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4. Transcription-driven DNA supercoiling counteracts H-NS-mediated gene silencing in bacterial chromatin.

Author

Universidad de Sevilla. Departamento de Microbiología y Parasitología, Universidad de Sevilla. Departamento de Genética, Centre national de la recherche scientifique (CNRS). France, Agence Nationale de la Recherche. France, Ministerio de Ciencia e Innovación (MICIN). España, European Commission (EC). Fondo Europeo de Desarrollo Regional (FEDER), Figueroa Bossi, Nara, Fernández Fernández, Rocío, Kerboriou, Patricia, Bouloc, Philippe, Casadesús Pursals, Josep, Sánchez Romero, María Antonia, Bossi, Lionello, Universidad de Sevilla. Departamento de Microbiología y Parasitología, Universidad de Sevilla. Departamento de Genética, Centre national de la recherche scientifique (CNRS). France, Agence Nationale de la Recherche. France, Ministerio de Ciencia e Innovación (MICIN). España, European Commission (EC). Fondo Europeo de Desarrollo Regional (FEDER), Figueroa Bossi, Nara, Fernández Fernández, Rocío, Kerboriou, Patricia, Bouloc, Philippe, Casadesús Pursals, Josep, Sánchez Romero, María Antonia, and Bossi, Lionello

Abstract

In all living cells, genomic DNA is compacted through interactions with dedicated proteins and/or the formation of plectonemic coils. In bacteria, DNA compaction is achieved dynamically, coordinated with dense and constantly changing transcriptional activity. H-NS, a major bacterial nucleoid structuring protein, is of special interest due to its interplay with RNA polymerase. H-NS:DNA nucleoprotein filaments inhibit transcription initiation by RNA polymerase. However, the discovery that genes silenced by H-NS can be activated by transcription originating from neighboring regions has suggested that elongating RNA polymerases can disassemble H-NS:DNA filaments. In this study, we present evidence that transcription-induced counter-silencing does not require transcription to reach the silenced gene; rather, it exerts its effect at a distance. Counter-silencing is suppressed by introducing a DNA gyrase binding site within the intervening segment, suggesting that the long-range effect results from transcription-driven positive DNA supercoils diffusing toward the silenced gene. We propose a model wherein H-NS:DNA complexes form in vivo on negatively supercoiled DNA, with H-NS bridging the two arms of the plectoneme. Rotational diffusion of positive supercoils generated by neighboring transcription will cause the H-NS-bound negativelysupercoiled plectoneme to “unroll” disrupting the H-NS bridges and releasing H-NS.

Published
2024

5. Whole genome mapping of 5' RNA ends in bacteria by tagged sequencing : A comprehensive view in Enterococcus faecalis

Author

Innocenti, Nicolas, Golumbeanu, Monica, d'Hérouël, Aymeric Fouquier, Lacoux, Caroline, Bonnin, Rémy A., Kennedy, Sean P., Wessner, Françoise, Serror, Pascale, Bouloc, Philippe, Repoila, Francis, and Aurell, Erik

Subjects
Quantitative Biology - Genomics, Quantitative Biology - Biomolecules, Quantitative Biology - Quantitative Methods
Abstract

Enterococcus faecalis is the third cause of nosocomial infections. To obtain the first comprehensive view 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 and 352 processing sites in E. faecalis. A blind motif search retrieved canonical features of SigA- and SigN-dependent promoters preceding TSSs mapped. We discovered 95 novel putative regulatory RNAs, small- and antisense RNAs, and 72 transcriptional antisense organisations. Presented data constitute a significant insight into bacterial RNA landscapes and a step towards the inference of regulatory processes at transcriptional and post-transcriptional levels in a comprehensive manner.

