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51. Isolation of RNA polymerase from Clostridiurn difficile and characterization of glutamate dehydrogenase and rRNA gene promoters in vitro and in vivo

Author

Mani, Nagraj, Dupuy, Bruno, and Sonenshein, Abraham L.

Subjects
Clostridium difficile -- Research, Bacterial genetics -- Research, Genetic transcription -- Research, Biological sciences
Abstract

Clostridium difficile is the primary causative agent of antibiotic-associated diarrheal disease. To facilitate molecular genetic analysis of gene expression in this organism, methods were developed to study transcriptional regulation in vitro and in vivo. That is, C. difficile RNA polymerase was partially purified and shown to bind to and initiate transcription in vitro from bona fide C. difficile promoters for rRNA and glutamate dehydrogenase genes. In addition, primer extension analyses and a [beta]-glucuronidase reporter system were used to quantitate transcription from these promoters in vivo. With these tools in hand, it is now possible to characterize the behavior of any C. difficile gene in vivo and to study the regulation of its expression in detail.

Published
2006

52. Identification of RNAs bound by Hfq reveals widespread RNA partners and a sporulation regulator in the human pathogen Clostridioides difficile

Author

Boudry, Pierre, primary, Piattelli, Emma, additional, Drouineau, Emilie, additional, Peltier, Johann, additional, Boutserin, Anaïs, additional, Lejars, Maxence, additional, Hajnsdorf, Eliane, additional, Monot, Marc, additional, Dupuy, Bruno, additional, Martin-Verstraete, Isabelle, additional, Gautheret, Daniel, additional, Toffano-Nioche, Claire, additional, and Soutourina, Olga, additional

Published
2021
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54. The spatial organization of the VirR boxes is critical for VirR-mediated expression of the perfringolysin O gene, pfoA, from Clostridium perfringens

Author

Cheung, Jackie K., Dupuy, Bruno, Deveson, Deanna S., and Rood, Julian I.

Subjects
Transduction -- Research, Genetic transcription -- Research, Clostridium -- Research, Clostridium -- Genetic aspects, Bacterial genetics, Biological sciences
Abstract

The transcriptional regulation of toxin production in the gram-positive anaerobe Clostridium perfringens involves a two-component signal transduction system that comprises the VirS sensor histidine kinase and its cognate response regulator, VirR. Previous studies showed that VirR binds independently to a pair of imperfect direct repeats, now designated VirR box 1 and VirR box 2, located immediately upstream of the promoter of the pfoA gene, which encodes the cholesterol-dependent cytolysin, perfringolysin O. For this study, we introduced mutated VirR boxes into a C. perfringens pfoA mutant and found that both VirR boxes are essential for transcriptional activation. Furthermore, the spacing between the VirR boxes and the distance between the VirR boxes and the -35 region are shown to be critical for perfringolysin O production. Other VirR boxes that were previously identified from the strain 13 genome sequence were also analyzed, with perfringolysin O production used as a reporter system. The results showed that placement of the different VirR boxes at the same position upstream of the pfoA promoter yields different levels of perfringolysin O activity. In all of these constructs, VirR was still capable of binding to the target DNA, indicating that DNA binding alone is not sufficient for transcriptional activation. Finally, we show that the C. perfringens RNA polymerase binds more efficiently to the pfoA promoter in the presence of VirR, indicating that interactions must occur between these proteins. We propose that these interactions are required for VirR-mediated transcriptional activation.

Published
2004

57. Environmental response and autoregulation of Clostridium difficile TxeR, a sigma factor for toxin gene expression

Author

Mani, Nagraj, Lyras, Dena, Barroso, Lisa, Howarth, Pauline, Wilkins, Tracy, Rood, Julian I., Sonenshein, Abraham L., and Dupuy, Bruno

Subjects
Bacteriology -- Research, Clostridium -- Genetic aspects, Clostridium -- Physiological aspects, Clostridium -- Environmental aspects, Toxins -- Physiological aspects, Toxins -- Genetic aspects, Gene expression -- Physiological aspects, Genetic regulation -- Research, Biological sciences
Abstract

Research has been conducted on sigma factor Clostridium difficile TxeR for toxin gene expression. The role of environmental conditions in tox gene expression and the possibility that these conditions control TxeR synthesis and regulate tox genes indirectly have been tested, and the results are reported.

Published
2002

61. Identification of RNAs bound by Hfq reveals widespread RNA partners and a sporulation regulator in the human pathogenClostridioides difficile

Author

Boudry, Pierre, primary, Piattelli, Emma, additional, Drouineau, Emilie, additional, Peltier, Johann, additional, Boutserin, Anaïs, additional, Lejars, Maxence, additional, Hajnsdorf, Eliane, additional, Monot, Marc, additional, Dupuy, Bruno, additional, Martin-Verstraete, Isabelle, additional, Gautheret, Daniel, additional, Toffano-Nioche, Claire, additional, and Soutourina, Olga, additional

Published
2020
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62. Ser/Thr kinase-dependent phosphorylation of the peptidoglycan hydrolase CwlA controls its export and modulates cell division in Clostridioides difficile

Author

Garcia-Garcia, Transito, primary, Poncet, Sandrine, additional, Cuenot, Elodie, additional, Douché, Thibaut, additional, Gianetto, Quentin Giai, additional, Peltier, Johann, additional, Courtin, Pascal, additional, Chapot-Chartier, Marie-Pierre, additional, Matondo, Mariette, additional, Dupuy, Bruno, additional, Candela, Thomas, additional, and Martin-Verstraete, Isabelle, additional

Published
2020
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65. Predictive regulatory and metabolic network models for systems analysis of Clostridioides difficile

Author

Arrieta-Ortiz, Mario L., primary, Immanuel, Selva Rupa Christinal, additional, Turkarslan, Serdar, additional, Wu, Wei Ju, additional, Girinathan, Brintha P., additional, Worley, Jay N., additional, DiBenedetto, Nicholas, additional, Soutourina, Olga, additional, Peltier, Johann, additional, Dupuy, Bruno, additional, Bry, Lynn, additional, and Baliga, Nitin S., additional

Published
2020
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70. In vivocommensal control ofClostridioides difficilevirulence

Author

Girinathan, Brintha P., primary, DiBenedetto, Nicholas, additional, Worley, Jay N., additional, Peltier, Johann, additional, Arrieta-Ortiz, Mario L., additional, Immanuel, Rupa, additional, Lavin, Richard, additional, Delaney, Mary L., additional, Cummins, Christopher, additional, Hoffmann, Maria, additional, Luo, Yan, additional, Escalona, Narjol Gonzalez, additional, Allard, Marc, additional, Onderdonk, Andrew B., additional, Gerber, Georg K., additional, Sonenshein, Abraham L., additional, Baliga, Nitin, additional, Dupuy, Bruno, additional, and Bry, Lynn, additional

Published
2020
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71. An RNA-Binding Protein Secreted by a Bacterial Pathogen Modulates RIG-I Signaling

Author

Pagliuso, Alessandro, primary, Tham, To Nam, additional, Allemand, Eric, additional, Robertin, Stevens, additional, Dupuy, Bruno, additional, Bertrand, Quentin, additional, Bécavin, Christophe, additional, Koutero, Mikael, additional, Najburg, Valérie, additional, Nahori, Marie-Anne, additional, Tangy, Frédéric, additional, Stavru, Fabrizia, additional, Bessonov, Sergey, additional, Dessen, Andréa, additional, Muchardt, Christian, additional, Lebreton, Alice, additional, Komarova, Anastassia V., additional, and Cossart, Pascale, additional

