{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,4]],"date-time":"2026-10-04T04:38:00Z","timestamp":1791088680772,"version":"4.1.0"},"reference-count":33,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2016,9,13]],"date-time":"2016-09-13T00:00:00Z","timestamp":1473724800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"},{"start":{"date-parts":[[2016,9,13]],"date-time":"2016-09-13T00:00:00Z","timestamp":1473724800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Sci Rep"],"abstract":"<jats:title>Abstract<\/jats:title><jats:p>The whooping cough agent<jats:italic>Bordetella pertussis<\/jats:italic>regulates the production of its virulence factors by the BvgA\/S system. Phosphorylated BvgA activates the virulence-activated genes (<jats:italic>vag<\/jats:italic>s) and represses the expression of the virulence-repressed genes (<jats:italic>vrg<\/jats:italic>s) via the activation of the<jats:italic>bvgR<\/jats:italic>gene. In modulating conditions, with MgSO<jats:sub>4<\/jats:sub>, the BvgA\/S system is inactive, and the<jats:italic>vrg<\/jats:italic>s are expressed. Here, we show that the expression of almost all<jats:italic>vrg<\/jats:italic>s depends on RisA, another transcriptional regulator. We also show that some<jats:italic>vag<\/jats:italic>s are surprisingly no longer modulated by MgSO<jats:sub>4<\/jats:sub>in the<jats:italic>risA<\/jats:italic><jats:sup>\u2212<\/jats:sup>background. RisA also regulates the expression of other genes, including chemotaxis and flagellar operons, iron-regulated genes, and genes of unknown function, which may or may not be controlled by BvgA\/S. We identified RisK as the likely cognate RisA kinase and found that it is important for expression of most, but not all RisA-regulated genes. This was confirmed using the phosphoablative RisAD<jats:sup>60<\/jats:sup>N and the phosphomimetic RisAD<jats:sup>60<\/jats:sup>E analogues. Thus the RisA regulon adds a new layer of complexity to<jats:italic>B. pertussis<\/jats:italic>virulence gene regulation.<\/jats:p>","DOI":"10.1038\/srep32774","type":"journal-article","created":{"date-parts":[[2016,9,13]],"date-time":"2016-09-13T09:32:10Z","timestamp":1473759130000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":44,"title":["The multifaceted RisA regulon of Bordetella pertussis"],"prefix":"10.1038","volume":"6","author":[{"given":"Lo\u00efc","family":"Coutte","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ludovic","family":"Huot","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rudy","family":"Antoine","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Stephanie","family":"Slupek","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tod J.","family":"Merkel","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Qing","family":"Chen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Scott","family":"Stibitz","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"David","family":"Hot","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Camille","family":"Locht","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2016,9,13]]},"reference":[{"key":"BFsrep32774_CR1","unstructured":"World Health Organisation. WHO vaccine-preventable diseases: monitoring system, 2016 global summary. http:\/\/apps.who.int\/immunization_monitoring\/globalsummary\/Date of access: 02\/08\/2016."},{"key":"BFsrep32774_CR2","unstructured":"Stibitz, S. The bvg regulon in Bordetella Molecular Microbiology. (ed. Locht, C. ) 47\u201367 (Horizon Bioscience, 2007)."