks of viral illness due to contamination of the surfaces of foods, or food preparation surfaces by for example infected food handlers are also common. Virus analysis of food matrices can contribute towards risk management for these hazards and a two-part technical specification for determination of Hepatitis A virus and norovirus in food matrices (ISO/TS 15216:2013) was published jointly by the European Committee for Standardisation and the International Organization for Standardization in 2013.As part of the European Mandate No. M381 to validate 15 standards in the field of food microbiology, an international validation study involving 18 laboratories from 11 countries in Europe was conducted between 2012 and 2014. This study aimed to generate method characteristics including limit of detection, limit of quantification, repeatability and reproducibility for ISO 15216 – Part 1, the method for quantification, in seven food matrices.The organization and results of this study, including observations that led to improvements in the standard method are presented here. After its conclusion, the method characteristics generated were added to the revised international standard, ISO 15216-1:2017, published in March 2017.
Published: 2019
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38. In vitro Assessment of the Probiotic Properties and Bacteriocinogenic Potential of Pediococcus pentosaceus MZF16 Isolated From Artisanal Tunisian Meat 'Dried Ossban'

Author: Emeline Bouffartigues, Nathalie Connil, Mounir Ferchichi, Khaled Sebei, Mohamed Zommiti, Marc G. J. Feuilloley, Magalie Barreau, Sabine Szunerits, Olivier Maillot, Laboratoire de Microbiologie du Froid – Signaux et Micro-Environnement (LMDF-SME), Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-Normandie Université (NU), Laboratoire de Microbiologie Signaux et Microenvironnement (LMSM), Institut d’Électronique, de Microélectronique et de Nanotechnologie - UMR 8520 (IEMN), Centrale Lille-Institut supérieur de l'électronique et du numérique (ISEN)-Université de Valenciennes et du Hainaut-Cambrésis (UVHC)-Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Université Polytechnique Hauts-de-France (UPHF), NanoBioInterfaces - IEMN (NBI - IEMN), Centrale Lille-Institut supérieur de l'électronique et du numérique (ISEN)-Université de Valenciennes et du Hainaut-Cambrésis (UVHC)-Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Université Polytechnique Hauts-de-France (UPHF)-Centrale Lille-Institut supérieur de l'électronique et du numérique (ISEN)-Université de Valenciennes et du Hainaut-Cambrésis (UVHC)-Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Université Polytechnique Hauts-de-France (UPHF), Oniris, Secalim UMR1014, LUNAM Université [Nantes Angers Le Mans], Centrale Lille-Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Université Polytechnique Hauts-de-France (UPHF)-JUNIA (JUNIA), Université catholique de Lille (UCL)-Université catholique de Lille (UCL), Université catholique de Lille (UCL)-Université catholique de Lille (UCL)-Centrale Lille-Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Université Polytechnique Hauts-de-France (UPHF)-JUNIA (JUNIA), SECurité des ALIments et Microbiologie, Institut National de la Recherche Agronomique (INRA)-École nationale d'ingénieurs des techniques des industries agricoles et alimentaires (ENITIAA)-École nationale vétérinaire, agroalimentaire et de l'alimentation Nantes-Atlantique (ONIRIS), and We thank Nicolas Barrois from the Center for Infection and Immunity of Lille (UMR8204—INSERM U1019) for helping with scanning electronic microscopy.
Subjects: 0301 basic medicine, Microbiology (medical), Dried Ossban, 030106 microbiology, lcsh:QR1-502, [SDV.TOX.TCA]Life Sciences [q-bio]/Toxicology/Toxicology and food chain, medicine.disease_cause, Microbiology, lcsh:Microbiology, law.invention, 03 medical and health sciences, Probiotic, Bacteriocin, Listeria monocytogenes, law, [SDV.BC.IC]Life Sciences [q-bio]/Cellular Biology/Cell Behavior [q-bio.CB], medicine, Food science, ComputingMilieux_MISCELLANEOUS, Original Research, Pediococcus pentosaceus, biology, Chemistry, food and beverages, biology.organism_classification, pediocin MZF16, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, 3. Good health, 030104 developmental biology, Tunisian fermented meat, Coagulin, Listeria, Bacillus coagulans, Pediococcus, Bacteria, probiotic
Abstract: International audience; Pediococcus pentosaceus MZF16 has been isolated from artisanal Tunisian meat so called “Dried Ossban,” an original ecological niche, and identified by MALDI-TOF mass spectrometry and 16S rDNA sequencing. This bacterium showed a high tolerance to gastric stress conditions, and toward bile salts. P. pentosaceus MZF16 also demonstrated a hydrophobic surface profile (high adhesion to xylene), autoaggregation, and adhesive abilities to the human intestinal Caco-2/TC7 cell line. These properties may help the bacterium colonizing the gut. Furthermore, MZF16 was found to be resistant to gentamycin and chloramphenicol but did not harbor any transferable resistance determinants and/or virulence genes. The data also demonstrated absence of cytotoxicity of this strain. Conversely, P. pentosaceus MZF16 can slightly stimulate the immune system and enhance the intestinal epithelial barrier function. Moreover, this bacterium has been shown to be highly active against Listeria spp. due to bacteriocin production. Characterization of the bacteriocin by PCR amplification, sequencing and bioinformatic analyses revealed that MZF16 produces a bacteriocin 100% identical to coagulin, a pediocin-like inhibitory substance produced by Bacillus coagulans. To our knowledge, this is the first report that highlights the production of a pediocin 100% identical to coagulin in a Pediococcus strain. As coagulin, pediocin MZF16 has the consensus sequence YYGNGVXCXXXXCXVXXXXA (X denotes any amino acid), which confirms its belonging to class IIa bacteriocins, and its suitability to preserve foods from Listeria monocytogenes development. According to these results, P. pentosaceus MZF16 can be proposed as a probiotic and bioprotective agent for fermented foods, including Tunisian dry meat and sausages. Further investigations will aim to study the behavior of this strain in meat products as a component of functional food.