Published
2019
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74. Contributors

Author

Adachi, Hideki, primary, Adachi, Osao, additional, Adam, Zach, additional, Adams, Michael W.W., additional, Adang, Michael J., additional, Adham, Ibrahim M., additional, Aducci, Patrizia, additional, Agard, David A., additional, Agranovsky, Alexey A., additional, Ahn, Kyunghye, additional, Akiyama, Yoshinori, additional, Alejo, Alí, additional, Amberg, Sean M., additional, Amerik, Alexander Y., additional, Andrés, Germán, additional, Andrews, Robert K., additional, Antalis, Toni M., additional, Apte, Suneel S., additional, Arima, Kazunari, additional, Arlaud, Gérard J., additional, Aronson, Nathan N., additional, Asano, Yasuhisa, additional, Ascenzi, Paolo, additional, Assakura, Marina T., additional, Auld, David S., additional, Avilés, Francesc X., additional, Awad, William M., additional, Babé, Lilia M., additional, Badorff, Cornel, additional, Bai, Shan, additional, Baird, Teaster T., additional, Paul Bajaj, S., additional, Baker, Rohan T., additional, Baker, Susan C., additional, Ballinger, Marcus D., additional, Banbula, Agnieszka, additional, Bannikov, Gregory A., additional, Barrett, Alan J., additional, Bartlett, John D., additional, Baskova, Isolda P., additional, Bauer, Karl, additional, Baumann, Ulrich, additional, Baumeister, Wolfgang, additional, Beauvais, Anne, additional, Belas, Robert, additional, Beppu, Teruhiko, additional, Bergmann, Ernst M., additional, Bergo, Martin O., additional, Berndt, Michael C., additional, Berry, Colin, additional, Bertenshaw, Greg P., additional, Betzel, Ch., additional, Bierbaum, Gabriele, additional, Bieth, Joseph G., additional, Bjarnason, Jón B., additional, Blaber, M., additional, Blaber, S.I., additional, Black, Roy A., additional, Blackman, M.J., additional, Blinkovsky, Alexander, additional, Blobel, Carl P., additional, Boatright, Kelly M., additional, Böck, August, additional, Boeke, Jef D., additional, Boileau, Guy, additional, Bolken, Tové C., additional, Bond, Judith S., additional, Bordallo, Javier, additional, Bordusa, Frank, additional, Boucaut, Kerry J., additional, Bouvier, Jacques, additional, Bowman, Barry J., additional, Bradshaw, Ralph A., additional, Braun, Hans-Peter, additional, Breddam, Klaus, additional, Brindley, Paul J., additional, Broadhurst, Anne, additional, Brocklehurst, Keith, additional, Broder, Dan H., additional, Brömme, Dieter, additional, Bron, Sierd, additional, Broom, Murray, additional, Brown, Kenneth D., additional, Brown, Mark A., additional, Bunn, Rhonda, additional, Burleigh, Barbara A., additional, Butler, Michael J., additional, Buttle, David J., additional, Byrd, Chelsea M., additional, Byun, Tony, additional, Cadel, Sandrine, additional, Caffrey, Conor R., additional, Caldentey, Javier, additional, Caprioglio, Daniel R., additional, Carbonell, Juan, additional, Carpentier, Mélanie, additional, Carter, Ruth E., additional, Casey, Patrick J., additional, Castellino, Francis J., additional, Catanese, Joseph J., additional, Caterson, Bruce, additional, Caughey, George H., additional, Cawley, Niamh X., additional, Cawston, Tim E., additional, Jose Cazzulo, Juan, additional, Cercós, Manuel, additional, Chakraborty, Trinad, additional, Chambers, Henry F., additional, Chang, L.S., additional, Chan, Michael K., additional, Chan, Sunney I., additional, Chao, Julie, additional, Chapot-Chartier, Marie-Pierre, additional, Chave, Karen J., additional, Chen, Jian-Min, additional, Chen, Jinq-May, additional, Chesneau, Valérie, additional, Chevrier, Bernard, additional, Chich, Jean-François, additional, Yong Choi, Kwan, additional, Chrétien, Michel, additional, Ha Chung, Chin, additional, Chung, Dominic W., additional, Clamagirand, Christine, additional, Clark, Ian M., additional, Clarke, Adrian K., additional, Clarke, Steven, additional, Cleary, Paul P., additional, Clements, Judith A., additional, Cleuziat, Philippe, additional, Cohen, Paul, additional, Colige, Alain, additional, Collen, D., additional, Collier, Ivan E., additional, Colloms, Sean D., additional, Colman, Robert W., additional, Conner, Gregory E., additional, Conzelmann, Andreas, additional, Coolbear, Tim, additional, Coombs, Graham H., additional, Cooper, Jonathan B., additional, Cooper, Max D., additional, Copeland, Nikki A., additional, Corvol, Pierre, additional, Cottrell, Graeme S., additional, Coyle, Joseph T., additional, Craik, Charles S., additional, Creemers, John W.M., additional, Croce, Jenifer, additional, Cueva, Rosario, additional, Cutting, Simon, additional, d′Enfert, Christophe, additional, D′Orchymont, Hugues, additional, Daenke, S., additional, Dahlbäck, Björn, additional, Dalbey, Ross E., additional, Dalton, John P., additional, Dando (Deceased), Pamela M., additional, Daniel, R.M., additional, Darke, Paul L., additional, Lagerblad de Oliveira, Pedro, additional, de Vos, Sarah, additional, Deghmane, Ala-Eddine, additional, Dekker, Niek, additional, DeLotto, Robert, additional, DeMartino, George N., additional, den Boon, Johan A., additional, Denison, Mark R., additional, DesGroseillers, Luc, additional, Deussing, Jan, additional, Devi, Lakshmi A., additional, Diamandis, Eleftherios P., additional, Dickson, Robert B., additional, Dingwall, Colin, additional, Dixon, Jack E., additional, Dodt, Johannes, additional, Dolenc, Iztoc, additional, Cat Dong, Tran, additional, Dong, Ying, additional, Dubois, Jean-Yves F., additional, Dudley, Edward G., additional, Dunn, Ben M., additional, Dupuy, Bruno, additional, Conceicão Duque-Magalhães, Maria, additional, Eeckhout, Yves, additional, Egelrud, Torbjörn, additional, Eijsink, Vincent, additional, Ellis, Vincent, additional, Engel, Wolfgang, additional, Erdös, Ervin G., additional, Etscheid, Michael, additional, Evans (Deceased), Herbert J., additional, Everett, Roger D., additional, Eyries, Mélanie, additional, Fahrenholz, Falk, additional, Fenster, Kurt M., additional, Férec, Claude, additional, Henrique Ferreira Sorgine, Marcos, additional, Fink, Doran, additional, Fives-Taylor, Paula M., additional, Foltmann, Bent, additional, Foster, Simon J., additional, Foulon, Thierry, additional, Foundling, Stephen I., additional, Fox, Jay W., additional, Freeze, Hudson H., additional, Frère, Jean-Marie, additional, Frey, Teryl K., additional, Flicker, Lloyd D., additional, Fritsche, Erich, additional, Froelich, Christopher J., additional, Fuhrmann, Cynthia N., additional, Fujimura, Satoshi, additional, Fukushima, J., additional, Fuller, Robert S., additional, Gaboriaud, Christine, additional, Gache, Christian, additional, Galivan, John, additional, Gary, Jonathan D., additional, Gaucher, G.M., additional, Ghuysen, Jean-Marie, additional, Gil, María J., additional, Giller, Thomas, additional, Goffin, Colette, additional, Gohda, Eiichi, additional, Goldberg, Alfred L., additional, Goldberg, Daniel E., additional, Goldberg, Gregory I., additional, Gorbalenya, Alexander E., additional, Gordon, Stuart G., additional, Götz, Friedrich, additional, Gráf, László, additional, Granados, Robert R., additional, Granell, Antonio, additional, Graycar, Thomas P., additional, Green, Jonathan, additional, Greenspan, Daniel S., additional, Grubman, Marvin J., additional, Grunden, Amy M., additional, Guillemain, Bernard, additional, Guinand, Micheline, additional, Gutiérrez, José Maria, additional, Haeggström, Jesper Z., additional, Hageman, James H., additional, Hagmann, Marie-Luise, additional, Halfon, Sherin, additional, Hamilton, Andrew J., additional, Seon Han, Ji, additional, Hara-Nishimura, Ikuko, additional, Harada, Minoru, additional, Hartzell, William O., additional, Hay, Rod J., additional, Hayashi, Kiyoshi, additional, Hendriks, Dirk F., additional, Henrich, Bernhard, additional, Henriet, Patrick, additional, Hernández-Arana, Andrés, additional, Herrera-Camacho, Irma, additional, Heusipp, Gerhard, additional, Hicks, P.M., additional, Hillman, Bradley I., additional, Yukihiro Hiraoka, B., additional, Hiratake, Jun, additional, Ho, Heng-Chien, additional, Thi Hoa, Ngo, additional, Hochstrasser, Mark, additional, Hofmann, Theo, additional, Hohn, Thomas, additional, Hoidal, John R., additional, Holbrook, Joanna D., additional, Höltje, Joachim-Volker, additional, Homma, Koichi J., additional, Hook, Vivian Y.H., additional, Hooper, John D., additional, Hooper, Nigel M., additional, Hosoi, Kazuo, additional, Hospital, Véronique, additional, Howe, Christopher J., additional, Hruby, Dennis E., additional, Huang, H.