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Accueil > Départements > Biologie des Génomes > Philippe BOULOC : Signalisation et Réseaux de Régulations Bactériens

Publications de l’équipe

2019


  • Y. Deng, X. Luo, M. Xie, P. Bouloc, C. Chen, et A. Jacq, « The ilvGMEDA Operon Is Regulated by Transcription Attenuation in Vibrio alginolyticus ZJ-T », Applied and Environmental Microbiology, vol. 85, nᵒ 19, oct. 2019.
    Résumé : Bacteria synthesize amino acids according to their availability in the environment or, in the case of pathogens, within the host. We explored the regulation of the biosynthesis of branched-chain amino acids (BCAAs) (l-leucine, l-valine, and l-isoleucine) in Vibrio alginolyticus, a marine fish and shellfish pathogen and an emerging opportunistic human pathogen. In this species, the ilvGMEDA operon encodes the main pathway for biosynthesis of BCAAs. Its upstream regulatory region shows no sequence similarity to the corresponding region in Escherichia coli or other Enterobacteriaceae, and yet we show that this operon is regulated by transcription attenuation. The translation of a BCAA-rich peptide encoded upstream of the structural genes provides an adaptive response similar to the E. coli canonical model. This study of a nonmodel Gram-negative organism highlights the mechanistic conservation of transcription attenuation despite the absence of primary sequence conservation.IMPORTANCE This study analyzes the regulation of the biosynthesis of branched-chain amino acids (leucine, valine, and isoleucine) in Vibrio alginolyticus, a marine bacterium that is pathogenic to fish and humans. The results highlight the conservation of the main regulatory mechanism with that of the enterobacterium Escherichia coli, suggesting that such a mechanism appeared early during the evolution of Gram-negative bacteria, allowing adaptation to a wide range of environments.
    Mots-clés : acetolactate synthase (AHAS), branched-chain amino acids, DBG, ilvGMEDA operon, leader attenuator, SRRB, transcription attenuation, Vibrio alginolyticus.

  • T. Rubio, D. Oyanedel, Y. Labreuche, E. Toulza, X. Luo, M. Bruto, C. Chaparro, M. Torres, J. de Lorgeril, P. Haffner, J. Vidal-Dupiol, A. Lagorce, B. Petton, G. Mitta, A. Jacq, F. Le Roux, G. M. Charrière, et D. Destoumieux-Garzón, « Species-specific mechanisms of cytotoxicity toward immune cells determine the successful outcome of Vibrio infections », Proceedings of the National Academy of Sciences of the United States of America, juin 2019.
    Résumé : Vibrio species cause infectious diseases in humans and animals, but they can also live as commensals within their host tissues. How Vibrio subverts the host defenses to mount a successful infection remains poorly understood, and this knowledge is critical for predicting and managing disease. Here, we have investigated the cellular and molecular mechanisms underpinning infection and colonization of 2 virulent Vibrio species in an ecologically relevant host model, oyster, to study interactions with marine Vibrio species. All Vibrio strains were recognized by the immune system, but only nonvirulent strains were controlled. We showed that virulent strains were cytotoxic to hemocytes, oyster immune cells. By analyzing host and bacterial transcriptional responses to infection, together with Vibrio gene knock-outs, we discovered that Vibrio crassostreae and Vibrio tasmaniensis use distinct mechanisms to cause hemocyte lysis. Whereas V. crassostreae cytotoxicity is dependent on a direct contact with hemocytes and requires an ancestral gene encoding a protein of unknown function, r5.7, V. tasmaniensis cytotoxicity is dependent on phagocytosis and requires intracellular secretion of T6SS effectors. We conclude that proliferation of commensal vibrios is controlled by the host immune system, preventing systemic infections in oysters, whereas the successful infection of virulent strains relies on Vibrio species-specific molecular determinants that converge to compromise host immune cell function, allowing evasion of the host immune system.
    Mots-clés : cytolysis, DBG, dual RNA-seq, pathogenesis, SRRB, T6SS, toxin.