},{"key":"BFsrep32774_CR3","first-page":"423","volume":"31","author":"BW Lacey","year":"1960","unstructured":"Lacey, B. W. Antigenic modulation of Bordetella pertussis. J Hyg 31, 423\u2013434 (1960).","journal-title":"J Hyg"},{"key":"BFsrep32774_CR4","doi-asserted-by":"publisher","first-page":"6206","DOI":"10.1128\/jb.171.11.6206-6212.1989","volume":"171","author":"AR Melton","year":"1989","unstructured":"Melton, A. R. & Weiss, A. A. Environmental regulation of expression of virulence determinants in Bordetella pertussis. J. Bacteriol 171, 6206\u20136212 (1989).","journal-title":"J. Bacteriol"},{"key":"BFsrep32774_CR5","doi-asserted-by":"publisher","first-page":"5059","DOI":"10.1128\/jb.170.11.5059-5066.1988","volume":"170","author":"S Knapp","year":"1988","unstructured":"Knapp, S. & Mekalanos, J. J. Two trans-acting regulatory genes (vir and mod) control antigenic modulation in Bordetella pertussis. J. Bacteriol 170, 5059\u20135066 (1988).","journal-title":"J. Bacteriol"},{"key":"BFsrep32774_CR6","doi-asserted-by":"publisher","first-page":"2727","DOI":"10.1128\/jb.177.10.2727-2736.1995","volume":"177","author":"TJ Merkel","year":"1995","unstructured":"Merkel, T. J. & Stibitz, S. Identification of a locus required for the regulation of bvg-repressed genes in Bordetella pertussis. J. Bacteriol 177, 2727\u20132736 (1995).","journal-title":"J. Bacteriol"},{"key":"BFsrep32774_CR7","doi-asserted-by":"publisher","first-page":"1648","DOI":"10.1128\/JB.187.5.1648-1658.2005","volume":"187","author":"TO Croinin","year":"2005","unstructured":"Croinin, T. O., Grippe, V. K. & Merkel, T. J. Activation of the vrg6 promoter of Bordetella pertussis by RisA. J. Bacteriol 187, 1648\u20131658 (2005).","journal-title":"J. Bacteriol"},{"key":"BFsrep32774_CR8","doi-asserted-by":"publisher","first-page":"5995","DOI":"10.1128\/IAI.73.9.5995-6004.2005","volume":"73","author":"TH Stenson","year":"2005","unstructured":"Stenson, T. H., Allen, A. G., Al-Meer, J. A., Maskell, D. & Peppler, M. S. Bordetella pertussis risA, but not risS, is required for maximal expression of Bvg-repressed genes. Infect Immun 73, 5995\u20136004 (2005).","journal-title":"Infect Immun"},{"key":"BFsrep32774_CR9","doi-asserted-by":"crossref","first-page":"4640","DOI":"10.1128\/IAI.66.10.4640-4650.1998","volume":"66","author":"H Jungnitz","year":"1998","unstructured":"Jungnitz, H., West, N. P., Walker, M. J., Chhatwal, G. S. & Guzman, C. A. A second two-component regulatory system of Bordetella bronchiseptica required for bacterial resistance to oxidative stress, production of acid phosphatase, and in vivo persistence. Infect Immun 66, 4640\u20134650 (1998).","journal-title":"Infect Immun"},{"key":"BFsrep32774_CR10","doi-asserted-by":"publisher","first-page":"1775","DOI":"10.1128\/JB.188.5.1775-1785.2006","volume":"188","author":"CA Cummings","year":"2006","unstructured":"Cummings, C. A., Bootsma, H. J., Relman, D. A. & Miller, J. F. Species- and strain-specific control of a complex, flexible regulon by Bordetella BvgAS. J. Bacteriol 188, 1775\u20131785 (2006).","journal-title":"J. Bacteriol"},{"key":"BFsrep32774_CR11","doi-asserted-by":"publisher","first-page":"5902","DOI":"10.1128\/JB.182.20.5902-5905.2000","volume":"182","author":"R Antoine","year":"2000","unstructured":"Antoine, R. et al. New virulence-activated and virulence-repressed genes identified by systematic gene inactivation and generation of transcriptional fusions in Bordetella pertussis. J. Bacteriol 182, 5902\u20135905 (2000).","journal-title":"J. Bacteriol"},{"key":"BFsrep32774_CR12","doi-asserted-by":"publisher","first-page":"4798","DOI":"10.1128\/JB.05136-11","volume":"193","author":"TJ Brickman","year":"2011","unstructured":"Brickman, T. J., Cummings, C. A., Liew, S. Y., Relman, D. A. & Armstrong, S. K. Transcriptional profiling of the iron starvation response in Bordetella pertussis provides new insights into siderophore utilization and virulence gene expression. J. Bacteriol 193, 4798\u20134812 (2011).","journal-title":"J. Bacteriol"},{"key":"BFsrep32774_CR13","doi-asserted-by":"publisher","first-page":"8731","DOI":"10.1016\/j.vaccine.2011.07.143","volume":"29","author":"J Alvarez Hayes","year":"2011","unstructured":"Alvarez Hayes, J. et al. Identification of a new protective antigen of Bordetella pertussis. Vaccine 29, 8731\u20138739 (2011).","journal-title":"Vaccine"},{"key":"BFsrep32774_CR14","doi-asserted-by":"publisher","first-page":"2518","DOI":"10.1021\/pr060681i","volume":"6","author":"ML Vidakovics","year":"2007","unstructured":"Vidakovics, M. L. et al. Profiling the Bordetella pertussis proteome during iron starvation. J. Proteome Res 6, 2518\u20132528 (2007).","journal-title":"J. Proteome