-C., additional, Huber, Robert, additional, Hughes, Clare E., additional, Ibrahim-Granet, Oumaïma, additional, Ichishima, Eiji, additional, Ikehara, Yukio, additional, Imamura, Takahisa, additional, Inagaki, Noritoshi, additional, Inagami, Tadashi, additional, Isaac, R.E., additional, Isaya, Grazia, additional, Ishihara, Kohji, additional, Ishii, Shin-ichi, additional, Itoh, Yoshifumi, additional, Ito, Kiyoshi, additional, Ito, Koreaki, additional, Iwanaga, Sadaaki, additional, Jack, Ralph W., additional, Jackson, Mel C., additional, James, Michael N.G., additional, Jeffrey (Deceased), John, additional, Jiang, Ping, additional, Johnson, Gary D., additional, Johnson, John E., additional, Johnson, Michael, additional, Albert Johnston, Stephen, additional, Jones, Elizabeth W., additional, Jongbloed, Jan D.H., additional, Joshua-Tor, Leemor, additional, Joudiou, Carine, additional, Juliano, Luiz, additional, Jupp, Ray, additional, Kaminogawa, Shuichi, additional, Kamio, Yoshiyuki, additional, Kan, Chen-Chen, additional, Kaneda, Makoto, additional, Gyun Kang, Sung, additional, Kania, Mary, additional, Kanjanahaluethai, Amornrat, additional, Kawabata, Shun-ichiro, additional, Kay, John, additional, Keiler, Kenneth C., additional, Kelly, R.M., additional, Kerr, Michael A, additional, Kervinen, Jukka, additional, Kessler, Efrat, additional, Kidd, Simon, additional, Kilian, Mogens, additional, Kim, Do-Hyung, additional, Seop Kim, In, additional, Kimura, Yukio, additional, Kirisako, Takayoshi, additional, Kirschke, Heidrun, additional, Kishi, Tadaaki, additional, Kitamura, Naomi, additional, Kitazono, Ana A., additional, Kleanthous, Colin, additional, Klein, Jürgen R., additional, Kobayashi, Hideyuki, additional, Koelsch, Gerald, additional, Kok, Jan, additional, Kolattukudy, P.E., additional, Kolmar, Harald, additional, Komori, Yumiko, additional, Konvalinka, Jan, additional, Korhonen, Timo K., additional, Kortt, Alexander A., additional, Kräusslich, Hans-Georg, additional, Kress, Lawrence F., additional, Kubo, Takeaki, additional, Kukkonen, Maini, additional, Kumagai, Hidehiko, additional, Kumazaki, Takashi, additional, Kümmerer, Beate M., additional, Kuno, Kouji, additional, Kurachi, Kotoku, additional, Kurkinen, Markku, additional, Lähteenmäki, Kaarina, additional, Laing, Gavin D., additional, Lambkin, Imelda J., additional, Lamppa, Gayle K., additional, Lång, Hannu, additional, Langer, Thomas, additional, Laursen, Richard A., additional, Le Bonniec, Bernard F., additional, Luel Lee, Bok, additional, Joon Lee, Kye, additional, Young Lee, So, additional, Lee, Soohee, additional, Leis, Jonathan, additional, LeMosy, Ellen K., additional, Lepage, Thierry, additional, Leppla, Stephen H., additional, Lessard, Ivan A.D., additional, Lhomond, Guy, additional, Liao, Ta-Hsiu, additional, Lieber, Toby, additional, Lijnen, H.R., additional, Lima, Christopher D., additional, Lin, Chen-Yong, additional, Lin, Xinli, additional, Lindsay, L.L., additional, Lipscomb, William N., additional, Little, Christopher B., additional, Little, John W., additional, Lively, Mark O., additional, Lobel, Peter, additional, Peng Loh, Y., additional, Lohi, Jouko, additional, Lomonossoff, G.P., additional, Looze, Yvan, additional, López-García, Alma, additional, López-Otín, Carlos, additional, Luo, Liu-Ying, additional, Lupas, Andrei, additional, MacKay, Vivian L., additional, Mains, Richard E., additional, Mäkinen, Kauko K., additional, Mäkinen, Pirkko-Liisa, additional, Mandelbaum, Fajga R., additional, Manning, James M., additional, Marcotrigiano, Joseph, additional, Markland, Francis S., additional, Maruyama, M., additional, Maruyama, Sususmu, additional, Masaki, Takeharu, additional, Mathew, Zacharia, additional, Matrisian, Lynn M., additional, Matsuda, Yoshihiro, additional, Matsuka, Yury V., additional, Matsushita, Osamu, additional, Matsuzawa, Hiroshi, additional, Maurizi, Michael R., additional, Mbikay, Majambu, additional, Ken McDonald, J., additional, McKerrow, James H., additional, McMillan, David, additional, Mecham, Robert P., additional, Mehta, Darshini P., additional, Meighan, Paul, additional, Mellors, Alan, additional, Melton, Roger G., additional, Ménard, Armelle, additional, Ménard, Robert, additional, Menéndez-Arias, Luis, additional, Meyer, Diane H., additional, Meyers, Gregor, additional, Michaelis, Susan, additional, Mielicki, Wojciech P., additional, Mierau, Igor, additional, Millán-Pérez-Peña, Lourdes, additional, Miller, Charles G., additional, Mills, John, additional, Mills, Kenneth V., additional, Mistou, Michel-Yves, additional, Misumi, Yoshio, additional, Miyoshi, Shin-ichi, additional, Mizutani, Shigehiko, additional, Mock, William L., additional, Möhrlen, Frank, additional, Moiré, Nathalie, additional, Monnet, Véronique, additional, Monod, Michel, additional, Montecucco, Cesare, additional, Morita, Takashi, additional, Morrissey, James H., additional, Mort, John S., additional, Mortensen, Uffe H., additional, Morty, Rory E., additional, Motoshima, Hidemasa, additional, Mottram, Jeremy C., additional, Mundt, Egbert, additional, Murakami, Kazuo, additional, Murakami-Murofushi, Kimiko, additional, Murao, Sawao, additional, Murata, Christina, additional, Murphy, Gillian, additional, Muta, Tatsushi, additional, Mzhavia, Nino, additional, Nagase, Hideaki, additional, Naik, Rajesh R., additional, Nakajima, Nobuyoshi, additional, Nakamura, Hiroyuki, additional, Nakamura, Yukio, additional, Nasmyth, Kim, additional, Navarro-García, Fernando, additional, Netzel-Arnett, Sarah, additional, Nguyen-Distéche, Martine, additional, Nicholson, Donald, additional, Nikai, Toshiaki, additional, Nirasawa, Satoru, additional, Nishii, Wataru, additional, Nishiyama, Makoto, additional, Niven, Gordon W., additional, Nomura, Seiji, additional, Norioka, Shigemi, additional, North, Michael J., additional, Nuss, Donald L., additional, O′Connor, Michael B., additional, Oberst, Michael, additional, Oda, Kohei, additional, Odorico, Dimitri M., additional, Oetjen, Joyce, additional, Ogura, Teru, additional, Ohkubo, Iwao, additional, Ohlendorf, Douglas H., additional, Ohman, Dennis E., additional, Ohsumi, Yoshinori, additional, Okabe, Akinobu, additional, Okuda, K., additional, Olesen, Kjeld, additional, Oroszlan, Stephen, additional, Orth, Kim, additional, Ota, Nobuyuki, additional, Ovadia, Michael, additional, Overgaard, Michael T., additional, O-Wang, Jiyang, additional, Oxvig, Claus, additional, Packer, Jeremy C.L., additional, Paetzel, Mark, additional, Paine, Mark J.I., additional, Park, John E., additional, Woo Park, Pyong, additional, Soo Park, Sung, additional, Parkin, Kirk L., additional, Parks, William C., additional, Pascall, John C., additional, Paschos, Athanasios, additional, Paul, Sudhir, additional, Pearce, David A., additional, Pei, Duanqing, additional, Pemberton, Alan D., additional, Peters, Jan-Michael, additional, Phylip, Lowri H., additional, Pichová, Iva, additional, Pieper, Michael, additional, Piesse, Christophe, additional, Pike, Rob, additional, Pinck, Lothaire, additional, Pirzad, Ramin, additional, Pitot, Henry