Published
2014
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10. sRNA-controlled iron sparing response in Staphylococci

Author

Coronel-Tellez, Rodrigo H, primary, Pospiech, Mateusz, additional, Barrault, Maxime, additional, Liu, Wenfeng, additional, Bordeau, Valérie, additional, Vasnier, Christelle, additional, Felden, Brice, additional, Sargueil, Bruno, additional, and Bouloc, Philippe, additional

Published
2022
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12. sRNA-controlled iron sparing response in Staphylococci

Author

Coronel-Tellez, Rodrigo H., primary, Pospiech, Mateusz, additional, Barrault, Maxime, additional, Liu, Wenfeng, additional, Bordeau, Valérie, additional, Vasnier, Christelle, additional, Felden, Brice, additional, Sargueil, Bruno, additional, and Bouloc, Philippe, additional

Published
2022
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15. Pervasive transcription enhances the accessibility of H-NS–silenced promoters and generates bistability in Salmonella virulence gene expression

Author

Universidad de Sevilla. Departamento de Microbiología y Parasitología, Universidad de Sevilla. Departamento de Genética, Agence Nationale de la Recherche. France, Ministerio de Ciencia e Innovación (MICIN). España, Agencia Estatal de Investigación. España, Figueroa Bossi, Nara, Sánchez Romero, María Antonia, Kerboriou, Patricia, Naquin, Delphine, Mendes, Clara, Bouloc, Philippe, Casadesus Pursals, Josep, Bossi, Lionello, Universidad de Sevilla. Departamento de Microbiología y Parasitología, Universidad de Sevilla. Departamento de Genética, Agence Nationale de la Recherche. France, Ministerio de Ciencia e Innovación (MICIN). España, Agencia Estatal de Investigación. España, Figueroa Bossi, Nara, Sánchez Romero, María Antonia, Kerboriou, Patricia, Naquin, Delphine, Mendes, Clara, Bouloc, Philippe, Casadesus Pursals, Josep, and Bossi, Lionello

Abstract

In Escherichia coli and Salmonella, many genes silenced by the nucleoid structuring protein H-NS are activated upon inhibiting Rho-dependent transcription termination. This response is poorly understood and difficult to reconcile with the view that H-NS acts mainly by blocking transcription initiation. Here we have analyzed the basis for the up-regulation of H-NS–silenced Salmonella pathogenicity island 1 (SPI-1) in cells depleted of Rho-cofactor NusG. Evidence from genetic experiments, semiquantitative 50 rapid amplification of complementary DNA ends sequencing (5’ RACE-Seq), and chromatin immunoprecipitation sequencing (ChIP-Seq) shows that transcription originating from spurious antisense promoters, when not stopped by Rho, elongates into a H-NS–bound regulatory region of SPI-1, displacing H-NS and rendering the DNA accessible to the master regulator HilD. In turn, HilD’s ability to activate its own transcription triggers a positive feedback loop that results in transcriptional activation of the entire SPI-1. Significantly, single-cell analyses revealed that this mechanism is largely responsible for the coexistence of two subpopulations of cells that either express or do not express SPI-1 genes. We propose that cell-to-cell differences produced by stochastic spurious transcription, combined with feedback loops that perpetuate the activated state, can generate bimodal gene expression patterns in bacterial populations.

Published
2022

16. 6S RNA-dependent antibiotic susceptibility

Author

Esberard, Marick, primary, Hallier, Marc, additional, Liu, Wenfeng, additional, Morvan, Claire, additional, Bossi, Lionello, additional, Figueroa-Bossi, Nara, additional, Felden, Brice, additional, and Bouloc, Philippe, additional

Published
2022
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23. Dynamic insights on transcription initiation and RNA processing during bacterial adaptation

Author

Lacoux, Caroline, D'Herouel, Aymeric Fouquier, Wessner-Le Bohec, Francoise, Innocenti, Nicolas, Bohn, Chantal, Kennedy, Sean P., Rochat, Tatiana, Bonnin, Remy A., Serror, Pascale, Aurell, Erik, Bouloc, Philippe, Repoila, Francis, Lacoux, Caroline, D'Herouel, Aymeric Fouquier, Wessner-Le Bohec, Francoise, Innocenti, Nicolas, Bohn, Chantal, Kennedy, Sean P., Rochat, Tatiana, Bonnin, Remy A., Serror, Pascale, Aurell, Erik, Bouloc, Philippe, and Repoila, Francis