2018



  • W. Briand, O. Dao, G. Garnier, R. Guegan, B. Marta, C. Maupu, J. Miesch, K. Papadopoulo, A. Radoux, J. Rojahn, Y. Zhu, C. Aubry, P. Bouloc, S. Bury-Moné, A. Ferré, S. Lautru, O. Namy, et M. Sabeti-Azad, « Dégradation d’un anticancéreux dans les eaux usées - Une médaille d’or pour l’équipe GO Paris-Saclay », Medecine Sciences: M/S, vol. 34, nᵒ 12, p. 1111-1114, déc. 2018.
    Résumé : iGEM (pour <i>international genetically engineered machine)<i/> est un concours international autour de la biologie synthétique réunissant des étudiants de toutes disciplines (mathématiques, physique, biologie, arts, etc.). « L’objectif est de construire un système biologique fonctionnel complexe, en assemblant des composants individuels moléculaires simples et standardisés (fragments d’ADN), appelés « briques biologiques » (biobriques), sorte de « legos » moléculaires, entreposés au MIT (<i>Massachusetts Institute of Technology<i/>) (le <i>registry of standard biological parts<i/> contient environ 20 000 biobriques). C’est une démarche proche de celle de l’ingénieur qui assemble des circuits électroniques ». En 2004, lors de sa création par le MIT (<b>→<b/>), la compétition iGEM regroupait une quarantaine de projets ; 14 ans plus tard, elle accueille 350 équipes (6 000 étudiants, avec leurs instructeurs) issues des universités du monde entier. Elle culmine en un <i>Giant Jamboree<i/> de quatre jours à Boston en novembre, au cours duquel les équipes présentent leur projet. Le « wiki » de la compétition (www.igem.org) présente l’ensemble des projets ainsi que le palmarès. Cette année, ont été décernées 114 médailles d’or, 68 d’argent et 107 de bronze. Neuf équipes françaises étaient engagées.<b>(→) Voir l’article de J. Peccoud et L. Coulombel, dont certains passages sont repris dans ce « chapo », m/s n° 5, mai 2007, page 551<b/>
    Mots-clés : ACTINO, Animals, Antineoplastic Agents, Biodegradation, Environmental, Bioreactors, CHERDIR, DBG, Escherichia coli, Escherichia coli Proteins, gamma-Glutamyl Hydrolase, GST, Humans, I2BC, Metabolic Engineering, Methotrexate, MICROBIO, Multienzyme Complexes, Organisms, Genetically Modified, Peptide Synthases, RNASTR, SRRB, Waste Water, Water Pollutants, Chemical, Water Purification.
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  • G. M. Dias, A. Bidault, P. Le Chevalier, G. Choquet, C. Der Sarkissian, L. Orlando, C. Medigue, V. Barbe, S. Mangenot, C. C. Thompson, F. L. Thompson, A. Jacq, V. Pichereau, et C. Paillard, « Vibrio tapetis Displays an Original Type IV Secretion System in Strains Pathogenic for Bivalve Molluscs », Frontiers in Microbiology, vol. 9, p. 227, 2018.
    Résumé : The Brown Ring Disease (BRD) caused high mortality rates since 1986 in the Manila clamVenerupis philippinarumintroduced and cultured in Western Europe from the 1970s. The causative agent of BRD is a Gram-Negative bacterium,Vibrio tapetis, which is also pathogenic to fish. Here we report the first assembly of the complete genome ofV. tapetisCECT4600T, together with the genome sequences of 16 additional strains isolated across a broad host and geographic range. Our extensive genome dataset allowed us to describe the pathogen pan- and core genomes and to identify putative virulence factors. TheV. tapetiscore genome consists of 3,352 genes, including multiple potential virulence factors represented by haemolysins, transcriptional regulators, Type I restriction modification system, GGDEF domain proteins, several conjugative plasmids, and a Type IV secretion system. Future research on the coevolutionary arms race betweenV. tapetisvirulence factors and host resistance mechanisms will improve our understanding of how pathogenicity develops in this emerging pathogen.
    Mots-clés : comparative genomics, core genome, DBG, pangenome, pathogenicity, SRRB, T4SS, Venerupis philippinarum, Vibrio tapetis.

  • W. Liu, T. Rochat, C. Toffano-Nioche, T. N. Le Lam, P. Bouloc, et C. Morvan, « Assessment of Bona Fide sRNAs in Staphylococcus aureus », Frontiers in Microbiology, vol. 9, p. 228, 2018.
    Résumé : Bacterial regulatory RNAs have been extensively studied for over a decade, and are progressively being integrated into the complex genetic regulatory network. Transcriptomic arrays, recent deep-sequencing data and bioinformatics suggest that bacterial genomes produce hundreds of regulatory RNAs. However, while some have been authenticated, the existence of the others varies according to strains and growth conditions, and their detection fluctuates with the methodologies used for data acquisition and interpretation. For example, several small RNA (sRNA) candidates are now known to be parts of UTR transcripts. Accurate annotation of regulatory RNAs is a complex task essential for molecular and functional studies. We definedbona fidesRNAs as those that (i) likely act intransand (ii) are not expressed from the opposite strand of a coding gene. Using published data and our own RNA-seq data, we reviewed hundreds ofStaphylococcus aureusputative regulatory RNAs using the DETR'PROK computational pipeline and visual inspection of expression data, addressing the question of which transcriptional signals correspond to sRNAs. We conclude that the model strain HG003, a NCTC8325 derivative commonly used forS. aureusgenetic regulation studies, has only about 50bona fidesRNAs, indicating that these RNAs are less numerous than commonly stated. Among them, about half are associated to theS. aureussp. core genome and a quarter are possibly expressed in otherStaphylococci. We hypothesize on their features and regulation using bioinformatic approaches.
    Mots-clés : bona fide sRNA, DBG, gene regulation, RNA-seq, SRRB, SSFA, Staphylococcus aureus HG003, transcription factors.