C., additional, Plaut, Andrew G., additional, Polgár, László, additional, Postina, Rolf, additional, Potempa, Jan, additional, Poulsen, Knud, additional, Pritchard, David G., additional, Pshezhetsky, Alexey V., additional, Abul Qasim, M., additional, Rader, Stephen D., additional, Rando, Robert R., additional, Rao, Mala, additional, Rao, Narayanam V., additional, Ratnoff, Oscar D., additional, Rawlings, Neil D., additional, Rawson, Robert B., additional, Reddy, Vijay, additional, Redman, Colvin M., additional, Reichl (Deceased), Antonia P., additional, Reid, Julian R., additional, Reid, Kenneth B.M., additional, Remaut, Han, additional, James Remington, S., additional, Rettig, Wolfgang J., additional, Rholam, Mohamed, additional, Rice, Charles M., additional, Richter, Stefan, additional, Riezman, Howard, additional, Ritchie, Alison, additional, Ro, Hyo-Sung, additional, Robert-Baudouy, Janine, additional, Michael Roberts, R., additional, Robinson, Michael, additional, Rodríguez-Romero, Adela, additional, Rogers, John C., additional, Rosenthal, Philip J., additional, Rose, A.M., additional, Rosing, J., additional, Rossetto, Ornella, additional, Rossi, Cesare, additional, Rossi, Véronique, additional, Roth, Richard A., additional, Rowan, Andrew D., additional, Rozanov, Mikhail, additional, Rucavado, Alexandra, additional, Rul, Françoise, additional, Rümenapf, Tillmann, additional, Ryan, Martin D., additional, Ryan, Thomas J., additional, Sacco, Elena, additional, Evan Sadler, J., additional, Saenger, W., additional, Sahl, Hans-Georg, additional, Sajid, Mohammed, additional, Sakiyama, Fumio, additional, Salas, María L., additional, Salter, Jason P., additional, Salvesen, Guy S., additional, Sanchez, Eladio F., additional, Sang, Qing-Xiang Amy, additional, Sankaran, Krishnan, additional, Sarras, Michael P., additional, Sasagawa, Yoshikiyo, additional, Satoh, Kimiyuki, additional, Sauer, Robert T., additional, Sawada, Hitoshi, additional, Scarisbrick, I.A., additional, Schauer-Vukasinovic, Vesna, additional, Schlievert, Patrick M., additional, Schlösser, Manfred, additional, Schmidt, Amy E., additional, Schmidt, Brian F., additional, Schmidt, Walter K., additional, Schmitz, Udo K., additional, Schneemann, Anette, additional, Scholze, Henning, additional, Schomburg, Lutz, additional, Schwaeble, Wilhelm J., additional, Sedlacek, Radislav, additional, Seemüller, Erika, additional, Seidah, Nabil G., additional, Seiki, Motoharu, additional, Selistre de Araujo, Heloisa S., additional, Senior, Robert M., additional, Sik Seong, Ihn, additional, Serpe, Mihaela, additional, Serrano, Solange M.T., additional, Setlow, Peter, additional, Shanks, M., additional, Shao, Feng, additional, Shapiro, Steven D., additional, Shen, Lei, additional, Sherwood (Deceased), Roger F., additional, Shi, Yun-Bo, additional, Shimoi, Hitoshi, additional, Shinoda, Sumio, additional, Siigur, Ene, additional, Siigur, Jüri, additional, Sim, Robert B., additional, Simmer, James P., additional, Simmons, William H., additional, Sirakova, Tatiana D., additional, Skern, Tim, additional, Skidgel, Randal A., additional, Slack, Jeffrey, additional, Sleat, David E., additional, Smith, Janet L., additional, Smyth, Mark J., additional, Snijder, Eric J., additional, Söderhäll, Kenneth, additional, Sohar, Istvan, additional, Sorimachi, Hiroyuki, additional, Sottrup-Jensen, Lars, additional, Soubrier, Florent, additional, Soukhodolets, Karen E., additional, Springman, Eric B., additional, Geme, Joseph W. St., additional, Leger, Raymond J. St., additional, Steele, James L., additional, Steinkühler, Christian, additional, Stenberg, Leisa M., additional, Stenflo, Johan, additional, Stennicke, Henning R., additional, Stepanov (Deceased), Valentin M., additional, Steven, Frank, additional, Stevenson, Kenneth J., additional, Stewart, David J., additional, Storer, Andrew C., additional, Stover, Cordula, additional, Sträter, Norbert, additional, Strauss, Ellen G., additional, Strauss, James H., additional, Stöcker, Walter, additional, Stříšovský, Kvido, additional, Suárez-Rendueles, Paz, additional, Sugimoto, Manabu, additional, Sulea, Traian, additional, Suzuki, Fumiaki, additional, Suzuki, Hideyuki, additional, Swenson, Stephen, additional, Szecsi, Pal B., additional, Szilágyi, László, additional, Taha, Muhamed-Kheir, additional, Takahashi, Kenji, additional, Takio, Koji, additional, Tamura, Tomohiro, additional, Tan, Fulong, additional, Hong Tan, Nget, additional, Tanase, Carmen, additional, Tang, Jordan, additional, Tanizaki, Martha M., additional, Tannich, Egbert, additional, Tans, G., additional, Tarentino (Deceased), Anthony L., additional, Tatnell, Peter J., additional, Tatsumi, Hiroki, additional, Tautz, Norbert, additional, Templin, Markus F., additional, Terada, Shigeyuki, additional, Thacker, C., additional, Theodoratou, Ekaterini, additional, Thiel, Heinz-Jürgen, additional, Thielens, Nicole M., additional, Thierry, Gonzales, additional, Thomas, Mark D., additional, Thornberry, Nancy A., additional, Thorsness, Mary K., additional, Thorsness, Peter E., additional, Tigue, Natalie J., additional, Tjalsma, Harold, additional, Tomkinson, Birgitta, additional, Tonello, Fiorella, additional, Toogood, H.S., additional, Toombs, Christopher, additional, Tortora, Paolo, additional, Tözsér, József, additional, Travis, James, additional, Tschesche, Harald, additional, Tsujimoto, Masafumi, additional, Tsunasawa, Susumu, additional, Tsu, Christopher A., additional, Tu, Anthony T., additional, Turk, Boris, additional, Turk, Dusan, additional, Turk, Vito, additional, Turner, Anthony J., additional, Uchikoba, Tetsuya, additional, Uitto, Veli-Jukka, additional, Ullmann, Dirk, additional, Valdenaire, Olivier, additional, Van Beeumen, Jozef, additional, Van de Ven, Wim J.M., additional, van den Burg, Bertus, additional, Maarten van Dijl, Jan, additional, van Roosmalen, Maarten L., additional, Van Wart, Harold E., additional, Vanoni, Marco, additional, Vath, Gregory M., additional, Velasco, Gloria, additional, Vendrell, Josep, additional, Venekei, István, additional, Vera, Pablo, additional, Verchot-Lubicz, Jeanmarie, additional, Vines, Richard R., additional, Volanakis, John E., additional, Wagner, Fred W., additional, Wainwright, Shane W., additional, Walker, Kenneth W., additional, Walker, Stephen J., additional, Wallach, Jean, additional, Walling, Linda L., additional, Walsh, Peter N., additional, Wang, P., additional, May Wang, Q., additional, Wassenaar, Alfred L.M., additional, Watts, Aaron B., additional, Weber, Joseph M., additional, Webster, Daniel R., additional, Weiss, Stephen J., additional, Wells, James A., additional, Wenzel, Herbert, additional, Wewer, Ulla M., additional, White, Judith M., additional, Wilk, Sherwin, additional, Wilkin, Jean-Marc, additional, Wilkins, Tracy D., additional, Wilkinson, Keith D., additional, Winther, Jakob R., additional, Wlodawer, Alexander, additional, Fred Woessner, J., additional, Wolfe, Michael S., additional, Wolfsberg, Tyra G., additional, Woodgate, Roger, additional, Wright, G.D., additional, Wu, Qingyu, additional, Xie, Sancai, additional, Yamagami, Kenjiro, additional, Yamaguchi, Nozomi, additional, Yamakawa, Yoshio, additional, Yamamoto, Kei, additional, Yamamoto, Shigeo, additional, Yana, Ikuo, additional, Yang, Maozhou, additional, Yasuda, Noriko, additional, Yasuhara, Toshimasa, additional, Yasumasu, Shigeki, additional, Yi, Elizabeth, additional, Yiallouros, Irene, additional, Yonezawa, Hiroo, additional, Ji Yoo, Soon, additional, Yoshimoto, Tadashi, additional, Young, Michael W., additional, Young, Stephen G., additional, Zavalova, Ludmila L., additional, Zdanov, Alexander, additional, and Zhang, Hong-Zhong, additional

