{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,9]],"date-time":"2025-10-09T21:16:29Z","timestamp":1760044589180},"reference-count":60,"publisher":"Springer Science and Business Media LLC","issue":"1","content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Genomics"],"published-print":{"date-parts":[[2014,12]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:sec><jats:title>Background<\/jats:title><jats:p>Upon infection of a mammalian host,<jats:italic>Bacillus anthracis<\/jats:italic>responds to host cues, and particularly to elevated temperature (37\u00b0C) and bicarbonate\/CO<jats:sub>2<\/jats:sub>concentrations, with increased expression of virulence factors that include the anthrax toxins and extracellular capsular layer. This response requires the presence of the pXO1 virulence plasmid-encoded pleiotropic regulator AtxA. To better understand the genetic basis of this response, we utilized a controlled<jats:italic>in vitro<\/jats:italic>system and Next Generation sequencing to determine and compare RNA expression profiles of the parental strain and an isogenic AtxA-deficient strain in a 2\u2009\u00d7\u20092 factorial design with growth environments containing or lacking carbon dioxide.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>We found 15 pXO1-encoded genes and 3 chromosomal genes that were strongly regulated by the separate or synergistic actions of AtxA and carbon dioxide. The majority of the regulated genes responded to both AtxA and carbon dioxide rather than to just one of these factors. Interestingly, we identified two previously unrecognized small RNAs that are highly expressed under physiological carbon dioxide concentrations in an AtxA-dependent manner. Expression levels of the two small RNAs were found to be higher than that of any other gene differentially expressed in response to these conditions. Secondary structure and small RNA-mRNA binding predictions for the two small RNAs suggest that they may perform important functions in regulating<jats:italic>B. anthracis<\/jats:italic>virulence.<\/jats:p><\/jats:sec><jats:sec><jats:title>Conclusions<\/jats:title><jats:p>A majority of genes on the virulence plasmid pXO1 that are regulated by the presence of either CO<jats:sub>2<\/jats:sub>or AtxA separately are also regulated synergistically in the presence of both. These results also elucidate novel pXO1-encoded small RNAs that are associated with virulence conditions.<\/jats:p><\/jats:sec>","DOI":"10.1186\/1471-2164-15-229","type":"journal-article","created":{"date-parts":[[2014,3,25]],"date-time":"2014-03-25T05:18:14Z","timestamp":1395724694000},"update-policy":"http:\/\/dx.doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":20,"title":["Transcriptome analysis identifies Bacillus anthracis genes that respond to CO2through an AtxA-dependent mechanism"],"prefix":"10.1186","volume":"15","author":[{"given":"Andrew T","family":"McKenzie","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Andrei P","family":"Pomerantsev","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Inka","family":"Sastalla","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Craig","family":"Martens","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Stacy M","family":"Ricklefs","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Kimmo","family":"Virtaneva","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Sarah","family":"Anzick","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Stephen F","family":"Porcella","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Stephen H","family":"Leppla","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2014,3,25]]},"reference":[{"key":"5953_CR1","doi-asserted-by":"crossref","first-page":"6509","DOI":"10.1128\/JB.181.20.6509-6515.1999","volume":"181","author":"RT Okinaka","year":"1999","unstructured":"Okinaka RT, Cloud K, Hampton O, Hoffmaster AR, Hill KK, Keim P, Koehler TM, Lamke G, Kumano S, Mahillon J, Manter D, Martinez Y, Ricke D, Svensson R, Jackson PJ: Sequence and organization of pXO1, the large Bacillus anthracis plasmid harboring the anthrax toxin genes. J Bacteriol. 