  • A. N. Nguyen, E. Disconzi, G. M. Charriere, D. Destoumieux-Garzon, P. Bouloc, F. Le Roux, et A. Jacq, « csrB Gene Duplication Drives the Evolution of Redundant Regulatory Pathways Controlling Expression of the Major Toxic Secreted Metalloproteases in Vibrio tasmaniensis LGP32 », Msphere, vol. 3, nᵒ 6, p. e00582-18, déc. 2018.
    Résumé : CsrBs are bacterial highly conserved and multiple-copy noncoding small RNAs (sRNAs) that play major roles in cell physiology and virulence. In the Vibrio genus, they are known to be regulated by the two-component system VarSNarA. They modulate the well-characterized quorum sensing pathway controlling virulence and luminescence in Vibrio cholerae and Vibrio harveyi, respectively. Remarkably, Vibrio tasmaniensis LGP32, an oyster pathogen that belongs to the Splendidus Glade, was found to have four copies of csrB, named csrB1-4, compared to two to three copies in other Vibrio species. Here, we show that the extra csrB4 copy results from a csrB3 gene duplication, a characteristic of the Splendidus Glade. Interestingly, csrB genes are regulated in different ways in V. tasmaniensis, with csrB1 expression being independent of the VarSNarA system. We found that a complex regulatory network involving CsrBs, quorum sensing, and the stationary-phase sigma factor sigma S redundantly but differentially controls the production of two secreted metalloproteases, Vsm and PrtV, the former being a major determinant of the V. tasmaniensis extracellular product toxicity. In particular, we identified a novel VarS/VarA-dependent but CsrB-independent pathway that controls positively both Vsm production and PrtV production as well as rpoS expression. Altogether, our data show that a csrB gene duplication event in V. tasmaniensis supported the evolution of the regulatory network controlling the expression of major toxic secreted metalloproteases, thereby increasing redundancy and enabling the integration of additional input signals. IMPORTANCE The conserved CsrB sRNAs are an example of sibling sRNAs, i.e., sRNAs which are present in multiple copies in genomes. This report illustrates how new copies arise through gene duplication events and highlights two evolutionary advantages of having such multiple copies: differential regulation of the multiple copies allows integration of different input signals into the regulatory network of which they are parts, and the high redundancy that they provide confers a strong robustness to the system.
    Mots-clés : bacterial gene regulation, bacterial sRNAs, cholerae, crassostrea-gigas, DBG, escherichia-coli, flhdc expression, Gene Duplication, Gene Expression Regulation, Bacterial, host-pathogen interactions, Metalloproteases, protein csra, Quorum Sensing, RNA, Untranslated, rpos, sequence, small rnas, splendidus, SRRB, transcriptomics, Vibrio, Vibrio pathogenic to oysters, Vibrio pathogenic to oysters, virulence.


  • N. Raghunathan, R. M. Kapshikar, J. K. Leela, J. Mallikarjun, P. Bouloc, et J. Gowrishankar, « Genome-wide relationship between R-loop formation and antisense transcription in Escherichia coli », Nucleic Acids Research, févr. 2018.

  • T. Rochat, C. Bohn, C. Morvan, T. N. L. Lam, F. Razvi, A. Pain, C. Toffano-Nioche, P. Ponien, A. Jacq, E. Jacquet, P. D. Fey, D. Gautheret, et P. Bouloc, « The conserved regulatory RNA RsaE down-regulates the arginine degradation pathway in Staphylococcus aureus », Nucleic Acids Research, vol. 46, nᵒ 17, p. 8803-8816, sept. 2018.
    Résumé : RsaE is a regulatory RNA highly conserved amongst Firmicutes that lowers the amount of mRNAs associated with the TCA cycle and folate metabolism. A search for new RsaE targets in Staphylococcus aureus revealed that in addition to previously described substrates, RsaE down-regulates several genes associated with arginine catabolism. In particular, RsaE targets the arginase rocF mRNA via direct interactions involving G-rich motifs. Two duplicated C-rich motifs of RsaE can independently downregulate rocF expression. The faster growth rate of Delta rsaE compared to its parental strain in media containing amino acids as sole carbon source points to an underlying role for RsaE in amino acid catabolism. Collectively, the data support a model in which RsaE acts as a global regulator of functions associated with metabolic adaptation.
    Mots-clés : accessibility, DBG, discovery, identification, prediction, reveals, SRRB, SSFA, virulence.

2017

2016


  • P. Bouloc et F. Repoila, « Fresh layers of RNA-mediated regulation in Gram-positive bacteria », Current Opinion in Microbiology, vol. 30, p. 30-35, avr. 2016.
    Résumé : Bacterial regulatory RNAs have been defined as diverse classes of cis and trans elements that may intervene at each step of gene expression, from RNA and protein synthesis to degradation. Here, we report on a few examples from Gram-positive bacteria that extend the definition of regulatory RNAs to include 5' and 3' UTRs that also act as cis and trans regulators. New examples unveil the existence of cis and trans acting regulatory RNAs on a single molecule. Also, we highlight data showing that a key RNA chaperone in Enterobacteriaceae, Hfq, does not fulfill the same role in Gram-positive Firmicutes.
    Mots-clés : Bacterial Proteins, DBG, Gene Expression Regulation, Bacterial, Gram-Positive Bacteria, RNA, Bacterial, SRRB.