Published
2004
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81. Micro-nano-bio acoustic system for the detection of foodborne pathogens in real samples

Author

Papadakis, George, Krulišová, Pavla, Hamiot, Audrey, Tsougeni, Katerina, Kaprou, Georgia, Eck, Michael, Rabus, David, Bílková, Zuzana, Dupuy, Bruno, Jobst, Gerhardt, Tserepi, Angeliki, Gogolides, Evangelos, Gizeli, Electra, Papadakis, George, Krulišová, Pavla, Hamiot, Audrey, Tsougeni, Katerina, Kaprou, Georgia, Eck, Michael, Rabus, David, Bílková, Zuzana, Dupuy, Bruno, Jobst, Gerhardt, Tserepi, Angeliki, Gogolides, Evangelos, and Gizeli, Electra

Abstract

The fast and efficient detection of foodborne pathogens is a societal priority, given the large number of food-poisoning outbreaks, and a scientific and technological challenge, given the need to detect as little as 1 viablecell in 25 gr of food. Here, we present thefirst approach that achieves the above goal, thanks to the use of amicro/nano-technology and the detection capability of acoustic wave sensors. Starting from 1Salmonellacell in25 ml of milk, we employ immuno-magnetic beads to capture cells after only 3 h of pre-enrichment and sub-sequently demonstrate efficient DNA amplification using the Loop Mediated Isothermal Amplification method(LAMP) and acoustic detection in an integrated platform, within an additional ½ h. The demonstrated 4 hsample-to-analysis time comes as a huge improvement to the current need of few days to obtain the same result.In addition, the work presents thefirst reported Lab-on-Chip platform that comprises an acoustic device as thesensing element, exhibiting impressive analytical features, namely, an acoustic limit of detection of 2 cells/μlor3 aM of the DNA target and ability to detect in a label-free manner dsDNA amplicons in impure samples. The useof food samples together with the incorporation of the necessary pre-enrichment step and ability for multipleanalysis with an internal control, make the proposed methodology highly relevant to real-world applications.Moreover, the work suggests that acoustic wave devices can be used as an attractive alternative to electro-chemical sensors in integrated platforms for applications in food safety and the point-of-care diagnostics., Rychlá a účinná detekce patogenů v potravinách je prioritou jak omezit rizika spojená s otravou obyvatel jídlem a je výzvou, jak využít vědeckých i technologických poznatků k sestavení analyzátoru, který by umožnil stanovit 1 bakteriální buňku v normovaných 25 g potraviny. Tento článek představuje nový analytický systém, využívající nové mikro a nanotechnologie a principu akustického biosenzoru. Průkaz je založen na nabohacení bakteriálních buněk pomocí imunosenzoru na bázi magnetických mikročástic po 3 hodinovém nabohacení v kultivačním médiu a poté jsou patogenní buŇky lyzovány a bakteriální DNA je amplifikována pomocí procesu LAMP a to již v samotném chipu spojeného elektronicky s detekční jednotkou, tj. akustickým biosenzorem. Celá detekce patogenů v tomto případě trvá 4 - 6 hodin, což je nespornou výhodou ve srovnání s dnes běžnými postupy závislým na předkultivaci a namnožení izolovaných patogenů po dobu min. 24 hodin. Tento systém má potenciál se uplatnit v praxi při kontrole bezpečnosti potravin tak i v rámci POCT systémů v klinické praxi.