Abstract

Transcription initiation and RNA processing govern gene expression and enable bacterial adaptation by reshaping the RNA landscape. The aim of this study was to simultaneously observe these two fundamental processes in a transcriptome responding to an environmental signal. A controlled sigma(E) system in E. coli was coupled to our previously described tag RNAseq method to yield process kinetics information. Changes in transcription initiation frequencies (TIF) and RNA processing frequencies (PF) were followed using 5' RNA tags. Changes in TIF showed a binary increased/decreased pattern that alternated between transcriptionally activated and repressed promoters, providing the bacterial population with transcriptional oscillation. PF variation fell into three categories of cleavage activity: (i) constant and independent of RNA levels, (ii) increased once RNA has accumulated, and (iii) positively correlated to changes in TIF. This work provides a comprehensive and dynamic view of major events leading to transcriptomic reshaping during bacterial adaptation. It unveils an interplay between transcription initiation and the activity of specific RNA cleavage sites. This study utilized a well-known genetic system to analyze fundamental processes and can serve as a blueprint for comprehensive studies that exploit the RNA metabolism to decipher and understand bacterial gene expression control., QC 20200407

Published
2020
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25. Dynamic insights on transcription initiation and RNA processing during bacterial adaptation

Author

Lacoux, Caroline, primary, Fouquier d'Hérouël, Aymeric, additional, Wessner-Le Bohec, Françoise, additional, Innocenti, Nicolas, additional, Bohn, Chantal, additional, Kennedy, Sean P., additional, Rochat, Tatiana, additional, Bonnin, Rémy A., additional, Serror, Pascale, additional, Aurell, Erik, additional, Bouloc, Philippe, additional, and Repoila, Francis, additional

Published
2020
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28. Degradation of carboxy-terminal-tagged cytoplasmic proteins by the Escherichia coli protease HflB (FtsH)

Author

Herman, Christophe, Thevenet, Danielle, Bouloc, Philippe, Walker, Graham C., and D'Ari, Richard

Subjects
Proteolysis -- Research, Proteases -- Research, Biological sciences
Abstract

The ATP-dependent zinc protease HflB and Clp proteases recognize tail-specific pathways and are involved in the process of removing abnormal cytoplasmic proteins in Escherichia coli. HflB degrades four unstable derivatives, three with nonpolar pentapeptide tails and one with the SsrA tag. HflB can compensate loss of ClpP by overproducing.

Published
1998

29. The HflB protease of Escherichia coli degrades its inhibitor lambdacIII

Author

Herman, Christophe, Thevenet, Danielle, D'Ari, Richard, and Bouloc, Philippe

Subjects
Bacterial proteins -- Analysis, Microbial enzymes -- Analysis, Proteases -- Analysis, Enzyme inhibitors -- Analysis, Biological sciences
Abstract

The effects of reduced HflB protease on the stability of lambdacIII protein and the proteolytic degradation of lambdacIII bacteriophage proteins were analyzed in Escherichia coli. The half-life of the lamdacIII protein was increased in vivo in response to reduced levels of HflB protease. On the other hand, the stability of the bacteriophage protein was reduced in the presence of high concentrations of HflB protease. The effects of HflB on lambdacIII indicated the ability of the essential host protease to degrade the bacteriophage protein and suppress its lethality.

Published
1997

33. Degradation of sigma(super 32), the heat shock regulator in Escherichia coli is governed by Hfl

Author

Herman, Christophe, Thevenet, Danielle, D'Ari, Richard, and Bouloc, Philippe

Subjects
Heat shock proteins -- Analysis, Escherichia coli -- Research, Science and technology
Abstract

The gamma-cIII protein regulates the heat shock response, stabilizes the unstable sigma factor, the sigma(super 32), and inhibits the HflB-mediated proteolytic activities. The concentration of sigma factor, sigma(super 32), mediates the heat shock response in Escherichia coli, and HflB governs the proteolysis of phage lambda-cII protein. The degradation of sigma(super 32) is also mediated by HflB protein.