  • Y. Deng, C. Chen, Z. Zhao, J. Zhao, A. Jacq, X. Huang, et Y. Yang, « The RNA Chaperone Hfq Is Involved in Colony Morphology, Nutrient Utilization and Oxidative and Envelope Stress Response in Vibrio alginolyticus », PloS One, vol. 11, nᵒ 9, p. e0163689, 2016.
    Résumé : Hfq is a global regulator that is involved in environmental adaptation of bacteria and in pathogenicity. To gain insight into the role of Hfq in Vibrio alginolyticus, an hfq deletion mutant was constructed in V. alginolyticus ZJ-T strain and phenotypically characterized. Deletion of hfq led to an alteration of colony morphology and reduced extracellular polysaccharide production, a general impairment of growth in both rich medium and minimal media with different carbon sources or amino acids, enhanced sensitivity to oxidative stress and to several antibiotics. Furthermore, a differential transcriptomic analysis showed significant changes of transcript abundance for 306 protein coding genes, with 179 genes being up regulated and 127 down-regulated. Several of these changes could be related to the observed phenotypes of the mutant. Transcriptomic data also provided evidence for the induction of the extracytoplasmic stress response in absence of Hfq. Altogether, these findings point to broad regulatory functions for Hfq in V. alginolyticus cells, likely to underlie an important role in pathogenicity.
    Mots-clés : DBG, SRRB.

  • A. S. Vanhove, T. P. Rubio, A. N. Nguyen, A. Lemire, D. Roche, J. Nicod, A. Vergnes, A. C. Poirier, E. Disconzi, E. Bachère, F. Le Roux, A. Jacq, G. M. Charrière, et D. Destoumieux-Garzón, « Copper homeostasis at the host vibrio interface: lessons from intracellular vibrio transcriptomics », Environmental Microbiology, vol. 18, nᵒ 3, p. 875-888, mars 2016.
    Résumé : Recent studies revealed that several vibrio species have evolved the capacity to survive inside host cells. However, it is still often ignored if intracellular stages are required for pathogenicity. Virulence of Vibrio tasmaniensis LGP32, a strain pathogenic for Crassostrea gigas oysters, depends on entry into hemocytes, the oyster immune cells. We investigated here the mechanisms of LGP32 intracellular survival and their consequences on the host-pathogen interaction. Entry and survival inside hemocytes were required for LGP32-driven cytolysis of hemocytes, both in vivo and in vitro. LGP32 intracellular stages showed a profound boost in metabolic activity and a major transcription of antioxidant and copper detoxification genes, as revealed by RNA sequencing. LGP32 isogenic mutants showed that resistance to oxidative stress and copper efflux are two main functions required for vibrio intracellular stages and cytotoxicity to hemocytes. Copper efflux was also essential for host colonization and virulence in vivo. Altogether, our results identify copper resistance as a major mechanism to resist killing by phagocytes, induce cytolysis of immune cells and colonize oysters. Selection of such resistance traits could arise from vibrio interactions with copper-rich environmental niches including marine invertebrates, which favour the emergence of pathogenic vibrios resistant to intraphagosomal killing across animal species.
    Mots-clés : Animals, Bacterial Proteins, Base Sequence, Copper, Crassostrea, Cytoplasm, DBG, Hemocytes, Homeostasis, Host-Pathogen Interactions, Sequence Analysis, RNA, Shellfish, SRRB, Superoxide Dismutase, Vibrio, Virulence.

  • A. Vingadassalon, P. Bouloc, et S. Rimsky, « Removing nucleic acids from nucleoid-associated proteins purified by affinity column », Journal of Biological Methods, vol. 3, nᵒ 1, p. e35, 2016.
    Résumé : In bacteria, DNA is tightly compacted in a supercoiled organization, which is mediated in part by nucleoid-associated proteins (NAPs). NAPs are well characterized for their ability to bind nucleic acids and for their involvement in gene regulation. A method commonly used to study protein-nucleic acid interactions involves immunoprecipitation of the protein of interest which is subsequently incubated with nucleic acids. A common cause of artifact is due to nucleic acids that remains bound to the protein of interest during the whole purification process. We developed an optimized method for the purification of tagged NAPs on affinity columns. The combination of three known methods allows removal of most of the nucleic acids bound to proteins during the purification process. This protocol is designed to improve the quality and specificity of results of in vitro experiments involving nucleic acid binding tests on purified NAPs. It can be used for in vitro studies of other RNA/DNA binding proteins.
    Mots-clés : affinity, DBG, nucleic acids, nucleoid-associated proteins, purification, SRRB.
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2015