Published
2019

82. An RNA-Binding Protein Secreted by a Bacterial Pathogen Modulates RIG-I Signaling

Author

Pagliuso, Alessandro, Allemand, Eric, Robertin, Stevens, Dupuy, Bruno, Bertrand, Quentin, Becavin, Christophe, Koutero, Mikael, Najburg, Valerie, Nahori, Marie-Anne, Tangy, Frederic, Stavru, Fabrizia, Bessonov, Sergey, Dessen, Andrea, Muchardt, Christian, Lebreton, Alice, Komarova, Anastassia, V, Cossart, Pascale, Pagliuso, Alessandro, Allemand, Eric, Robertin, Stevens, Dupuy, Bruno, Bertrand, Quentin, Becavin, Christophe, Koutero, Mikael, Najburg, Valerie, Nahori, Marie-Anne, Tangy, Frederic, Stavru, Fabrizia, Bessonov, Sergey, Dessen, Andrea, Muchardt, Christian, Lebreton, Alice, Komarova, Anastassia, V, and Cossart, Pascale

Abstract

RNA-binding proteins (RBPs) perform key cellular activities by controlling the function of bound RNAs. The widely held assumption that RBPs are strictly intracellular has been challenged by the discovery of secreted RBPs. However, extracellular RBPs have been described in eukaryotes, while secreted bacterial RBPs have not been reported. Here, we show that the bacterial pathogen Listeria monocytogenes secretes a small RBP that we named Zea. We show that Zea binds a subset of L. monocytogenes RNAs, causing their accumulation in the extracellular medium. Furthermore, during L. monocytogenes infection, Zea binds RIG-I, the non-self-RNA innate immunity sensor, potentiating interferon-beta production. Mouse infection studies reveal that Zea affects L. monocytogenes virulence. Together, our results unveil that bacterial RNAs can be present extracellularly in association with RBPs, acting as social RNAs to trigger a host response during infection.

Published
2019

83. Advanced immunocapture of milk-borne Salmonella by microfluidic magnetically stabilized fluidized bed

Author

Srbová, Jana, Krulišová, Pavla, Holubová, Lucie, Pereiro, Iago, Bendali, Amel, Hamiot, Audrey, Podzemná, Veronika, Macák, Jan, Dupuy, Bruno, Descroix, Stephanie, Viovy, Jean-Louis, Bílková, Zuzana, Srbová, Jana, Krulišová, Pavla, Holubová, Lucie, Pereiro, Iago, Bendali, Amel, Hamiot, Audrey, Podzemná, Veronika, Macák, Jan, Dupuy, Bruno, Descroix, Stephanie, Viovy, Jean-Louis, and Bílková, Zuzana

Abstract

The success of microfluidic immunocapture based on magnetic beads depends primarily on a sophisticated microscale separation system and on the quality of the magnetic immunosorbent. A microfluidic chip containing a magnetically stabilized fluidized bed (MSFB), developed for the capture and on-chip amplification of bacteria, was recently described by Pereiro etal.. The present work shows the thorough development of anti-Salmonella magnetic immunosorbents with the optimal capture efficiency and selectivity. Based on the corresponding ISO standards, these parameters have to be high enough to capture even a few cells of bacteria in a proper aliquot of sample, e.g. milk. The selection of specific anti-Salmonella IgG molecules and the conditions for covalent bonding were the key steps in preparing an immunosorbent of the desired quality. The protocol for immunocapturing was first thoroughly optimized and studied in a batchwise arrangement, and then the carrier was integrated into the MSFB chip. The combination of the unique design of the chip (guaranteeing the collision of cells with magnetic beads) with the advanced immunosorbent led to a Salmonella cell capture efficiency of up to 99%. These high values were achieved repeatedly even in samples of milk differing in fat content. The rate of nonspecific capture of Escherichia coli (i.e. the negative control) was only 2%., Účinnost vychytávání patogenních bakterií z mléka je silně závislá na kvalitě imunosorbentu, nosiči na bázi superparamagnetických částic, jejichž povrch je biofunkcionalizován specifickými protilátkami. MSFB systém - mikrofluidní separátor s integrovaným magnetem stabilizovaným fluidním ložem byl použit k izolaci a také k namnožení počtu patogenních bakterií pro další analýzu, např. PCR metodu pro průkaz bakteirální DNA. Selekttivita i specificita záchytu je klíčová pro praktické využití analyzátoru, je nutné dosáhnout parametrů, které vyžadují ISO standardy pro průkaz patogenů v potravinách. V práci je popsána biofunkcionalizace magnetických částic a jejich použití pro izolaci patogenů, buněk Salmonella sp. Sledovali jsme účinnost záchytu, výtěžnost, ale i specificitu záchytu, křížová reaktivita nebyla prokázána, míra nespecifické sorpce (směs Salmonella, E. coli) byla pouze 2%.

Published
2019

84. Rapid expansion of the physical and genetic map of the chromosome of Clostridium perfringens CPN50

Author

Katayama, Sei-Chi, Dupuy, Bruno, Garnier, Thierry, and Cole, Stewart T.

Subjects
Clostridium -- Observations, Chromosome mapping -- Research, Cloning -- Analysis, Virulence (Microbiology) -- Research, Biological sciences
Abstract

An expanded genetic map of the chromosome in Clostridium perfringens CPN50 indicated that the virulence genes were located near oriC and the pleiotropic virulence factor virRS was located near the putative replication terminus. Other bacilli appear to have similar arrangement of heat shock and sporulation genes. Researchers expanded the genetic map by cutting the chromosome into fragments, and then cloning, sequencing, and determining the function of the fragments.

Published
1995

85. Type IV prepilin peptidase gene of Neisseria gonorrhoeae MS11: presence of a related gene in other piliated and nonpiliated Neisseria strains

Author

Dupuy, Bruno and Pugsley, Anthony P.

Subjects
Polymerase chain reaction -- Observations, Neisseria gonorrhoeae -- Genetic aspects, Proteases -- Analysis, Biological sciences
Abstract

PCR amplification method yields the N. gonorrhoeae prepilin gene, pilD-Ng, which splits and subsequently N-methylates the precursor pilin subunits before assembling into pili. Accurate splitting of the gonococcal prepilin in Escherichia coli cells containing the prepilin peptidase gene and the pilin structural gene is promoted by the pilD-Ng product.