Published: 2018
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39. Evaluation of Probiotic Properties and Safety of Enterococcus faecium Isolated From Artisanal Tunisian Meat 'Dried Ossban'

Author: Marc G. J. Feuilloley, Magalie Barreau, Olivier Maillot, Mohamed Zommiti, Mélyssa Cambronel, Mounir Ferchichi, Khaled Sebei, Nathalie Connil, Université de Tunis, Laboratoire de Microbiologie Signaux et Microenvironnement (LMSM), Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-Normandie Université (NU), Laboratoire de Microbiologie du Froid – Signaux et Micro-Environnement (LMDF-SME), Oniris, Secalim UMR1014, and LUNAM Université [Nantes Angers Le Mans]
Subjects: 0301 basic medicine, Microbiology (medical), Dried Ossban, safety, antibiotic resistance, medicine.drug_class, 030106 microbiology, Antibiotics, Enterococcus faecium, lcsh:QR1-502, Virulence, Microbiology, lcsh:Microbiology, law.invention, 03 medical and health sciences, Probiotic, Antibiotic resistance, law, [SDV.BC.IC]Life Sciences [q-bio]/Cellular Biology/Cell Behavior [q-bio.CB], medicine, Food science, ComputingMilieux_MISCELLANEOUS, Original Research, biology, [SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, biology.organism_classification, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, 3. Good health, probiotics, Listeria, Vancomycin, virulence determinants, Bacteria, medicine.drug
Abstract: Enterococcus faecium strains were isolated from an original biotope, artisanal dried Tunisian meat “Dried Ossban,” and evaluated for safety and capacity as probiotics. Gram-positive, catalase negative, and bacteriocin-producing bacteria were screened using selective microbiological media. All isolates were identified by phenotypic and molecular tools. Five E. faecium strains (MZF1, MZF2, MZF3, MZF4, and MZF5) were selected and further assessed for their probiotic properties. They were found to be resistant to the physiological concentrations of bile salts, and the harsh conditions of the gastrointestinal tract, and showed autoaggregation and adhesion ability. All these isolates possess at least one enterocin and could efficiently inhibit the growth of Listeria innocua HPB13. The analysis of their safety profile revealed for almost all the strains the absence of cytotoxicity and virulence determinants, and susceptibility to clinically important antibiotics such as vancomycin. These data suggest that these bacteria, isolated from “Dried Ossban,” do not present a risk to human health, and may be considered as interesting candidates for future use as probiotics and bioprotective cultures for application in the food and/or feed industries.
Published: 2018
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40. Nascent teichoic acids insertion into the cell wall directs the localization and activity of the major pneumococcal autolysin LytA

Author: Kari Helene Berg, Nathalie Campo, Thierry Vernet, J. Bonnet, Daniel Straume, Yung-Sing Wong, Maxime Jacq, A. M. Di Guilmi, Leiv Sigve Håvarstein, Claire Durmort, Isabelle Mortier-Barrière, Christine Moriscot, Institut de biologie structurale [1992-2019] (IBS - UMR 5075 [1992-2019]), Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Laboratoire de microbiologie et génétique moléculaires (LMGM), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Département de pharmacochimie moléculaire [1999-2015] (DPM [1999-2015]), Centre National de la Recherche Scientifique (CNRS)-Université Joseph Fourier - Grenoble 1 (UJF), Institut de biologie structurale (IBS - UMR 5075 ), Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS), Centre de Biologie Intégrative (CBI), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Département de pharmacochimie moléculaire (DPM ), Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019]), Laboratoire de microbiologie et génétique moléculaires - UMR5100 (LMGM), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), and Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0301 basic medicine, animal structures, 030106 microbiology, Cell, Streptococcus pneumoniae cell wall, Context (language use), Choline-Binding Proteins, Applied Microbiology and Biotechnology, Microbiology, Bacterial cell structure, Article, Cell wall, 03 medical and health sciences, chemistry.chemical_compound, medicine, Amidase activity, lcsh:QH573-671, Molecular Biology, ComputingMilieux_MISCELLANEOUS, ComputingMethodologies_COMPUTERGRAPHICS, Teichoic acid, Major autolysin LytA localization, lcsh:Cytology, Autolysin, [SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, Cell Biology, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, 3. Good health, Cell biology, Teichoic acids localization, medicine.anatomical_structure, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, chemistry, Peptidoglycan, Peptidoglycan hydrolases
Abstract: Graphical abstract, Highlights • Peptidoglycan which sustains bacterial growth is targeted by b-lactam antibiotics. • Spread of antibiotic resistance requires the development of new antibacterial drugs. • The cell wall of Gram-positive bacteria carries teichoic acids and virulence factors. • Function and surface localization of virulence factors are regulated by teichoic acids. • Anti-bacterial strategy should target the localization of surface virulence factors., The bacterial cell wall is in part composed of the peptidoglycan (PG) layer that maintains the cell shape and sustains the basic cellular processes of growth and division. The cell wall of Gram-positive bacteria also carries teichoic acids (TAs). In this work, we investigated how TAs contribute to the structuration of the PG network through the modulation of PG hydrolytic enzymes in the context of the Gram-positive Streptococcus pneumoniae bacterium. Pneumococcal TAs are decorated by phosphorylcholine residues which serve as anchors for the Choline-Binding Proteins, some of them acting as PG hydrolases, like the major autolysin LytA. Their binding is non covalent and reversible, a property that allows easy manipulation of the system. In this work, we show that the release of LytA occurs independently from its amidase activity. Furthermore, LytA fused to GFP was expressed in pneumococcal cells and showed different localization patterns according to the growth phase. Importantly, we demonstrate that TAs modulate the enzymatic activity of LytA since a low level of TAs present at the cell surface triggers LytA sensitivity in growing pneumococcal cells. We previously developed a method to label nascent TAs in live cells revealing that the insertion of TAs into the cell wall occurs at the mid-cell. In conclusion, we demonstrate that nascent TAs inserted in the cell wall at the division site are the specific receptors of LytA, tuning in this way the positioning of LytA at the appropriate place at the cell surface.