  • R. A. Bonnin et P. Bouloc, « RNA Degradation in Staphylococcus aureus: Diversity of Ribonucleases and Their Impact », International Journal of Genomics, vol. 2015, p. 395753, 2015.
    Résumé : The regulation of RNA decay is now widely recognized as having a central role in bacterial adaption to environmental stress. Here we present an overview on the diversity of ribonucleases (RNases) and their impact at the posttranscriptional level in the human pathogen Staphylococcus aureus. RNases in prokaryotes have been mainly studied in the two model organisms Escherichia coli and Bacillus subtilis. Based on identified RNases in these two models, putative orthologs have been identified in S. aureus. The main staphylococcal RNases involved in the processing and degradation of the bulk RNA are (i) endonucleases RNase III and RNase Y and (ii) exonucleases RNase J1/J2 and PNPase, having 5' to 3' and 3' to 5' activities, respectively. The diversity and potential roles of each RNase and of Hfq and RppH are discussed in the context of recent studies, some of which are based on next-generation sequencing technology.
    Mots-clés : DBG, SRRB.

  • D. Goudenège, M. A. Travers, A. Lemire, B. Petton, P. Haffner, Y. Labreuche, D. Tourbiez, S. Mangenot, A. Calteau, D. Mazel, J. L. Nicolas, A. Jacq, et F. Le roux, « A single regulatory gene is sufficient to alter Vibrio aestuarianus pathogenicity in oysters », Environmental Microbiology, vol. 17, nᵒ 11, p. 4189-4199, nov. 2015.
    Résumé : Oyster diseases caused by pathogenic vibrios pose a major challenge to the sustainability of oyster farming. In France, since 2012 a disease affecting specifically adult oysters has been associated with the presence of Vibrio aestuarianus. Here, by combining genome comparison, phylogenetic analyses and high-throughput infections of strains isolated before or during the recent outbreaks, we show that virulent strains cluster into two V. aestuarianus lineages independently of the sampling dates. The bacterial lethal dose was not different between strains isolated before or after 2012. Hence, the emergence of a new highly virulent clonal strain is unlikely. Each lineage comprises nearly identical strains, the majority of them being virulent, suggesting that within these phylogenetically coherent virulent lineages a few strains have lost their pathogenicity. Comparative genomics allowed the identification of a single frameshift in a non-virulent strain. This mutation affects the varS gene that codes for a signal transduction histidine-protein kinase. Genetic analyses confirmed that varS is necessary for infection of oysters and for a secreted metalloprotease expression. For the first time in a Vibrio species, we show here that VarS is a key factor of pathogenicity.
    Mots-clés : Animals, DBG, Frameshift Mutation, France, Genes, Regulator, Genomics, Ostreidae, Phylogeny, Protein Kinases, SRRB, Vibrio, Virulence.

  • N. Innocenti, M. Golumbeanu, A. Fouquier d'Hérouël, C. Lacoux, R. A. Bonnin, S. P. Kennedy, F. Wessner, P. Serror, P. Bouloc, F. Repoila, et E. Aurell, « Whole-genome mapping of 5' RNA ends in bacteria by tagged sequencing: a comprehensive view in Enterococcus faecalis », RNA (New York, N.Y.), vol. 21, nᵒ 5, p. 1018-1030, mai 2015.
    Résumé : Enterococcus faecalis is the third cause of nosocomial infections. To obtain the first snapshot of transcriptional organizations in this bacterium, we used a modified RNA-seq approach enabling to discriminate primary from processed 5' RNA ends. We also validated our approach by confirming known features in Escherichia coli. We mapped 559 transcription start sites (TSSs) and 352 processing sites (PSSs) in E. faecalis. A blind motif search retrieved canonical features of SigA- and SigN-dependent promoters preceding transcription start sites mapped. We discovered 85 novel putative regulatory RNAs, small- and antisense RNAs, and 72 transcriptional antisense organizations. Presented data constitute a significant insight into bacterial RNA landscapes and a step toward the inference of regulatory processes at transcriptional and post-transcriptional levels in a comprehensive manner.
    Mots-clés : 5' Untranslated Regions, Chromosome Mapping, DBG, Enterococcus faecalis, Gene Expression Regulation, Bacterial, Genome, Bacterial, Nucleic Acid Denaturation, primary RNA, processed RNA, promoter, Promoter Regions, Genetic, RNA degradation, RNA Processing, Post-Transcriptional, RNA, Bacterial, Sequence Analysis, RNA, Sequence Tagged Sites, SRRB, Transcription Initiation Site, Transcriptome.

