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

Publications de l’équipe

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, 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.


  • T. N. Le Lam, C. Morvan, W. Liu, C. Bohn, Y. Jaszczyszyn, et P. Bouloc, « Finding sRNA-associated phenotypes by competition assays: An example with Staphylococcus aureus », Methods, 2016.
    Mots-clés : DBG, NGS, PF, 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, 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.

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, 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, 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, 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, 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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