Res"},{"key":"BFsrep32774_CR15","first-page":"e00657","volume":"3","author":"CJ Boinett","year":"2015","unstructured":"Boinett, C. J. et al. Complete Genome Sequence of Bordetella pertussis D420. Genome Announc 3, e00657\u201315 (2015).","journal-title":"Genome Announc"},{"key":"BFsrep32774_CR16","doi-asserted-by":"publisher","first-page":"343","DOI":"10.1128\/JB.00596-15","volume":"198","author":"Hanawa","year":"2016","unstructured":"Hanawa et al. Glutamate Limitation, BvgAS Activation, and (p)ppGpp Regulate the Expression of the Bordetella pertussis Type 3 Secretion System. J. Bacteriol 198, 343\u2013351 (2016).","journal-title":"J. Bacteriol"},{"key":"BFsrep32774_CR17","doi-asserted-by":"publisher","first-page":"5537","DOI":"10.1128\/IAI.00781-06","volume":"74","author":"MM Nakamura","year":"2006","unstructured":"Nakamura, M. M. et al. Growth phase- and nutrient limitation-associated transcript abundance regulation in Bordetella pertussis. Infect. Immun. 74, 5537\u20135548 (2006).","journal-title":"Infect. Immun."},{"key":"BFsrep32774_CR18","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1128\/MMBR.00043-12","volume":"77","author":"U R\u00f6mling","year":"2013","unstructured":"R\u00f6mling, U., Galperin, M. Y. & Gomelsky, M. Cyclic di-GMP: the first 25 years of a universal bacterial second messenger. Microbiol Mol Biol Rev 77, 1\u201352 (2013).","journal-title":"Microbiol Mol Biol Rev"},{"key":"BFsrep32774_CR19","doi-asserted-by":"publisher","first-page":"3468","DOI":"10.1128\/jb.175.11.3468-3479.1993","volume":"175","author":"BJ Akerley","year":"1993","unstructured":"Akerley, B. J. & Miller, J. F. Flagellin gene transcription in Bordetella brobchispetica is regulated by the BvgAS virulence control system. J. Bacteriol 175, 3468\u20133479 (1993).","journal-title":"J. Bacteriol"},{"key":"BFsrep32774_CR20","doi-asserted-by":"publisher","first-page":"980","DOI":"10.1128\/jb.174.3.980-990.1992","volume":"174","author":"BJ Akerley","year":"1992","unstructured":"Akerley, B. J., Monack, D. M., Falkow, S. & Miller, J. F. The bvgAS locus negatively controls motility and synthesis of flagella in Bordetella bronchiseptica. J Bacteriol 174, 980\u2013990 (1992).","journal-title":"J Bacteriol"},{"key":"BFsrep32774_CR21","doi-asserted-by":"publisher","first-page":"869","DOI":"10.1099\/mic.0.064345-0","volume":"159","author":"F Sisti","year":"2013","unstructured":"Sisti, F., Ha, D. G., O\u2019Toole, G. A., Hozbor, D. & Fernandez, J. Cyclic-di-GMP signalling regulates motility and biofilm formation in Bordetella bronchiseptica. Microbiology 159, 869\u2013879 (2013).","journal-title":"Microbiology"},{"key":"BFsrep32774_CR22","doi-asserted-by":"publisher","first-page":"788","DOI":"10.1111\/j.1365-2958.2004.04418.x","volume":"55","author":"WL Veal-Carr","year":"2005","unstructured":"Veal-Carr, W. L. & Stibitz, S. Demonstration of differential virulence gene promoter activation in vivo in Bordetella pertussis using RIVET. Mol Microbiol 55, 788\u2013798 (2005).","journal-title":"Mol Microbiol"},{"key":"BFsrep32774_CR23","doi-asserted-by":"crossref","first-page":"769","DOI":"10.1128\/iai.62.3.769-778.1994","volume":"62","author":"FD Menozzi","year":"1994","unstructured":"Menozzi, F. D. et al. Heparin-inhibitable lectin activity of the filamentous hemagglutinin adhesin of Bordetella pertussis. Infect Immun 62, 769\u2013778 (1994).","journal-title":"Infect Immun"},{"key":"BFsrep32774_CR24","doi-asserted-by":"publisher","first-page":"4288","DOI":"10.1128\/jb.173.14.4288-4296.1991","volume":"173","author":"S Stibitz","year":"1991","unstructured":"Stibitz, S. & Yang, M. S. Subcellular localization and immunological detection of proteins encoded by the vir locus of Bordetella pertussis. J Bacteriol 173, 4288\u20134296 (1991).","journal-title":"J Bacteriol"},{"key":"BFsrep32774_CR25","doi-asserted-by":"publisher","first-page":"15","DOI":"10.1016\/0378-1119(93)90611-6","volume":"127","author":"J Quandt","year":"1993","unstructured":"Quandt, J. & Hynes, M. F. Versatile suicide vectors which allow direct selection for gene replacement in Gram-negative bacteria. Gene 127, 15\u201321 (1993).","journal-title":"Gene"},{"key":"BFsrep32774_CR26","doi-asserted-by":"publisher","first-page":"133","DOI":"10.1016\/0378-1119(86)90318-5","volume":"50","author":"S Stibitz","year":"1986","unstructured":"Stibitz, S., Black, W. & Falkow, S. The construction of a cloning vector designed for gene replacement in Bordetella pertussis. Gene 50, 133\u2013140 (1986).","journal-title":"Gene"},{"key":"BFsrep32774_CR27","doi-asserted-by":"publisher","first-page":"458","DOI":"10.1016\/0076-6879(94)35161-9","volume":"235","author":"S Stibitz","year":"1994","unstructured":"Stibitz, S. Use of conditionally counterselectable suicide vectors for allelic exchange. Methods Enzymol 235, 458\u2013465 (1994).","journal-title":"Methods Enzymol"},{"key":"BFsrep32774_CR28","doi-asserted-by":"publisher","first-page":"784","DOI":"10.1038\/nbt1183-784","volume":"1","author":"R Simon","year":"1983","unstructured":"Simon, R., Priefer, U. & P\u00fchler, A. A broad host range mobilization system for in vivo genetic engineering: transposon mutagenesis in gram negative bacteria. Biotechnology 1, 784\u2013791 (1983).","journal-title":"Biotechnology"},{"key":"BFsrep32774_CR29","doi-asserted-by":"publisher","first-page":"3175","DOI":"10.1002\/j.1460-2075.1992.tb05394.x","volume":"11","author":"C Locht","year":"1992","unstructured":"Locht, C., Geoffroy, M. C. & Renauld, G. Common accessory genes for the Bordetella pertussis filamentous hemagglutinin and fimbriae share sequence similarities with the papC and papD gene families. EMBO J 11, 3175\u20133183 (1992).","journal-title":"EMBO J"},{"key":"BFsrep32774_CR30","doi-asserted-by":"publisher","first-page":"3057","DOI":"10.1093\/nar\/gkg426","volume":"31","author":"JM Rouillard","year":"2003","unstructured":"Rouillard, J. M., Zuker, M. & Gulari, E. OligoArray 2.0: design of oligonucleotide probes for DNA microarrays using a thermodynamic approach. Nucleic Acids Res 31, 3057\u20133062 (2003).","journal-title":"Nucleic Acids Res"},{"key":"BFsrep32774_CR31","first-page":"111","volume":"224","author":"GK Smyth","year":"2003","unstructured":"Smyth, G. K., Yang, Y. H. & Speed, T. Statistical issues in cDNA microarray data analysis. Methods Mol Biol 224, 111\u2013136 (2003).","journal-title":"Methods Mol Biol"},{"key":"BFsrep32774_CR32","first-page":"808","volume":"12","author":"I Lonnstedt","year":"2002","unstructured":"Lonnstedt, I. & Speed, T. Replicated microarray data. Stat Sinica 12, 808 (2002).","journal-title":"Stat Sinica"},{"key":"BFsrep32774_CR33","doi-asserted-by":"crossref","first-page":"289","DOI":"10.1111\/j.2517-6161.1995.tb02031.x","volume":"811","author":"Y Benjamini","year":"1995","unstructured":"Benjamini, Y. & Hochberg, Y. Controlling the False Discovery Rate - a Practical and Powerful Approach to Multiple Testing. J Roy Stat Soc B Met 811, 289\u2013300 (1995).","journal-title":"J Roy Stat Soc B Met"}],"container-title":["Scientific Reports"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.nature.com\/articles\/srep32774.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/srep32774","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/srep32774.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,6,19]],"date-time":"2024-06-19T09:56:37Z","timestamp":1718790997000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.nature.com\/articles\/srep32774"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2016,9,13]]},"references-count":33,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2016,12,16]]}},"alternative-id":["BFsrep32774"],"URL":"https:\/\/doi.org\/10.1038\/srep32774","relation":{},"ISSN":["2045-2322"],"issn-type":[{"value":"2045-2322","type":"electronic"}],"subject":[],"published":{"date-parts":[[2016,9,13]]},"assertion":[{"value":"10 March 2016","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"9 August 2016","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"13 September 2016","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"The authors declare no competing financial interests.","order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}],"article-number":"32774"}}