Published
1994

86. The Ser/Thr Kinase PrkC Participates in Cell Wall Homeostasis and Antimicrobial Resistance in Clostridium difficile

Author

Cuenot, Elodie, primary, Garcia-Garcia, Transito, additional, Douche, Thibaut, additional, Gorgette, Olivier, additional, Courtin, Pascal, additional, Denis-Quanquin, Sandrine, additional, Hoys, Sandra, additional, Tremblay, Yannick D. N., additional, Matondo, Mariette, additional, Chapot-Chartier, Marie-Pierre, additional, Janoir, Claire, additional, Dupuy, Bruno, additional, Candela, Thomas, additional, and Martin-Verstraete, Isabelle, additional

Published
2019
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90. An RNA-binding protein secreted byListeria monocytogenesactivates RIG-I signaling

Author

Pagliuso, Alessandro, primary, Tham, To Nam, additional, Allemand, Eric, additional, Robertin, Stevens, additional, Dupuy, Bruno, additional, Bertrand, Quentin, additional, Bécavin, Christophe, additional, Koutero, Mikael, additional, Najburg, Valérie, additional, Nahori, Marie-Anne, additional, Stavru, Fabrizia, additional, Dessen, Andréa, additional, Muchard, Christian, additional, Lebreton, Alice, additional, Komarova, Anastassia V., additional, and Cossart, Pascale, additional

Published
2019
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91. Structure and assembly of aClostridioides difficilespore polar appendage

Author

Antunes, Wilson, primary, Pereira, Fátima C., additional, Feliciano, Carolina, additional, Saujet, Laure, additional, Vultos, Tiago dos, additional, Couture-Tosi, Evelyne, additional, Péchiné, Severine, additional, Bruxelle, Jean-François, additional, Janoir, Claire, additional, Melo, Luís V., additional, Brito, Patrícia, additional, Martin-Verstraete, Isabelle, additional, Serrano, Mónica, additional, Dupuy, Bruno, additional, and Henriques, Adriano O., additional

Published
2018
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92. Global regulation of gene expression in response to cysteine availability in Clostridium perfringens

Author

André Gaelle, Haudecoeur Elise, Monot Marc, Ohtani Kaori, Shimizu Tohru, Dupuy Bruno, and Martin-Verstraete Isabelle

Subjects
Microbiology, QR1-502
Abstract

Abstract Background Cysteine has a crucial role in cellular physiology and its synthesis is tightly controlled due to its reactivity. However, little is known about the sulfur metabolism and its regulation in clostridia compared with other firmicutes. In Clostridium perfringens, the two-component system, VirR/VirS, controls the expression of the ubiG operon involved in methionine to cysteine conversion in addition to the expression of several toxin genes. The existence of links between the C. perfringens virulence regulon and sulfur metabolism prompted us to analyze this metabolism in more detail. Results We first performed a tentative reconstruction of sulfur metabolism in C. perfringens and correlated these data with the growth of strain 13 in the presence of various sulfur sources. Surprisingly, C. perfringens can convert cysteine to methionine by an atypical still uncharacterized pathway. We further compared the expression profiles of strain 13 after growth in the presence of cystine or homocysteine that corresponds to conditions of cysteine depletion. Among the 177 genes differentially expressed, we found genes involved in sulfur metabolism and controlled by premature termination of transcription via a cysteine specific T-box system (cysK-cysE, cysP1 and cysP2) or an S-box riboswitch (metK and metT). We also showed that the ubiG operon was submitted to a triple regulation by cysteine availability via a T-box system, by the VirR/VirS system via the VR-RNA and by the VirX regulatory RNA. In addition, we found that expression of pfoA (theta-toxin), nagL (one of the five genes encoding hyaluronidases) and genes involved in the maintenance of cell redox status was differentially expressed in response to cysteine availability. Finally, we showed that the expression of genes involved in [Fe-S] clusters biogenesis and of the ldh gene encoding the lactate dehydrogenase was induced during cysteine limitation. Conclusion Several key functions for the cellular physiology of this anaerobic bacterium were controlled in response to cysteine availability. While most of the genes involved in sulfur metabolism are regulated by premature termination of transcription, other still uncharacterized mechanisms of regulation participated in the induction of gene expression during cysteine starvation.

Published
2010
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94. A new microfluidic approach for the one-step capture, amplification and label-free quantification of bacteria in raw milk

Author

Pereiro, Iago, Bendali, Amel, Tabnaoui, Sanae, Alexandre, Lucile, Srbova, Jana, Bilkova, Zuzana, Deegan, Shane, Joshi, Lokesh, Viovy, Jean-Louis, Malaquin, Laurent, Dupuy, Bruno, Descroix, Stéphanie, Pereiro, Iago, Bendali, Amel, Tabnaoui, Sanae, Alexandre, Lucile, Srbova, Jana, Bilkova, Zuzana, Deegan, Shane, Joshi, Lokesh, Viovy, Jean-Louis, Malaquin, Laurent, Dupuy, Bruno, and Descroix, Stéphanie

Abstract

A microfluidic method to specifically capture and detect infectious bacteria based on immunorecognition and proliferative power is presented. It involves a microscale fluidized bed in which magnetic and drag forces are balanced to retain antibody-functionalized superparamagnetic beads in a chamber during sample perfusion. Captured cells are then cultivated in situ by infusing nutritionally-rich medium. The system was validated by the direct one-step detection of Salmonella Typhimurium in undiluted unskimmed milk, without pre-treatment. The growth of bacteria induces an expansion of the fluidized bed, mainly due to the volume occupied by the newly formed bacteria. This expansion can be observed with the naked eye, providing simple low-cost detection of only a few bacteria and in a few hours. The time to expansion can also be measured with a low-cost camera, allowing quantitative detection down to 4 cfu (colony forming unit), with a dynamic range of 100 to 107 cfu ml−1 in 2 to 8 hours, depending on the initial concentration. This mode of operation is an equivalent of quantitative PCR, with which it shares a high dynamic range and outstanding sensitivity and specificity, operating at the live cell rather than DNA level. Specificity was demonstrated by controls performed in the presence of a 500× excess of non-pathogenic Lactococcus lactis. The system's versatility was demonstrated by its successful application to the detection and quantitation of Escherichia coli O157:H15 and Enterobacter cloacae. This new technology allows fast, low-cost, portable and automated bacteria detection for various applications in food, environment, security and clinics., Práce popisuje mikrofluidní metodu pro specifické zachycení a detekci infekčních bakterií na základě imunorekognitivní a proliferační energie. Využívá se zde magnetické mikrofluidní lože, kde jsou magnetické a proudící síly vyrovnány tak, aby se udržely funkcionalizované superparamagnetické částice uvnitř komůrky čipu během průchodu vzorku. Zachycené buňky se pak kultivují in situ pomocí infuze živného média. Systém byl validován přímou jednostupňovou detekcí Salmonella Typhimurium v ​​nezředěném surovém mléce bez předchozího ošetření. Růst bakterií indukuje expanzi fluidního lože, zejména kvůli objemu který zaujímají nově vytvořené bakterie. Tato expanze může být pozorována pouhým okem, což umožňuje jednoduchou detekci pouze několika bakterií za několik málo hodin. Tato nová technologie umožňuje rychlou, přenosu a automatizovanou detekci bakterií pro různé aplikace v potravinách, životním prostředí, ale i klinických vzorcích.