  • F. Le Roux, K. M. Wegner, C. Baker-Austin, L. Vezzulli, C. R. Osorio, C. Amaro, J. M. Ritchie, T. Defoirdt, D. Destoumieux-Garzón, M. Blokesch, D. Mazel, A. Jacq, F. Cava, L. Gram, C. C. Wendling, E. Strauch, A. Kirschner, et S. Huehn, « The emergence of Vibrio pathogens in Europe: ecology, evolution, and pathogenesis (Paris, 11-12th March 2015) », Frontiers in Microbiology, vol. 6, p. 830, 2015.
    Résumé : Global change has caused a worldwide increase in reports of Vibrio-associated diseases with ecosystem-wide impacts on humans and marine animals. In Europe, higher prevalence of human infections followed regional climatic trends with outbreaks occurring during episodes of unusually warm weather. Similar patterns were also observed in Vibrio-associated diseases affecting marine organisms such as fish, bivalves and corals. Basic knowledge is still lacking on the ecology and evolutionary biology of these bacteria as well as on their virulence mechanisms. Current limitations in experimental systems to study infection and the lack of diagnostic tools still prevent a better understanding of Vibrio emergence. A major challenge is to foster cooperation between fundamental and applied research in order to investigate the consequences of pathogen emergence in natural Vibrio populations and answer federative questions that meet societal needs. Here we report the proceedings of the first European workshop dedicated to these specific goals of the Vibrio research community by connecting current knowledge to societal issues related to ocean health and food security.
    Mots-clés : animal model, aquaculture, bacterial disease, DBG, european network, genome plasticity, global warming, human health, interactions, SRRB.

  • N. Messaoudi, V. Gautier, J. Dairou, M. Mihoub, G. Lelandais, P. Bouloc, A. Landoulsi, et G. Richarme, « Fermentation and alternative respiration compensate for NADH dehydrogenase deficiency in a prokaryotic model of DJ-1-associated Parkinsonism », Microbiology (Reading, England), vol. 161, nᵒ 11, p. 2220-2231, nov. 2015.
    Résumé : YajL is the closest prokaryotic homologue of Parkinson's disease-associated DJ-1, a protein of undefined function involved in the oxidative stress response. We reported recently that YajL and DJ-1 protect cells against oxidative stress-induced protein aggregation by acting as covalent chaperones for the thiol proteome, including the NuoG subunit of NADH dehydrogenase 1, and that NADH dehydrogenase 1 activity is negligible in the yajL mutant. We report here that this mutant compensates for low NADH dehydrogenase activity by utilizing NADH-independent alternative dehydrogenases, including pyruvate oxidase PoxB and d-amino acid dehydrogenase DadA, and mixed acid aerobic fermentations characterized by acetate, lactate, succinate and ethanol excretion. The yajL mutant has a low adenylate energy charge favouring glycolytic flux, and a high NADH/NAD ratio favouring fermentations over pyruvate dehydrogenase and the Krebs cycle. DNA array analysis showed upregulation of genes involved in glycolytic and pentose phosphate pathways and alternative respiratory pathways. Moreover, the yajL mutant preferentially catabolized pyruvate-forming amino acids over Krebs cycle-related amino acids, and thus the yajL mutant utilizes pyruvate-centred respiro-fermentative metabolism to compensate for the NADH dehydrogenase 1 defect and constitutes an interesting model for studying eukaryotic respiratory complex I deficiencies, especially those associated with Alzheimer's and Parkinson's diseases.
    Mots-clés : Aerobiosis, DBG, Escherichia coli, Escherichia coli Proteins, Fermentation, Gene Expression Profiling, Humans, Metabolic Flux Analysis, Microarray Analysis, Models, Biological, Molecular Sequence Data, NADH Dehydrogenase, Parkinsonian Disorders, Ribosomal Proteins, Sequence Analysis, DNA, SRRB.

  • A. Pain, A. Ott, H. Amine, T. Rochat, P. Bouloc, et D. Gautheret, « An assessment of bacterial small RNA target prediction programs », RNA biology, vol. 12, nᵒ 5, p. 509-513, 2015.
    Résumé : Most bacterial regulatory RNAs exert their function through base-pairing with target RNAs. Computational prediction of targets is a busy research field that offers biologists a variety of web sites and software. However, it is difficult for a non-expert to evaluate how reliable those programs are. Here, we provide a simple benchmark for bacterial sRNA target prediction based on trusted E. coli sRNA/target pairs. We use this benchmark to assess the most recent RNA target predictors as well as earlier programs for RNA-RNA hybrid prediction. Moreover, we consider how the definition of mRNA boundaries can impact overall predictions. Recent algorithms that exploit both conservation of targets and accessibility information offer improved accuracy over previous software. However, even with the best predictors, the number of true biological targets with low scores and non-targets with high scores remains puzzling.
    Mots-clés : bacteria, Base Pairing, Computational Biology, DBG, Escherichia coli, RNA, Bacterial, RNA, Messenger, sRNA, sRNA target prediction, SRRB, SSFA, Untranslated Regions.