1999, 181: 6509-6515.","journal-title":"J Bacteriol"},{"key":"5953_CR2","doi-asserted-by":"publisher","first-page":"81","DOI":"10.1038\/nature01586","volume":"423","author":"TD Read","year":"2003","unstructured":"Read TD, Peterson SN, Tourasse N, Baillie LW, Paulsen IT, Nelson KE, Tettelin H, Fouts DE, Eisen JA, Gill SR, Holtzapple EK, Okstad OA, Helgason E, Rilstone J, Wu M, Kolonay JF, Beanan MJ, Dodson RJ, Brinkac LM, Gwinn M, DeBoy RT, Madpu R, Daugherty SC, Durkin AS, Haft DH, Nelson WC, Peterson JD, Pop M, Khouri HM, Radune D, et al: The genome sequence of Bacillus anthracis Ames and comparison to closely related bacteria. Nature. 2003, 423: 81-86. 10.1038\/nature01586.","journal-title":"Nature"},{"key":"5953_CR3","doi-asserted-by":"publisher","first-page":"87","DOI":"10.1038\/nature01582","volume":"423","author":"N Ivanova","year":"2003","unstructured":"Ivanova N, Sorokin A, Anderson I, Galleron N, Candelon B, Kapatral V, Bhattacharyya A, Reznik G, Mikhailova N, Lapidus A, Chu L, Mazur M, Goltsman E, Larsen N, D'Souza M, Walunas T, Grechkin Y, Pusch G, Haselkorn R, Fonstein M, Ehrlich SD, Overbeek R, Kyrpides N: Genome sequence of Bacillus cereus and comparative analysis with Bacillus anthracis. Nature. 2003, 423: 87-91. 10.1038\/nature01582.","journal-title":"Nature"},{"key":"5953_CR4","doi-asserted-by":"publisher","first-page":"439","DOI":"10.1016\/j.mam.2009.07.003","volume":"30","author":"M Moayeri","year":"2009","unstructured":"Moayeri M, Leppla SH: Cellular and systemic effects of anthrax lethal toxin and edema toxin. Mol Aspects Med. 2009, 30: 439-455. 10.1016\/j.mam.2009.07.003.","journal-title":"Mol Aspects Med"},{"key":"5953_CR5","doi-asserted-by":"publisher","first-page":"243","DOI":"10.1146\/annurev.biochem.75.103004.142728","volume":"76","author":"JA Young","year":"2007","unstructured":"Young JA, Collier RJ: Anthrax toxin: receptor-binding, internalization, pore formation, and translocation. Annu Rev Biochem. 2007, 76: 243-265. 10.1146\/annurev.biochem.75.103004.142728.","journal-title":"Annu Rev Biochem"},{"key":"5953_CR6","doi-asserted-by":"publisher","first-page":"227","DOI":"10.1086\/341299","volume":"186","author":"S Makino","year":"2002","unstructured":"Makino S, Watarai M, Cheun HI, Shirahata T, Uchida I: Effect of the lower molecular capsule released from the cell surface of Bacillus anthracis on the pathogenesis of anthrax. J Infect Dis. 2002, 186: 227-233. 10.1086\/341299.","journal-title":"J Infect Dis"},{"key":"5953_CR7","doi-asserted-by":"publisher","first-page":"386","DOI":"10.1016\/j.mam.2009.07.004","volume":"30","author":"TM Koehler","year":"2009","unstructured":"Koehler TM: Bacillus anthracis physiology and genetics. Mol Aspects Med. 2009, 30: 386-396. 10.1016\/j.mam.2009.07.004.","journal-title":"Mol Aspects Med"},{"key":"5953_CR8","doi-asserted-by":"crossref","first-page":"2295","DOI":"10.1128\/iai.57.8.2295-2300.1989","volume":"57","author":"JM Bartkus","year":"1989","unstructured":"Bartkus JM, Leppla SH: Transcriptional regulation of the protective antigen gene of Bacillus anthracis. Infect Immun. 1989, 57: 2295-2300.","journal-title":"Infect Immun"},{"key":"5953_CR9","doi-asserted-by":"crossref","first-page":"5188","DOI":"10.1128\/jb.176.16.5188-5192.1994","volume":"176","author":"JC Sirard","year":"1994","unstructured":"Sirard JC, Mock M, Fouet A: The three Bacillus anthracis toxin genes are coordinately regulated by bicarbonate and temperature. J Bacteriol. 1994, 176: 5188-5192.","journal-title":"J Bacteriol"},{"key":"5953_CR10","doi-asserted-by":"publisher","first-page":"5108","DOI":"10.1128\/JB.187.15.5108-5114.2005","volume":"187","author":"M Drysdale","year":"2005","unstructured":"Drysdale M, Bourgogne A, Koehler TM: Transcriptional analysis of the Bacillus anthracis capsule regulators. J Bacteriol. 