Published: 2018
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41. Different Dose-Dependent Modes of Action of C-Type Natriuretic Peptide on Pseudomonas aeruginosa Biofilm Formation

Author: Thomas Clamens, Jérôme Leprince, Ali Tahrioui, Sophie Rodrigues, Olivier Lesouhaitier, Jérémy Enault, Lucille Roquigny, Alexis Bazire, Alain Dufour, Sylvie Chevalier, Thibaut Rosay, Florie Desriac, Laure Taupin, Marc G. J. Feuilloley, Emeline Bouffartigues, Pierre-Jean Racine, Laboratoire de Microbiologie Signaux et Microenvironnement (LMSM), Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-Normandie Université (NU), Laboratoire de Biotechnologie et Chimie Marines (LBCM), Université de Bretagne Sud (UBS)-Université de Brest (UBO)-Institut Universitaire Européen de la Mer (IUEM), Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS), Différenciation et communication neuronale et neuroendocrine (DC2N), Normandie Université (NU)-Normandie Université (NU)-Institut National de la Santé et de la Recherche Médicale (INSERM), Laboratoire de Microbiologie du Froid – Signaux et Micro-Environnement (LMDF-SME), and Neuroendocrinologie cellulaire et moléculaire
Subjects: 0301 basic medicine, Microbiology (medical), medicine.drug_class, [SDV.NEU.NB]Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC]/Neurobiology, 030106 microbiology, bacterial adaptation, lcsh:Medicine, Peptide, [CHIM.THER]Chemical Sciences/Medicinal Chemistry, Bacterial growth, medicine.disease_cause, biofilm, lung, cystic fibrosis, 03 medical and health sciences, [SDV.BC.IC]Life Sciences [q-bio]/Cellular Biology/Cell Behavior [q-bio.CB], Membrane fluidity, medicine, Natriuretic peptide, Immunology and Allergy, Mode of action, Molecular Biology, ComputingMilieux_MISCELLANEOUS, chemistry.chemical_classification, General Immunology and Microbiology, hormones, Pseudomonas aeruginosa, lcsh:R, Biofilm, Adhesion, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, peptides, Infectious Diseases, chemistry, Biophysics, [SDV.SP.PHARMA]Life Sciences [q-bio]/Pharmaceutical sciences/Pharmacology
Abstract: International audience; We have previously shown that the C-type Natriuretic Peptide (CNP), a peptide produced by lungs, is able to impact Pseudomonasaeruginosa physiology. In the present work, the effect of CNP at different concentrations on P. aeruginosa biofilm formation was studied and the mechanisms of action of this human hormone on P. aeruginosa were deciphered. CNP was shown to inhibit dynamic biofilm formation in a dose-dependent manner without affecting the bacterial growth at any tested concentrations. The most effective concentrations were 1 and 0.1 µM. At 0.1 µM, the biofilm formation inhibition was fully dependent on the CNP sensor protein AmiC, whereas it was only partially AmiC-dependent at 1 µM, revealing the existence of a second AmiC-independent mode of action of CNP on P. aeruginosa. At 1 µM, CNP reduced both P. aeruginosa adhesion on glass and di-rhamnolipid production and also increased the bacterial membrane fluidity. The various effects of CNP at 1 µM and 0.1 µM on P. aeruginosa shown here should have major consequences to design drugs for biofilm treatment or prevention.
Published: 2018
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42. Clinical Assessment of a Nocardia PCR-Based Assay for Diagnosis of Nocardiosis

Author: Daniel Mathieu, Claire Rouzaud, David Lebeaux, Eric Farfour, Emilie Catherinot, Felipe Suarez, Emmanuelle Bergeron, Jean-Philippe Lengelé, Fabrice Larosa, Olivier Lortholary, Jean-Louis Christophe, Veronica Rodriguez-Nava, Anne Scemla, C. Delavaud, Sylvain Poirée, Frédéric Méchaï, Stéphane Durupt, Université Paris Descartes - Paris 5 (UPD5), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon, Service de pneumologie [Hôpital Foch], Hôpital Foch [Suresnes], Service des maladies infectieuses et tropicales, Université Paris 13 (UP13)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpital Avicenne [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Service de Transplantation Rénale, Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-CHU Necker - Enfants Malades [AP-HP], CHU Necker - Enfants Malades [AP-HP], Centre Hospitalier Universitaire de Lille (CHU de Lille), Centre Hospitalier Régional Universitaire de Besançon (CHRU Besançon), CHU Besancon, Dept Hematol, Besancon, France, Partenaires INRAE, Grand Hopital de Charleroi, Institut Pasteur [Paris], Centre National de Référence des Mycoses invasives et antifongiques - Mycologie moléculaire (CNRMA), Centre National de la Recherche Scientifique (CNRS)-Institut Pasteur [Paris], Bourse Junior 2015-Societe de Pathologie Infectieuse de Langue Francaise, We thank Frédéric Imbert (Montélimar) and Patrick Lamarche (Fontenay-le-Comte), Caroline Elie (Unité de Recherche Clinique/Centre d'Investigation Clinique Paris Descartes Necker Cochin, Assistance Publique-Hôpitaux de Paris, Hôpital Necker Enfants Malades, Paris, France), Emilie Cardot (Service de Microbiologie, Hôpital Foch, Suresnes, France), Hervé Lecuyer (Laboratoire de Microbiologie, Hôpital Necker-Enfants Malades, APHP, Paris, France), and Violaine Walewski (Laboratoire de Microbiologie, Hôpital Avicenne, APHP, Bobigny, France) for their help during the study. We thank Karen Pickett for her editorial suggestions., Institut Pasteur [Paris] (IP), and Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0301 basic medicine, Lung Diseases, Male, Opportunistic infection, SAMPLES, FEATURES, [SDV]Life Sciences [q-bio], Colony Count, Microbial, Positive control, Negative control, ANTIMICROBIAL SUSCEPTIBILITY PATTERNS, Gastroenterology, Polymerase Chain Reaction, Nocardia, law.invention, COLONIZATION, law, RNA, Ribosomal, 16S, Child, Polymerase chain reaction, Aged, 80 and over, biology, Nocardiosis, Middle Aged, 3. Good health, Hospitalization, PCR, Child, Preschool, Female, Nocardia Infections, Microbiology (medical), Adult, medicine.medical_specialty, Adolescent, 030106 microbiology, Opportunistic Infections, TRANSPLANT RECIPIENTS, Sensitivity and Specificity, 03 medical and health sciences, Immunocompromised Host, Young Adult, Internal medicine, medicine, Humans, nocardiosis, Aged, business.industry, Bacteriology, DNA, TAXONOMY, medicine.disease, biology.organism_classification, Multicenter study, immunocompromised hosts, business, SPP
Abstract: The diagnosis of nocardiosis, a severe opportunistic infection, is challenging. We assessed the specificity and sensitivity of a 16S rRNA Nocardia PCR-based assay performed on clinical samples. In this multicenter study (January 2014 to April 2015), patients who were admitted to three hospitals and had an underlying condition favoring nocardiosis, clinical and radiological signs consistent with nocardiosis, and a Nocardia PCR assay result for a clinical sample were included. Patients were classified as negative control (NC) (negative Nocardia culture results and proven alternative diagnosis or improvement at 6 months without anti- Nocardia treatment), positive control (PC) (positive Nocardia culture results), or probable nocardiosis (positive Nocardia PCR results, negative Nocardia culture results, and no alternative diagnosis). Sixty-eight patients were included; 47 were classified as NC, 8 as PC, and 13 as probable nocardiosis. PCR results were negative for 35/47 NC patients (74%). For the 12 NC patients with positive PCR results, the PCR assay had been performed with respiratory samples. These NC patients had chronic bronchopulmonary disease more frequently than did the NC patients with negative PCR results (8/12 patients [67%] versus 11/35 patients [31%]; P = 0.044). PCR results were positive for 7/8 PC patients (88%). There were 13 cases of probable nocardiosis, diagnosed solely using the PCR results; 9 of those patients (69%) had lung involvement (consolidation or nodule). Nocardia PCR testing had a specificity of 74% and a sensitivity of 88% for the diagnosis of nocardiosis. Nocardia PCR testing may be helpful for the diagnosis of nocardiosis in immunocompromised patients but interpretation of PCR results from respiratory samples is difficult, because the PCR assay may also detect colonization.