Published
1995

35. Cell growth and lambda phage development controlled by the same essential Escherichia coli gene, ftsH/hfl

Author

Herman, Christophe, Ogura, Teru, Toshifumi Tomoyasu, Hiraga, Sota, Yoshinori Akiyama, Ito, Koreaki, Thomas, Rene, D'Ari, Richard, and Bouloc, Philippe

Subjects
Cells -- Growth, Bacteriophages -- Growth, Escherichia coli -- Growth, Growth -- Genetic aspects, Science and technology
Abstract

The temperature-sensitive mutant ftsH1 exhibits an enhanced lysogenization of the frequency of lamda and is governed FtsH/HflB. The enhanced frequency is inhibited by the excessive synthesis of FtsH/HflB. The proteolytic pathway contains the FtsH/HflB protein, which may behave as a chaperone and regulate the phage cII activator protein.

Published
1993

36. Penicillin-binding protein 2 inactivation in Escherichia coli results in cell division inhibition, which is relieved by FtsZ overexpression

Author

Vinella, Daniel, Joseleau-Petit, Daniele, Thevenet, Danielle, Bouloc, Philippe, and D'Ari, Richard

Subjects
Escherichia coli -- Genetic aspects, Carrier proteins -- Research, Cell division -- Analysis, Penicillin -- Analysis, Gene expression -- Analysis, Biological sciences
Abstract

The cell division process in Escherichia coli is inhibited by inactivation of the penicillin-binding protein 2 (PBP-2), and is relieved by an increase in the amount of guanosine 5'-diphosphate 3'-diphosphate (ppGpp) present. ppGpp is an FtsZ protein distributed in a ring form around the cell center at the beginning of cell division. PBP-2 is responsible for the final steps of peptidoglycan layer synthesis around the cell membrane. The peptidoglycan layer is responsible for the shape of the cell.

Published
1993

37. Topology and subcellular localization of FtsH protein in Escherichia coli

Author

Tomoyasu, Toshifumi, Yamanaka, Kunitoshi, Murata, Kazuyoshi, Suzaki, Toshinobu, Bouloc, Philippe, Kato, Atsushi, Niki, Hironori, Hiraga, Sota, and Ogura, Teru

Subjects
Adenosine triphosphatase -- Research, Escherichia coli -- Physiological aspects, Membrane proteins -- Research, Biological sciences
Abstract

Western blot analysis and immunohistochemical techniques were utilized in the investigation of the subcellular distribution of the FtsH protein in Escherichia coli. Results show that the adenosine triphosphate-binding protein is putative in the cytoplasmic phase of the cell membrane. Analysis of the amino acid sequence and the predicted structure reveal that FtsH is an integralmembrane protein spanning the lipid bilayer twice. The carboxy terminal is cytoplasmic and contains the nucleotide binding region.

Published
1993

39. Assessment of Bona Fide sRNAs in Staphylococcus aureus

Author

Liu, Wenfeng, Rochat, Tatiana, Toffano-Nioche, Claire, Le Lam, Thao Nguyen, Bouloc, Philippe, and Morvan, Claire

Subjects
Microbiology (medical), bona fide sRNA, transcription factors, lcsh:QR1-502, Staphylococcus aureus HG003, RNA-seq, gene regulation, Microbiology, lcsh:Microbiology
Abstract

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 defined bona fide sRNAs as those that (i) likely act in trans and (ii) are not expressed from the opposite strand of a coding gene. Using published data and our own RNA-seq data, we reviewed hundreds of Staphylococcus aureus putative 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 for S. aureus genetic regulation studies, has only about 50 bona fide sRNAs, indicating that these RNAs are less numerous than commonly stated. Among them, about half are associated to the S. aureus sp. core genome and a quarter are possibly expressed in other Staphylococci. We hypothesize on their features and regulation using bioinformatic approaches.