  • T. Rochat, O. Delumeau, N. Figueroa-Bossi, P. Noirot, L. Bossi, E. Dervyn, et P. Bouloc, « Tracking the Elusive Function of Bacillus subtilis Hfq », PloS One, vol. 10, nᵒ 4, p. e0124977, 2015.
    Résumé : RNA-binding protein Hfq is a key component of the adaptive responses of many proteobacterial species including Escherichia coli, Salmonella enterica and Vibrio cholera. In these organisms, the importance of Hfq largely stems from its participation to regulatory mechanisms involving small non-coding RNAs. In contrast, the function of Hfq in Gram-positive bacteria has remained elusive and somewhat controversial. In the present study, we have further addressed this point by comparing growth phenotypes and transcription profiles between wild-type and an hfq deletion mutant of the model Gram-positive bacterium, Bacillus subtilis. The absence of Hfq had no significant consequences on growth rates under nearly two thousand metabolic conditions and chemical treatments. The only phenotypic difference was a survival defect of B. subtilis hfq mutant in rich medium in stationary phase. Transcriptomic analysis correlated this phenotype with a change in the levels of nearly one hundred transcripts. Albeit a significant fraction of these RNAs (36%) encoded sporulation-related functions, analyses in a strain unable to sporulate ruled out sporulation per se as the basis of the hfq mutant's stationary phase fitness defect. When expressed in Salmonella, B. subtilis hfq complemented the sharp loss of viability of a degP hfq double mutant, attenuating the chronic σE-activated phenotype of this strain. However, B. subtilis hfq did not complement other regulatory deficiencies resulting from loss of Hfq-dependent small RNA activity in Salmonella indicating a limited functional overlap between Salmonella and B. subtilis Hfqs. Overall, this study confirmed that, despite structural similarities with other Hfq proteins, B. subtilis Hfq does not play a central role in post-transcriptional regulation but might have a more specialized function connected with stationary phase physiology. This would account for the high degree of conservation of Hfq proteins in all 17 B. subtilis strains whose genomes have been sequenced.
    Mots-clés : Bacillus subtilis, DBG, Host Factor 1 Protein, Phenotype, RGSP, SRRB, Transcriptome.

  • I. Rosinski-Chupin, E. Sauvage, O. Sismeiro, A. Villain, V. Da Cunha, M. - E. Caliot, M. - A. Dillies, P. Trieu-Cuot, P. Bouloc, M. - F. Lartigue, et P. Glaser, « Single nucleotide resolution RNA-seq uncovers new regulatory mechanisms in the opportunistic pathogen Streptococcus agalactiae », BMC genomics, vol. 16, p. 419, mai 2015.
    Résumé : BACKGROUND: Streptococcus agalactiae, or Group B Streptococcus, is a leading cause of neonatal infections and an increasing cause of infections in adults with underlying diseases. In an effort to reconstruct the transcriptional networks involved in S. agalactiae physiology and pathogenesis, we performed an extensive and robust characterization of its transcriptome through a combination of differential RNA-sequencing in eight different growth conditions or genetic backgrounds and strand-specific RNA-sequencing. RESULTS: Our study identified 1,210 transcription start sites (TSSs) and 655 transcript ends as well as 39 riboswitches and cis-regulatory regions, 39 cis-antisense non-coding RNAs and 47 small RNAs potentially acting in trans. Among these putative regulatory RNAs, ten were differentially expressed in response to an acid stress and two riboswitches sensed directly or indirectly the pH modification. Strikingly, 15% of the TSSs identified were associated with the incorporation of pseudo-templated nucleotides, showing that reiterative transcription is a pervasive process in S. agalactiae. In particular, 40% of the TSSs upstream genes involved in nucleotide metabolism show reiterative transcription potentially regulating gene expression, as exemplified for pyrG and thyA encoding the CTP synthase and the thymidylate synthase respectively. CONCLUSIONS: This comprehensive map of the transcriptome at the single nucleotide resolution led to the discovery of new regulatory mechanisms in S. agalactiae. It also provides the basis for in depth analyses of transcriptional networks in S. agalactiae and of the regulatory role of reiterative transcription following variations of intra-cellular nucleotide pools.
    Mots-clés : DBG, Gene Expression Profiling, Gene Expression Regulation, Bacterial, Gene Regulatory Networks, Genes, Bacterial, High-Throughput Nucleotide Sequencing, Nucleotides, RNA, Bacterial, RNA, Messenger, Sequence Analysis, RNA, SRRB, Streptococcus agalactiae.
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Publications de l’équipe avant 2015

- Bergonier D., Sobral D., Feßler A.T., Jacquet E., Gilbert F.B., Schwarz S., Treilles M., Bouloc P., Pourcel C. & Vergnaud G. (2014) Staphylococcus aureus from 152 cases of bovine, ovine and caprine mastitis investigated by Multiple-locus variable number of tandem repeat analysis (MLVA) Vet Res. 45(1):97. (PMC4195859)

- Lartigue M-F. & Bouloc P. (2014) A tetracycline-inducible expression vector for Streptococcus agalactiae allowing controllable gene expression. J Microbiol Methods. 96C:16-8.