Published: 2018
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43. Insights into RNA-processing pathways and associated RNA-degrading enzymes in Archaea

Author: Lisa-Katharina Maier, Béatrice Clouet-d’Orval, Yves Quentin, Anita Marchfelder, Manon Batista, Marie Bouvier, Gwennaele Fichant, Génétique Diversité et Ecophysiologie des Céréales (GDEC), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Institut National de la Recherche Agronomique (INRA), Laboratoire de microbiologie et génétique moléculaires (LMGM), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Molekulare Botanik, Universität Ulm - Ulm University [Ulm, Allemagne], Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Institut National de la Recherche Agronomique (INRA), Centre de Biologie Intégrative (CBI), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Institut National de la Recherche Agronomique (INRA)-Université Blaise Pascal - Clermont-Ferrand 2 (UBP), Institut National de la Recherche Agronomique (INRA)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), Laboratoire de microbiologie et génétique moléculaires - UMR5100 (LMGM), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), and ANR-16-CE12-0016,CASPAR,Rôle Physiologique des Ribonucléases de type ß-CASP dans le Métabolisme des ARN chez les Archées(2016)
Subjects: 0301 basic medicine, Regulation of gene expression, Messenger RNA, biology, [SDV]Life Sciences [q-bio], RNA, Computational biology, Ribosomal RNA, biology.organism_classification, Microbiology, Archaea, 03 medical and health sciences, 030104 developmental biology, Infectious Diseases, Transfer RNA, Endoribonucleases, Exoribonucleases, CRISPR, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Guide RNA, RNA Processing, Post-Transcriptional, ComputingMilieux_MISCELLANEOUS
Abstract: RNA-processing pathways are at the centre of regulation of gene expression. All RNA transcripts undergo multiple maturation steps in addition to covalent chemical modifications to become functional in the cell. This includes destroying unnecessary or defective cellular RNAs. In Archaea, information on mechanisms by which RNA species reach their mature forms and associated RNA-modifying enzymes are still fragmentary. To date, most archaeal actors and pathways have been proposed in light of information gathered from Bacteria and Eukarya. In this context, this review provides a state of the art overview of archaeal endoribonucleases and exoribonucleases that cleave and trim RNA species and also of the key small archaeal proteins that bind RNAs. Furthermore, synthetic up-to-date views of processing and biogenesis pathways of archaeal transfer and ribosomal RNAs as well as of maturation of stable small non-coding RNAs such as CRISPR RNAs, small C/D and H/ACA box guide RNAs, and other emerging classes of small RNAs are described. Finally, prospective post-transcriptional mechanisms to control archaeal messenger RNA quality and quantity are discussed.
Published: 2018
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44. Biodegradation of Emiliania huxleyi aggregates by a natural Mediterranean prokaryotic community under increasing hydrostatic pressure

Author: Frédéric A. C. Le Moigne, Kazuyo Tachikawa, Virginie Riou, Christian Tamburini, Chiara Santinelli, Dominique Lefèvre, Badr Al Ali, Stephanie Jacquet, Madeleine Goutx, J. Para, Catherine Guigue, Jean-Pierre Gattuso, Marc Garel, Institut méditerranéen d'océanologie (MIO), Centre National de la Recherche Scientifique (CNRS)-Université de Toulon (UTLN)-Aix Marseille Université (AMU)-Institut de Recherche pour le Développement (IRD), Laboratoire de MicrobiologiE de Géochimie et d'Ecologie Marines (LMGEM), Centre National de la Recherche Scientifique (CNRS)-Université de la Méditerranée - Aix-Marseille 2, Istituto di Biofisica [Pisa] (IBF), Consiglio Nazionale delle Ricerche [Roma] (CNR), Laboratoire d'océanographie de Villefranche (LOV), Institut national des sciences de l'Univers (INSU - CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut de la Mer de Villefranche (IMEV), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), GEOMAR - Helmholtz Centre for Ocean Research [Kiel] (GEOMAR), Centre européen de recherche et d'enseignement des géosciences de l'environnement (CEREGE), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Collège de France (CdF)-Institut national des sciences de l'Univers (INSU - CNRS)-Aix Marseille Université (AMU)-Institut National de la Recherche Agronomique (INRA), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS), Institut de Recherche pour le Développement (IRD)-Institut National de la Recherche Agronomique (INRA)-Aix Marseille Université (AMU)-Collège de France (CdF (institution))-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS), Tishreen University, National Research Council of Italy | Consiglio Nazionale delle Ricerche (CNR), Helmholtz Centre for Ocean Research [Kiel] (GEOMAR), Université de la Méditerranée - Aix-Marseille 2-Centre National de la Recherche Scientifique (CNRS), Institut méditerranéen d'océanologie ( MIO ), Institut de Recherche pour le Développement ( IRD ) -Aix Marseille Université ( AMU ) -Université de Toulon ( UTLN ) -Centre National de la Recherche Scientifique ( CNRS ), CE, Institut de Recherche pour le Développement ( IRD ) -Aix Marseille Université ( AMU ) -Université de Toulon ( UTLN ) -Centre National de la Recherche Scientifique ( CNRS ) -Institut de Recherche pour le Développement ( IRD ) -Aix Marseille Université ( AMU ) -Université de Toulon ( UTLN ) -Centre National de la Recherche Scientifique ( CNRS ), Laboratoire de MicrobiologiE de Géochimie et d'Ecologie Marines ( LMGEM ), Centre National de la Recherche Scientifique ( CNRS ) -Université de la Méditerranée - Aix-Marseille 2, Istituto di Biofisica, Area della Ricerca di Pisa, Via Moruzzi, 1, 56124 Pisa, Italy, Université du Québec, Observatoire océanologique de Villefranche-sur-mer ( OOVM ), Université Pierre et Marie Curie - Paris 6 ( UPMC ) -Institut national des sciences de l'Univers ( INSU - CNRS ) -Centre National de la Recherche Scientifique ( CNRS ), Centre européen de recherche et d'enseignement de géosciences de l'environnement ( CEREGE ), Centre National de la Recherche Scientifique ( CNRS ) -Institut de Recherche pour le Développement ( IRD ) -Aix Marseille Université ( AMU ) -Collège de France ( CdF ) -Institut National de la Recherche Agronomique ( INRA ) -Institut national des sciences de l'Univers ( INSU - CNRS ), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire océanologique de Villefranche-sur-mer (OOVM), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), and Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Collège de France (CdF (institution))-Institut de Recherche pour le Développement (IRD)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA)