Published
2018

40. Assessment ofBona FidesRNAs inStaphylococcus aureus

Author

Liu, Wenfeng, Rochat, Tatiana, Toffano-Nioche, Claire, Le Lam, Thao Nguyen, Bouloc, Philippe, Morvan, Claire, Institut de Biologie Intégrative de la Cellule (I2BC), 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, Signalisation et Réseaux de Régulations Bactériens (SRRB), Département Biologie des Génomes (DBG), 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-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-Institut de Biologie Intégrative de la Cellule (I2BC), 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-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, Unité de recherche Virologie et Immunologie Moléculaires (VIM), Institut National de la Recherche Agronomique (INRA), Université Paris-Saclay, Séquence, Structure et Fonction des ARN (SSFA), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-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)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Unité de recherche Virologie et Immunologie Moléculaires (VIM (UR 0892)), Agence Nationale pour la Recherche (ANR) [ANR-15-CE12-0003-01], Fondation pour la Recherche Médicale (FRM) [DBE20160635724 'Bactéries et champignons face aux antibiotiques et antifongiques'], Chinese scholarship council, and ANR

Subjects
bona fide sRNA, transcription factors, [SDV]Life Sciences [q-bio], Staphylococcus aureus HG003, RNA-seq, gene regulation
Abstract

HYPOTHESIS AND THEORY ARTICLE; International audience; 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.

Published
2018

41. Dégradation d’un anticancéreux dans les eaux usées

Author

Briand, William, Dao, Ousmane, Garnier, Guillaume, Guegan, Raphaël, Marta, Britany, Maupu, Clémence, Miesch, Julie, Papadopoulo, Kenn, Radoux, Arthur, Rojahn, Julie, Zhu, Yueying, Aubry, Céline, Bouloc, Philippe, Bury-Moné, Stéphanie, Ferré, Arnaud, Lautru, Sylvie, Namy, Olivier, and Sabeti Azad, Mahnaz

Abstract

GEM (pour international genetically engineered machine) 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 (Massachusetts Institute of Technology) (le registry of standard biological parts 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 (→), 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 Giant Jamboree1 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.

Published
2018

42. The conserved regulatory RNA RsaE down-regulates the arginine degradation pathway in Staphylococcus aureus

Author

Rochat, Tatiana, Bohn, Chantal, Morvan, Claire, Le Lam, Thao Nguyen, Razvi, Fareha, Pain, Adrien, Toffano-Nioche, Claire, Ponien, Prishila, Jacq, Annick, Jacquet, Eric, Fey, Paul D, Gautheret, Daniel, Bouloc, Philippe, Unité de recherche Virologie et Immunologie Moléculaires (VIM (UR 0892)), Institut National de la Recherche Agronomique (INRA), Université Paris-Saclay, Institut de génétique et microbiologie [Orsay] (IGM), Université Paris-Sud - Paris 11 (UP11)-Centre National de la Recherche Scientifique (CNRS), Laboratoire d'Ecologie des Hydrosystèmes Naturels et Anthropisés (LEHNA), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-École Nationale des Travaux Publics de l'État (ENTPE)-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), Département Biologie des Génomes (DBG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Séquence, Structure et Fonction des ARN (SSFA), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Institut de Biologie Intégrative de la Cellule (I2BC), Institut de Chimie des Substances Naturelles (ICSN), Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Signalisation et Réseaux de Régulations Bactériens (SRRB), University of Nebraska Medical Center, University of Nebraska System, Agence Nationale pour la Recherche [ANR-2012-BLAN-1602, ANR-15-CE12-0003], Fondation pour la Recherche Medicale [DBF20160635724], National Institutes of Health [NIH/NIAID P01AI083211], Unité de recherche Virologie et Immunologie Moléculaires (VIM), Université Paris-Sud - Paris 11 (UP11)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Université Paris-Sud - Paris 11 (UP11)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université Paris-Sud - Paris 11 (UP11)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Institut de Biologie Intégrative de la Cellule (I2BC), Université Paris-Sud - Paris 11 (UP11)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université Paris-Sud - Paris 11 (UP11)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS), Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), 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, 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-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, 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-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-Institut de Biologie Intégrative de la Cellule (I2BC), Institute for Integrative Biology of the Cell (I2BC), and Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC)

Subjects
SRRB, Staphylococcus aureus, Organisms, Genetically Modified, DBG, [SDV]Life Sciences [q-bio], Gene regulation, Chromatin and Epigenetics, Down-Regulation, Gene Expression Regulation, Bacterial, prediction, Regulatory Sequences, Ribonucleic Acid, Arginine, Culture Media, accessibility, virulence, RNA, Bacterial, identification, Amino Acids, SSFA, reveals, Conserved Sequence, Metabolic Networks and Pathways, ComputingMilieux_MISCELLANEOUS, discovery
Abstract

International audience; 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.