Published
2018

95. The LexA regulated genes of the Clostridium difficile

Author

Walter, Beata Maria, Rupnik, Maja, Hodnik, Vesna, Anderluh, Gregor, Dupuy, Bruno, Paulič, Nejc, Žgur-Bertok, Darja, and Butala, Matej

Subjects
toxin regulation, antibiotic resistance, rezistenca na antibiotike, viruses, LexA repressor, SPR, represor LexA, Clostridium difficile, biochemical phenomena, metabolism, and nutrition, površinska plazmonska resonanca, regulacija toksinov, odpornost na antibiotike, udc:577.2, SOS system, enzymes and coenzymes (carbohydrates), sistem SOS, bacteria, surface plasmon resonance
Abstract

Background: The SOS response including two main proteins LexA and RecA, maintains the integrity of bacterial genomes after DNA damage due to metabolic or environmental assaults. Additionally, derepression of LexA-regulated genes can result in mutations, genetic exchange and expression of virulence factors. Here we describe the first comprehensive description of the in silico LexA regulon in Clostridium difficile, an important human pathogen. Results: We grouped thirty C. difficile strains from different ribotypes and toxinotypes into three clusters according to lexA gene/protein variability. We applied in silico analysis coupled to surface plasmon resonance spectroscopy (SPR) and determined 16 LexA binding sites in C. difficile. Our data indicate that strains within the cluster, as defined by LexA variability, harbour several specific LexA regulon genes. In addition to core SOS genes: lexA, recA, ruvCA and uvrBA, we identified a LexA binding site on the pathogenicity locus (PaLoc) and in the putative promoter region of several genes involved in housekeeping, sporulation and antibiotic resistance. Conclusions: Results presented here suggest that in C. difficile LexA is not merely a regulator of the DNA damage response genes but also controls the expression of dozen genes involved in various other biological functions. Our in vitro results indicate that in C. difficile inactivation of LexA repressor depends on repressor`s dissociation from the operators. We report that the repressor`s dissociation rates from operators differentiate, thus the determined LexA-DNA dissociation constants imply on the timing of SOS gene expression in C. difficile.

Published
2017

96. Sequence similarity of Clostridium difficile strains by analysis of conserved genes and genome content is reflected by their ribotype affiliation

Author

Kurka, Hedwig, Ehrenreich, Armin, Ludwig, Wolfgang, Monot, Marc, Rupnik, Maja, Barbut, Frédéric, Indra, Alexander, Dupuy, Bruno, and Liebl, Wolfgang

Subjects
RNA polymerase, comparative genomics, clostridium difficile, udc:579.852.13, RNA-polimeraza, primerjalna genomika
Abstract

PCR-ribotyping is a broadly used method for the classification of isolates of Clostridium difficile, an emerging intestinal pathogen, causing infections with increased disease severity and incidence in several European and North American countries. We have now carried out clustering analysis with selected genes of numerous C. difficile strains as well as gene content comparisons of their genomes in order to broaden our view of the relatedness of strains assigned to different ribotypes. We analyzed the genomic content of 48 C. difficile strains representing 21 different ribotypes. The calculation of distance matrix-based dendrograms using the neighbor joining method for 14 conserved genes (standard phylogenetic marker genes) from the genomes of the C. difficile strains demonstrated that the genes from strains with the same ribotype generally clustered together. Further, certain ribotypes always clustered together and formed ribotype groups, i.e. ribotypes 078, 033 and 126, as well as ribotypes 002 and 017, indicating their relatedness. Comparisons of the gene contents of the genomes of ribotypes that clustered according to the conserved gene analysis revealed that the number of common genes of the ribotypes belonging to each of these three ribotype groups were very similar for the 078/033/126 group (at most 69 specific genes between the different strains with the same ribotype) but less similar for the 002/017 group (86 genes difference). It appears that the ribotype is indicative not only of a specific pattern of the amplified 16S23S rRNA intergenic spacer but also reflects specific differences in the nucleotide sequences of the conserved genes studied here. It can be anticipated that the sequence deviations of more genes of C. difficile strains are correlated with their PCR-ribotype. In conclusion, the results of this study corroborate and extend the concept of clonal C. difficile lineages, which correlate with ribotypes affiliation.

Published
2017

97. The alternative sigma factor σ B plays a crucial role in adaptive strategies of Clostridium difficile during gut infection

Author

Kint, Nicolas, Janoir, Claire, Monot, Marc, Hoys, Sandra, Soutourina, Olga, Dupuy, Bruno, Martin-Verstraete, Isabelle, Pathogénèse des Bactéries Anaérobies / Pathogenesis of Bacterial Anaerobes (PBA (U-Pasteur_6)), Institut Pasteur [Paris]-Université Paris Diderot - Paris 7 (UPD7), Université Paris Diderot - Paris 7 (UPD7), Bactéries, Pathogènes et Santé (UBaPS), Faculté de Pharmacie, Université Paris-Sud - Paris 11 (UP11)-Université Paris-Sud - Paris 11 (UP11), This work was funded by the Institut Pasteur and the University Paris 7., We are thankful to Thomas Dubois and Al Claiborne for helpful discussions and to Jovana Mihajlovic and Jean-Marc Ghigo for their help with oxygen assays., Institut Pasteur [Paris] (IP)-Université Paris Diderot - Paris 7 (UPD7), and Université Paris-Sud - Paris 11 (UP11)-Université Paris-Saclay-Université Paris-Sud - Paris 11 (UP11)-Université Paris-Saclay

Subjects
MESH: DNA Repair, MESH: Gene Expression Regulation, Bacterial, MESH: Oxidative Stress, MESH: Sigma Factor, [SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, MESH: Drug Resistance, Multiple, Bacterial, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, MESH: Diarrhea, MESH: Gene Expression Profiling, MESH: Spores, Bacterial, MESH: Germ-Free Life, MESH: Up-Regulation, MESH: Animals, MESH: Gastrointestinal Tract, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], MESH: Mice, Inbred C3H, MESH: Bacterial Proteins, MESH: Mice, MESH: Female, MESH: Clostridium difficile, MESH: Virulence Factors
Abstract

International audience; Clostridium difficile is a major cause of diarrhoea associated with antibiotherapy. Exposed to stresses in the gut, C. difficile can survive by inducing protection, detoxification and repair systems. In several firmicutes, most of these systems are controlled by the general stress response involving σ(B) . In this work, we studied the role of σ(B) in the physiopathology of C. difficile. We showed that the survival of the sigB mutant during the stationary phase was reduced. Using a transcriptome analysis, we showed that σ(B) controls the expression of ∼25% of genes including genes involved in sporulation, metabolism, cell surface biogenesis and the management of stresses. By contrast, σ(B) does not control toxin gene expression. In agreement with the up-regulation of sporulation genes, the sporulation efficiency is higher in the sigB mutant than in the wild-type strain. sigB inactivation also led to increased sensitivity to acidification, cationic antimicrobial peptides, nitric oxide and ROS. In addition, we showed for the first time that σ(B) also plays a crucial role in oxygen tolerance in this strict anaerobe. Finally, we demonstrated that the fitness of colonisation by the sigB mutant is greatly affected in a dixenic mouse model of colonisation when compared to the wild-type strain.

Published
2017

99. Cwp19 Is a Novel Lytic Transglycosylase Involved in Stationary-Phase Autolysis Resulting in Toxin Release in Clostridium difficile

Author

Wydau-Dematteis, Sandra, primary, El Meouche, Imane, additional, Courtin, Pascal, additional, Hamiot, Audrey, additional, Lai-Kuen, René, additional, Saubaméa, Bruno, additional, Fenaille, François, additional, Butel, Marie-José, additional, Pons, Jean-Louis, additional, Dupuy, Bruno, additional, Chapot-Chartier, Marie-Pierre, additional, and Peltier, Johann, additional

Published
2018
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