Subjects: 0106 biological sciences, [ SDU.OCEAN ] Sciences of the Universe [physics]/Ocean, Atmosphere, 010504 meteorology & atmospheric sciences, [SDE.MCG]Environmental Sciences/Global Changes, Hydrostatic pressure, Alkalinity, Aquatic Science, Biology, 01 natural sciences, chemistry.chemical_compound, Water column, Total inorganic carbon, Organic matter, 14. Life underwater, [SDU.ENVI]Sciences of the Universe [physics]/Continental interfaces, environment, ComputingMilieux_MISCELLANEOUS, [SDU.STU.OC]Sciences of the Universe [physics]/Earth Sciences/Oceanography, 0105 earth and related environmental sciences, Emiliania huxleyi, chemistry.chemical_classification, [SDU.OCEAN]Sciences of the Universe [physics]/Ocean, Atmosphere, Atmospheric pressure, 010604 marine biology & hydrobiology, fungi, Geology, biology.organism_classification, [SDE.ES]Environmental Sciences/Environmental and Society, [ SDE.MCG ] Environmental Sciences/Global Changes, Calcium carbonate, Oceanography, chemistry, 13. Climate action, Biological carbon pump, Mesopelagic, Mineral ballast, Coccolithophorid, Prokaryotes, Biodegradation, [SDE.BE]Environmental Sciences/Biodiversity and Ecology
Abstract: In the deep ocean, fluxes of particulate organic carbon (POC) and calcium carbonate are positively correlated, suggesting that CaCO3 could increase sinking particle densities and/or protect the organic matter from degradation by prokaryotes, the so called "ballast effect". Here, we used the PArticle Sinking Simulator (PASS) system to investigate the effect of increasing pressure on the biodegradation of calcifying Emiliania huxleyi aggregates. Incubations were carried out over a period of 10 days, simulating the changes in temperature and pressure in the water column of the NW Mediterranean Sea. Aggregates sinking from a depth of 200 m to 1700 m (assuming an average sinking velocity of 150 m d(-1)) were exposed to a natural mesopelagic prokaryotic community collected from 200 m. In contrast to previous studies, where silicifying diatom aggregates were used, the calcifying E. huxleyi aggregates were found to be more sensitive to degradation with increasing hydrostatic pressure (relative to constant atmospheric pressure). This was confirmed by changes in lipid composition which suggested increased cell lysis. Changes in particulate inorganic carbon and total alkalinity indicated that CaCO3 dissolution might have been faster under pressure. Increased hydrostatic pressure also had a positive effect on particle aggregation, which may compensate for the effect of increased cell lysis. Our results imply that in coccolithophorid-dominated sinking aggregates, the ballasting and protection effects of coccoliths may collapse throughout the water column. The increased aggregation potential with pressure observed in these controlled conditions, may balance the loss of mineral ballast to a certain extent, although this needs to be confirmed in situ.
Published: 2018
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45. Sourdough microbial community dynamics: An analysis during French organic bread-making processes

Author: Emilie Lhomme, Xavier Dousset, Delphine Sicard, Bernard Onno, Charlotte Urien, Judith Legrand, Laboratoire de Microbiologie Alimentaire et Industrielle, PRES Université Nantes Angers Le Mans (UNAM), Génétique Quantitative et Evolution - Le Moulon (Génétique Végétale) (GQE-Le Moulon), Institut National de la Recherche Agronomique (INRA)-Université Paris-Sud - Paris 11 (UP11)-AgroParisTech-Centre National de la Recherche Scientifique (CNRS), UMR 1014 SECurité des ALIments et Microbiologie, Institut National de la Recherche Agronomique (INRA)-Département Microbiologie et Chaîne Alimentaire (MICA), Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire, Agroalimentaire et de l'alimentation Nantes-Atlantique (ONIRIS)-SECurité des ALIments et Microbiologie (SECALIM), ONIRIS Laboratoire de Microbiologie Alimentaire et Industrielle, Matrices Aliments Procédés Propriétés Structure - Sensoriel (GEPEA-MAPS2), Laboratoire de génie des procédés - environnement - agroalimentaire (GEPEA), Ecole Nationale Vétérinaire, Agroalimentaire et de l'alimentation Nantes-Atlantique (ONIRIS)-Université Bretagne Loire (UBL)-IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Université de Nantes (UN)-Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Vétérinaire, Agroalimentaire et de l'alimentation Nantes-Atlantique (ONIRIS)-Université Bretagne Loire (UBL)-IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Université de Nantes (UN)-Centre National de la Recherche Scientifique (CNRS), Ecole Nationale Vétérinaire, Agroalimentaire et de l'alimentation Nantes-Atlantique (ONIRIS), Sciences Pour l'Oenologie (SPO), Université Montpellier 1 (UM1)-Institut de Recherche pour le Développement (IRD [Nouvelle-Calédonie])-Institut National de la Recherche Agronomique (INRA)-Université de Montpellier (UM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Centre National de la Recherche Scientifique (CNRS)-AgroParisTech-Université Paris-Sud - Paris 11 (UP11)-Institut National de la Recherche Agronomique (INRA), Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire, Agroalimentaire et de l'alimentation Nantes-Atlantique (ONIRIS), Université de Nantes - UFR des Sciences et des Techniques (UN UFR ST), Université de Nantes (UN)-Université de Nantes (UN)-IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Centre National de la Recherche Scientifique (CNRS)-Ecole Polytechnique de l'Université de Nantes (EPUN), Université de Nantes (UN)-Université de Nantes (UN)-Institut Universitaire de Technologie - Nantes (IUT Nantes), Université de Nantes (UN)-Institut Universitaire de Technologie Saint-Nazaire (IUT Saint-Nazaire), Université de Nantes (UN)-Institut Universitaire de Technologie - La Roche-sur-Yon (IUT La Roche-sur-Yon), Université de Nantes (UN)-Ecole Nationale Vétérinaire, Agroalimentaire et de l'alimentation Nantes-Atlantique (ONIRIS)-Université Bretagne Loire (UBL)-Université de Nantes - UFR des Sciences et des Techniques (UN UFR ST), Université de Nantes (UN)-Ecole Nationale Vétérinaire, Agroalimentaire et de l'alimentation Nantes-Atlantique (ONIRIS)-Université Bretagne Loire (UBL), Université Montpellier 1 (UM1)-Institut National de la Recherche Agronomique (INRA)-Université de Montpellier (UM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Université de Nantes (UN)-Ecole Nationale Vétérinaire, Agroalimentaire et de l'alimentation Nantes-Atlantique (ONIRIS)-Centre National de la Recherche Scientifique (CNRS)-Université Bretagne Loire (UBL)-IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Université de Nantes (UN)-Ecole Nationale Vétérinaire, Agroalimentaire et de l'alimentation Nantes-Atlantique (ONIRIS)-Centre National de la Recherche Scientifique (CNRS)-Université Bretagne Loire (UBL)-IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT), and Institut National de la Recherche Agronomique (INRA)-Université de Montpellier (UM)-Université Montpellier 1 (UM1)-Institut de Recherche pour le Développement (IRD [Nouvelle-Calédonie])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)