Published
2018

45. No detectable effect of RNA-binding protein Hfq absence in Staphylococcus aureus

Author

Bouloc Philippe, Rigoulay Candice, and Bohn Chantal

Subjects
Microbiology, QR1-502
Abstract

Abstract Background The RNA-binding protein Hfq is involved in stress and virulence of several pathogens, probably due to its role as mediator in small RNA (sRNA)-mRNA interactions. In this study, we investigate the function of Hfq in the Gram-positive pathogen Staphylococcus aureus, by constructing hfq null mutant derivatives. Results We report that unexpectedly, in S. aureus, Hfq does not seem to play a crucial role in stress response, RNAIII or spa mRNA quantity and exoprotein expression, as tested in three virulent genetic backgrounds. Moreover, a global analysis of the RN6390 hfq mutant, which tests ~ 2000 phenotypes, supports our results concerning the non-implication of Hfq in stress response, and shows that Hfq is also not involved in resistance to several chemical agents and antibiotics and does not seem to be implicated in metabolic pathways. Conclusion Our data suggest that although sRNA-mRNA interactions in S. aureus are decisive for gene expression regulation, they do not require the RNA-chaperone protein Hfq. These interactions possibly require an RNA-chaperone protein other than Hfq, which remains to be found.

Published
2007
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46. csrB Gene Duplication Drives the Evolution of Redundant Regulatory Pathways Controlling Expression of the Major Toxic Secreted Metalloproteases in Vibrio tasmaniensis LGP32

Author

Nguyen, An Ngoc, Disconzi, Elena, Charriere, Guillaume, Destoumieux-garzon, Delphine, Bouloc, Philippe, Le Roux, Frederique, Jacq, Annick, Nguyen, An Ngoc, Disconzi, Elena, Charriere, Guillaume, Destoumieux-garzon, Delphine, Bouloc, Philippe, Le Roux, Frederique, and Jacq, Annick

Abstract

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 inpu

Published
2018
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48. RNA at 92°C

Author

Toffano-Nioche, Claire, Ott, Alban, Crozat, Estelle, Nguyen, An N., Zytnicki, Matthias, Leclerc, Fabrice, Forterre, Patrick, Bouloc, Philippe, and Gautheret, Daniel

Subjects
Base Composition, Pyrococcus abyssi, Hot Temperature, RNA, Untranslated, Base Sequence, Transcription, Genetic, archaea, non-coding RNA, High-Throughput Nucleotide Sequencing, Molecular Sequence Annotation, RNA, Archaeal, hyperthermophile, Untranslated Regions, Nucleic Acid Conformation, Promoter Regions, Genetic, Transcriptome, Phylogeny, Research Paper
Abstract

The non-coding transcriptome of the hyperthermophilic archaeon Pyrococcus abyssi is investigated using the RNA-seq technology. A dedicated computational pipeline analyzes RNA-seq reads and prior genome annotation to identify small RNAs, untranslated regions of mRNAs, and cis-encoded antisense transcripts. Unlike other archaea, such as Sulfolobus and Halobacteriales, P. abyssi produces few leaderless mRNA transcripts. Antisense transcription is widespread (215 transcripts) and targets protein-coding genes that appear to evolve more rapidly than average genes. We identify at least three novel H/ACA-like guide RNAs among the newly characterized non-coding RNAs. Long 5′ UTRs in mRNAs of ribosomal proteins and amino-acid biosynthesis genes strongly suggest the presence of cis-regulatory leaders in these mRNAs. We selected a high-interest subset of non-coding RNAs based on their strong promoters, high GC-content, phylogenetic conservation, or abundance. Some of the novel small RNAs and long 5′ UTRs display high GC contents, suggesting unknown structural RNA functions. However, we were surprised to observe that most of the high-interest RNAs are AU-rich, which suggests an absence of stable secondary structure in the high-temperature environment of P. abyssi. Yet, these transcripts display other hallmarks of functionality, such as high expression or high conservation, which leads us to consider possible RNA functions that do not require extensive secondary structure.

Published
2013

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