- Madec S., Pichereau V., Jacq A., Paillard M., Boisset C., Guérard F., Paillard C. & Nicolas JL. (2014) Characterization of the secretomes of two vibrios pathogenic to mollusks. PLoS One. 9(11):e113097. (PMID : 25401495)

- Goudenège D., Travers M., Lemire A., Petton B., Haffner P., Labreuche Y., Tourbiez D., Mangenot S., Calteau A., Mazel D., Nicolas J.-L., Jacq A., Le Roux F. (2014). A single regulatory gene is sufficient to alter Vibrio aestuarianus pathogenicity in oysters. Environ Microbiol. doi : 10.1111/1462-2920.12699.

- Nguyen N A. & Jacq A. (2014) sRNAs in the vibrionaceae : an ocean still to be explored. Wiley Interdiscip Rev RNA. 2014 Jan 23. doi : 10.1002/wrna.1218.

- Toffano-Nioche C., Luo Y., Kuchly C., Wallon C., Steinbach D., Zytnicki M., Jacq A. & Gautheret D. (2013) Detection of non-coding RNA in Bacteria and Archaea using the DETR’PROK Galaxy pipeline. Methods. PMID : 23806640

- Toffano-Nioche C., Ott A., Crozat E., Nguyen N.A., Zytnicki M., Leclerc F., Forterre P., Bouloc P. & Gautheret D. (2013) RNA at 92°C : the Non-Coding Transcriptome of the Hyperthermophilic Archaeon Pyrococcus abyssi. RNA Biology 10:1211-20. (PMC3849170)

- Messaoudi N., Gautier V., Kthiri F., Lelandais G., Mihoub M., Joseleau-Petit D., Caldas T., Bohn C., Tolosa L., Rao G., Tao K., Landoulsi A., Bouloc P. & Richarme G. (2013) Global stress response in prokaryotic model of DJ1 associated Parkinsonism. J. Bacteriol. 195:1167-78. (PMC3592003)

- Rochat T., Bouloc P. & Repoila F. (2013) Gene expression control by selective RNA processing and stabilization in bacteria. FEMS Microbiol. Letters. DOI : 10.1111/1574-6968.12162

- Toffano-Nioche C.*, Nguyen N.A.*, Kuchly C., Ott A., Gautheret D., Bouloc P. & Jacq A. (2012) Transcriptomic profiling of the oyster pathogen Vibrio splendidus opens a window on the evolutionary dynamics of the small RNA repertoire in the Vibrio genus. RNA 18:2201-19. (PMC3504672)

- Rochat T., Bouloc P., Qi Y., Bossi L. & Figueroa-Bossi N. (2012) Lack of interchangeability of Hfq-like proteins. Biochimie 94(7):1554-59

- Bouloc P. & Felden B. (2011) Les acides ribonucléiques : Régulation du staphylocoque doré et rôle dans la virulence. [Ribonucleic acids : regulators of Staphylococcus aureus and role in bacterial virulence] Med. Sci. (Paris) 27 : 238–41

- Felden B., Vandesnesch F., Bouloc P., & Romby P. (2011) The Staphylococcus aureus RNome and its commitment to virulence. PLoS Pathog. 7(3):e1002006. (PMC3504672)

- Erauso G.*, Lakhal F.*, Bidault-Toffin A., Le Chevalier P., Bouloc P., Paillard C. & Jacq A. (2011) Evidence for the role of horizontal transfer in generating pVT1, a large mosaic conjugative plasmid from the clam pathogen, Vibrio tapetis. PLoS One 6(2) : e16759. (PMC3504672)

- Paillard C., Jacq A. & Nicolas J.-L. (2011) Specificity of host−pathogen interactions in marine environment : comparison of mollusk vibrioses. J. Shellfish Res. 30 : 540

- Bohn C., Rigoulay C., Chabelskaya S., Sharma C., Marchais A., Borezée-Durant E., Skorski P., Barbet R., Jacquet E., Jacq. A., Gautheret D., Felden B., Vogel J. & Bouloc P. (2010) Experimental discovery of small RNAs in Staphylococcus aureus reveals a riboregulator of central metabolism. Nucleic Acid Res. 38(19):6620-36. (PMC2965222)

- Marchais A., Bohn C., Bouloc P. & Gautheret D. (2010) RsaOG, a new Staphylococcal family of highly transcribed non-coding RNA. RNA Biol. 7(2):116-9.

- Kthiri F., Le H.-T., Gautier V., Caldas T., Malki A., Landoulsi A, Bohn C., Bouloc P. & Richarme G.(2010) Protein aggregation in a mutant deficient in the bacterial homolog yajL of the parkinsonism-associated protein DJ-1. J. Biol. Chem. 285(14):10328-36. (PMC2856238)

- Bury-Moné S., Nomane Y., Reymond N., Barbet R., Jacquet E., Imbeaud S., Jacq A. & Bouloc P. (2009) Global analysis of extracytoplasmic stress signaling in Escherichia coli. PLoS Genet. 5(9):e1000651. (PMC2731931)

- Marchais A., Naville M., Bohn C., Bouloc P. & Gautheret D. (2009) Single-pass classification of all non-coding sequences in a bacterial genome using phylogenetic profiles. Genome Res. 19:1084-92. (PMC2694484)

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