Subjects: 0301 basic medicine, bactérie lactique, [SDV]Life Sciences [q-bio], Microbial Consortia, 030106 microbiology, Colony Count, Microbial, Lactobacillus sanfranciscensis, lactobacillus sanfranciscensis, yeast, Microbiology, Saccharomyces, saccharomyces, 03 medical and health sciences, kazachstania sp, RNA, Ribosomal, 16S, Yeasts, Lactobacillus, Food microbiology, Food science, saccharomyces sp, levure, Triticum, 2. Zero hunger, biology, digestive, oral, and skin physiology, food and beverages, Bread, Kazachstania, biology.organism_classification, Yeast, lactic acid bacteria, Microbial population biology, Fermentation, Food Microbiology, Food, Organic, Food Science
Abstract: Natural sourdoughs are commonly used in bread-making processes, especially for organic bread. Despite its role in bread flavor and dough rise, the stability of the sourdough microbial community during and between bread-making processes is debated. We investigated the dynamics of lactic acid bacteria (LAB) and yeast communities in traditional organic sourdoughs of five French bakeries during the bread-making process and several months apart using classical and molecular microbiology techniques. Sourdoughs were sampled at four steps of the bread-making process with repetition. The analysis of microbial density over 68 sourdough/dough samples revealed that both LAB and yeast counts changed along the bread-making process and between bread-making runs. The species composition was less variable. A total of six LAB and nine yeast species was identified from 520 and 1675 isolates, respectively. The dominant LAB species was Lactobacillus sanfranciscensis, found for all bakeries and each bread-making run. The dominant yeast species changed only once between bread-making processes but differed between bakeries. They mostly belonged to the Kazachstania clade. Overall, this study highlights the change of population density within the bread-making process and between bread-making runs and the relative stability of the sourdough species community during bread-making process.
Published: 2016
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46. Type III Secretion System and Virulence Markers Highlight Similarities and Differences between Human- and Plant-Associated Pseudomonads Related to Pseudomonas fluorescens and P. putida

Author: Victorien Decoin, Xavier Latour, Maïté Vicré-Gibouin, Corinne Barbey, Katy Jeannot, Alexandre Crépin, Dorian Bergeau, Annabelle Merieau, Sylvie Mazurier, Daniel Sperandio, Philippe Lemanceau, Patrick Plésiat, Agroécologie [Dijon], Institut National de la Recherche Agronomique (INRA)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Université Bourgogne Franche-Comté [COMUE] (UBFC), Laboratoire de Microbiologie Signaux et Microenvironnement (LMSM), Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-Normandie Université (NU), Université de Franche-Comté (UFC), Laboratoire de Glycobiologie et Matrice Extracellulaire Végétale (Glyco-MEV), Institut National de la Recherche Agronomique ( INRA ) -Université de Bourgogne ( UB ) -AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Université Bourgogne Franche-Comté ( UBFC ), Laboratoire de Microbiologie Signaux et Microenvironnement ( LMSM ), Université de Rouen Normandie ( UNIROUEN ), Normandie Université ( NU ) -Normandie Université ( NU ), Université de Franche-Comté ( UFC ), Laboratoire de Glycobiologie et Matrice Extracellulaire Végétale ( Glyco-MEV ), Institut National de la Recherche Agronomique (INRA)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Université Bourgogne Franche-Comté [COMUE] (UBFC), Service de bactériologie [Besançon], Centre Hospitalier Régional Universitaire de Besançon (CHRU Besançon), Conseil Regional de Haute-Normandie & Ministere delegue a l'Enseignement Superieur et a la Recherche, Reseau VASI (GRR TERA), Groupement de Recherche CNRS Pseudomonas, IOBC-WPRS, and FEDER
Subjects: POPULATION-DYNAMICS, Cystic Fibrosis, PATHOGENIC BACTERIA, Sequence Homology, Bacteremia, [ SDV.MP.BAC ] Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, medicine.disease_cause, Polymerase Chain Reaction, Applied Microbiology and Biotechnology, CAROTOVORA SUBSP ATROSEPTICA, Type three secretion system, RNA, Ribosomal, 16S, Genotype, Cluster Analysis, Dictyostelium, Bacterial Secretion Systems, Respiratory Tract Infections, Phylogeny, Ecology, biology, Public and Environmental Health Microbiology, Temperature, GENOME SEQUENCE, Plants, GENOTYPIC DIVERSITY, 3. Good health, Pseudomonas aeruginosa, Biotechnology, DNA, Bacterial, Virulence Factors, MICROBIAL-CONTAMINATION, Molecular Sequence Data, Virulence, NUCLEOTIDE-SEQUENCES, Pseudomonas fluorescens, DNA, Ribosomal, Microbiology, medicine, Humans, Pseudomonas Infections, Plant Diseases, PV. TOMATO DC3000, DICTYOSTELIUM-DISCOIDEUM, Pathogenic bacteria, Sequence Analysis, DNA, biology.organism_classification, 16S ribosomal RNA, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, CLINICAL STRAIN, Bacteria, Food Science
Abstract: Pseudomonas fluorescensis commonly considered a saprophytic rhizobacterium devoid of pathogenic potential. Nevertheless, the recurrent isolation of strains from clinical human cases could indicate the emergence of novel strains originating from the rhizosphere reservoir, which could be particularly resistant to the immune system and clinical treatment. The importance of type three secretion systems (T3SSs) in the relatedPseudomonas aeruginosanosocomial species and the occurrence of this secretion system in plant-associatedP. fluorescensraise the question of whether clinical isolates may also harbor T3SSs. In this study, isolates associated with clinical infections and identified in hospitals as belonging toP. fluorescenswere compared with fluorescent pseudomonads harboring T3SSs isolated from plants. Bacterial isolates were tested for (i) their genetic relationships based on their 16S rRNA phylogeny, (ii) the presence of T3SS genes by PCR, and (iii) their infectious potential on animals and plants under environmental or physiological temperature conditions. Two groups of bacteria were delineated among the clinical isolates. The first group encompassed thermotolerant (41°C) isolates from patients suffering from blood infections; these isolates were finally found to not belong toP. fluorescensbut were closely related and harbored highly conserved T3SS genes belonging to the Ysc-T3SS family, like the T3SSs fromP. aeruginosa. The second group encompassed isolates from patients suffering from cystic fibrosis; these isolates belonged toP. fluorescensand harbored T3SS genes belonging to the Hrp1-T3SS family found commonly in plant-associatedP. fluorescens.
Published: 2015
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47. The Sole DEAD-Box RNA Helicase of the Gastric Pathogen Helicobacter pylori Is Essential for Colonization

Author: Lamya El Mortaji, Karine Anger, Hilde De Reuse, Yves Quentin, Eloïse Galtier, Sylvie Aubert, Yulia Redko, Christine Schmitt, El Mortaji, Lamya, De Reuse, Hilde, Pathogenèse de Helicobacter - Helicobacter Pathogenesis, Institut Pasteur [Paris]-Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS), Imagopole (CITECH), Institut Pasteur [Paris], Laboratoire de microbiologie et génétique moléculaires (LMGM), Centre de Biologie Intégrative (CBI), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Roux fellowship, Carnot MI fellowship of the Institut Pasteur, Janssen, Agence National de la Recherche [ANR 09 BLAN 0287 01, ANR 12 BSV5-0025-02], Pasteur-Weizmann Consortium of 'The Roles of Noncoding RNAs in Regulation of Microbial Life Styles and Virulence', ANR-12-BSV5-0025,BacTox1,Rôle des systèmes toxine antitoxine de type I dans la persistence bactérienne(2012), Institut Pasteur [Paris] (IP)-Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS), Institut Pasteur [Paris] (IP), Laboratoire de microbiologie et génétique moléculaires - UMR5100 (LMGM), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), and Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0301 basic medicine, DEAD-box helicase, RNase P, [SDV]Life Sciences [q-bio], mouse model, Ribosome biogenesis, flagellar motility, Ribosome, Microbiology, Helicobacter Infections, Ribosome assembly, DEAD-box RNA Helicases, Mice, 03 medical and health sciences, RNA degradation, Bacterial Proteins, Transcription (biology), RNA, Ribosomal, 16S, Virology, Animals, Helicobacter pylori, 2. Zero hunger, biology, RNA, Helicase, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, RNA Helicase A, QR1-502, 3. Good health, Cell biology, 030104 developmental biology, biology.protein, Research Article
Abstract: Present in every kingdom of life, generally in multiple copies, DEAD-box RNA helicases are specialized enzymes that unwind RNA secondary structures. They play major roles in mRNA decay, ribosome biogenesis, and adaptation to cold temperatures. Most bacteria have multiple DEAD-box helicases that present both specialized and partially redundant functions. By using phylogenomics, we revealed that the Helicobacter genus, including the major gastric pathogen H. pylori, is among the exceptions, as it encodes a sole DEAD-box RNA helicase. In H. pylori, this helicase, designated RhpA, forms a minimal RNA degradosome together with the essential RNase, RNase J, a major player in the control of RNA decay. Here, we used H. pylori as a model organism with a sole DEAD-box helicase and investigated the role of this helicase in H. pylori physiology, ribosome assembly, and during in vivo colonization. Our data showed that RhpA is dispensable for growth at 37°C but crucial at 33°C, suggesting an essential role of the helicase in cold adaptation. Moreover, we found that a ΔrhpA mutant was impaired in motility and deficient in colonization of the mouse model. RhpA is involved in the maturation of 16S rRNA at 37°C and is associated with translating ribosomes. At 33°C, RhpA is, in addition, recruited to individual ribosomal subunits. Finally, via its role in the RNA degradosome, RhpA directs the regulation of the expression of its partner, RNase J. RhpA is thus a multifunctional enzyme that, in H. pylori, plays a central role in gene regulation and in the control of virulence., IMPORTANCE We present the results of our study on the role of RhpA, the sole DEAD-box RNA helicase encoded by the major gastric pathogen Helicobacter pylori. We observed that all the Helicobacter species possess such a sole helicase, in contrast to most free-living bacteria. RhpA is not essential for growth of H. pylori under normal conditions. However, deletion of rhpA leads to a motility defect and to total inhibition of the ability of H. pylori to colonize a mouse model. We also demonstrated that this helicase encompasses most of the functions of its specialized orthologs described so far. We found that RhpA is a key element of the bacterial adaptation to colder temperatures and plays a minor role in ribosome biogenesis. Finally, RhpA regulates transcription of the rnj gene encoding RNase J, its essential partner in the minimal H. pylori RNA degradosome, and thus plays a crucial role in the control of RNA decay.
Published: 2018
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48. A conserved mechanism drives partition complex assembly on bacterial chromosomes and plasmids

Author: Debaugny, Roxanne, Sanchez, Aurore, Rech, Jérôme, Labourdette, Delphine, Dorignac, Jerome, Geniet, Frederic, Palmeri, John, Parmeggiani, Andrea, Boudsocq, François, LE BERRE, Véronique, Walter, Jean-Charles, Bouet, Jean-yves, Laboratoire de microbiologie et génétique moléculaires (LMGM), Centre de Biologie Intégrative (CBI), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Laboratoire d'Ingénierie des Systèmes Biologiques et des Procédés (LISBP), Institut National de la Recherche Agronomique (INRA)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS), Laboratoire Charles Coulomb (L2C), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Dynamique des interactions membranaires normales et pathologiques (DIMNP), Université Montpellier 1 (UM1)-Université Montpellier 2 - Sciences et Techniques (UM2)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Systèmes Complexes et Phénomènes Nonlinéaires (SCPN), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), CNRS INPHYNITI program, Universite de Toulouse [APR14], Labex NUMEV [AAP 2013-2-005, 2015-2-055, 2016-1-024], ANR-14-CE09-0025,IBM,Visualisation et Modélisation de la Mitose Bactérienne(2014), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Institut National de la Recherche Agronomique (INRA), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), Laboratoire de microbiologie et génétique moléculaires - UMR5100 (LMGM), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), and Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)
Subjects: [PHYS.PHYS.PHYS-BIO-PH]Physics [physics]/Physics [physics]/Biological Physics [physics.bio-ph], plasmid partition, DNA segregation, Article, Bacterial Proteins, Chromosome Segregation, Escherichia coli, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, ParABS, Vibrio cholerae, Quantitative Biology & Dynamical Systems, bactérie, Stochastic Processes, F plasmid, Systems Biology, adn, DNA Replication, Repair & Recombination, Articles, partitionnement, Chromosomes, Bacterial, Models, Theoretical, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Microbiology, Virology & Host Pathogen Interaction, Autre (Sciences du Vivant), Plasmids
Abstract: Synopsis Chromosome and plasmid segregation in bacteria are mostly driven by ParABS systems. These DNA partitioning machineries rely on large nucleoprotein complexes assembled on centromere sites (parS). However, the mechanism of how a few parS-bound ParB proteins nucleate the formation of highly concentrated ParB clusters remains unclear despite several proposed physico-mathematical models. We discriminated between these different models by varying some key parameters in vivo using the F plasmid partition system. We found that "Nucleation & caging" is the only coherent model recapitulating in vivo data. We also showed that the stochastic self-assembly of partition complexes (i) is a robust mechanism, (ii) does not directly involve ParA ATPase, (iii) results in a dynamic structure of discrete size independent of ParB concentration, and (iv) is not perturbed by active transcription but is by protein complexes. We refined the "Nucleation & caging" model and successfully applied it to the chromosomally encoded Par system of Vibrio cholerae, indicating that this stochastic self-assembly mechanism is widely conserved from plasmids to chromosomes.
Published: 2018
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49. Large-Scale Measurement of mRNA Degradation in Escherichia coli: To Delay or Not to Delay

Author: Muriel Cocaign-Bousquet, Agamemnon J. Carpousis, Ignacio González, Annick Moisan, Marie Bouvier, Sébastien Nouaille, Nathalie Villa-Vialaneix, Christine Gaspin, Sandrine Laguerre, Laurence Girbal, Laboratoire d'Ingénierie des Systèmes Biologiques et des Procédés (LISBP), Centre National de la Recherche Scientifique (CNRS)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Institut National de la Recherche Agronomique (INRA), Unité de Mathématiques et Informatique Appliquées de Toulouse (MIAT INRA), Institut National de la Recherche Agronomique (INRA), Laboratoire de microbiologie et génétique moléculaires (LMGM), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Institut National de la Recherche Agronomique (INRA)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de microbiologie et génétique moléculaires - UMR5100 (LMGM), Centre de Biologie Intégrative (CBI), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), and Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0301 basic medicine, RNA half-life, Chemistry, [SDV]Life Sciences [q-bio], Linear model, Bacterial growth, medicine.disease_cause, Correlation, Genome-wide measurement, 03 medical and health sciences, 030104 developmental biology, Exponential decay, Linear regression, MRNA degradation, Biophysics, medicine, RNA decay modeling, Delay in the degradation kinetics, Scale measurement, Escherichia coli
Abstract: International audience; In this study, we compared different computational methods used for genome-wide determination of mRNA half-lives in Escherichia coli with a special focus on the impact on considering a delay before the onset of mRNA decay after transcription arrest. A wide variety of datasets were analyzed coming from different technical methods for mRNA quantification (microarrays, RNA-seq, and RT-qPCR) and different bacterial growth conditions. The exponential decay of mRNA levels was fitted using both linear and exponential models and with or without a delay. We showed that for all the models, independently of mRNA quantification methods and growth conditions, ignoring the delay resulted in only a modest overestimation of the half-life. For approximately 80% of the mRNAs, differences in mRNA half-life values were less than 34 s. The correlation between half-lives estimated with and without a delay was extremely high. However, the slope of the linear regression between the half-lives with and without a delay tended to decrease with the delay. For the few mRNAs for which taking into account the delay influenced the estimated half-life, the impact was dependent on the model and the growth condition. The smallest impact was obtained for the linear model.
Published: 2018
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50. Evolutionary Success of Prokaryotes

Author: Anne Godfroy, Philippe Normand, Karine Alain, Patricia Bonin, Bernard Ollivier, Nathalie Pradel, Jean-Claude Bertrand, Institut Pythéas (OSU PYTHEAS), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut méditerranéen d'océanologie (MIO), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de microbiologie des environnements extrêmophiles (LM2E), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS), Laboratoire d'Ecologie Microbienne - UMR 5557 (LEM), Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Ecole Nationale Vétérinaire de Lyon (ENVL)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Bertrand, J.C. (ed.), Normand, P. (ed.), Ollivier, Bernard (ed.), Sime-Ngando, T. (ed.), Centre National de la Recherche Scientifique (CNRS)-Université de Brest (UBO)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Ecole Nationale Vétérinaire de Lyon (ENVL), Laboratoire d'océanographie et de biogéochimie (LOB), Université de la Méditerranée - Aix-Marseille 2-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de MicrobiologiE de Géochimie et d'Ecologie Marines (LMGEM), Centre National de la Recherche Scientifique (CNRS)-Université de la Méditerranée - Aix-Marseille 2, Laboratoire de Microbiologie et Biotechnologie des Environnements Chauds, Université de la Méditerranée - Aix-Marseille 2-Université de Provence - Aix-Marseille 1, Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS), Département informatique (INFO), and Institut Mines-Télécom [Paris] (IMT)-Télécom Bretagne-Université européenne de Bretagne - European University of Brittany (UEB)
Subjects: 0303 health sciences, 03 medical and health sciences, Race (biology), Red queen, 030306 microbiology, Ecology, [SDV]Life Sciences [q-bio], [SDV.BC]Life Sciences [q-bio]/Cellular Biology, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Biology, ComputingMilieux_MISCELLANEOUS, Organism, 030304 developmental biology
Abstract: How can the evolutionary success of prokaryotes be explained ? How did they manage to survive conditions that have fluctuated, with drastic events over 3.5 billion years ? Which significant metabolisms and mechanisms have appeared over the course of evolution that have permitted them to survive the most inhospitable conditions from the physicochemical point of view ? In a 'Red Queen Race', prokaryotes have always run sufficiently fast to adapt to constraints imposed by the environment and the other living species with which they have established interactions. If the criterion retained to define the level of evolution of an organism is its capacity to survive and to yield the largest number of offsprings, prokaryotes must be considered highly evolved organisms.
Published: 2018
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