2005, 187: 5108-5114. 10.1128\/JB.187.15.5108-5114.2005.","journal-title":"J Bacteriol"},{"key":"5953_CR11","doi-asserted-by":"publisher","first-page":"735","DOI":"10.1016\/j.resmic.2010.09.006","volume":"161","author":"A Fouet","year":"2010","unstructured":"Fouet A: AtxA, a Bacillus anthracis global virulence regulator. Res Microbiol. 2010, 161: 735-742. 10.1016\/j.resmic.2010.09.006.","journal-title":"Res Microbiol"},{"key":"5953_CR12","doi-asserted-by":"publisher","first-page":"e4904","DOI":"10.1371\/journal.pone.0004904","volume":"4","author":"KD Passalacqua","year":"2009","unstructured":"Passalacqua KD, Varadarajan A, Byrd B, Bergman NH: Comparative transcriptional profiling of Bacillus cereus sensu lato strains during growth in CO2-bicarbonate and aerobic atmospheres. PLoS ONE. 2009, 4: e4904-10.1371\/journal.pone.0004904.","journal-title":"PLoS ONE"},{"key":"5953_CR13","doi-asserted-by":"publisher","first-page":"1626","DOI":"10.1128\/IAI.06061-11","volume":"80","author":"ZP Weiner","year":"2012","unstructured":"Weiner ZP, Glomski IJ: Updating perspectives on the initiation of Bacillus anthracis growth and dissemination through Its host. Infect Immun. 2012, 80: 1626-1633. 10.1128\/IAI.06061-11.","journal-title":"Infect Immun"},{"key":"5953_CR14","doi-asserted-by":"crossref","first-page":"5329","DOI":"10.1128\/jb.175.17.5329-5338.1993","volume":"175","author":"I Uchida","year":"1993","unstructured":"Uchida I, Hornung JM, Thorne CB, Klimpel KR, Leppla SH: Cloning and characterization of a gene whose product is a trans-activator of anthrax toxin synthesis. J Bacteriol. 1993, 175: 5329-5338.","journal-title":"J Bacteriol"},{"key":"5953_CR15","doi-asserted-by":"crossref","first-page":"586","DOI":"10.1128\/jb.176.3.586-595.1994","volume":"176","author":"TM Koehler","year":"1994","unstructured":"Koehler TM, Dai Z, Kaufman-Yarbray M: Regulation of the Bacillus anthracis protective antigen gene: CO2 and a trans-acting element activate transcription from one of two promoters. J Bacteriol. 1994, 176: 586-595.","journal-title":"J Bacteriol"},{"key":"5953_CR16","doi-asserted-by":"crossref","first-page":"2576","DOI":"10.1128\/iai.65.7.2576-2582.1997","volume":"65","author":"Z Dai","year":"1997","unstructured":"Dai Z, Koehler TM: Regulation of anthrax toxin activator gene (atxA) expression in Bacillus anthracis: temperature, not CO2\/bicarbonate, affects AtxA synthesis. Infect Immun. 1997, 65: 2576-2582.","journal-title":"Infect Immun"},{"key":"5953_CR17","doi-asserted-by":"publisher","first-page":"370","DOI":"10.1128\/JB.184.2.370-380.2002","volume":"184","author":"E Saile","year":"2002","unstructured":"Saile E, Koehler TM: Control of anthrax toxin gene expression by the transition state regulator abrB. J Bacteriol. 2002, 184: 370-380. 10.1128\/JB.184.2.370-380.2002.","journal-title":"J Bacteriol"},{"key":"5953_CR18","doi-asserted-by":"publisher","first-page":"6483","DOI":"10.1128\/JB.00766-08","volume":"190","author":"C Bongiorni","year":"2008","unstructured":"Bongiorni C, Fukushima T, Wilson AC, Chiang C, Mansilla MC, Hoch JA, Perego M: Dual promoters control the expression of the Bacillus anthracis virulence factor AtxA. J Bacteriol. 2008, 190: 6483-6492. 10.1128\/JB.00766-08.","journal-title":"J Bacteriol"},{"key":"5953_CR19","doi-asserted-by":"publisher","first-page":"109","DOI":"10.1111\/j.1365-2958.2009.06627.x","volume":"72","author":"AC Wilson","year":"2009","unstructured":"Wilson AC, Hoch JA, Perego M: Two small c-type cytochromes affect virulence gene expression in Bacillus anthracis. Mol Microbiol. 2009, 72: 109-123. 10.1111\/j.1365-2958.2009.06627.x.","journal-title":"Mol Microbiol"},{"key":"5953_CR20","doi-asserted-by":"publisher","first-page":"644","DOI":"10.1111\/j.1365-2958.2006.05543.x","volume":"63","author":"B Tsvetanova","year":"2007","unstructured":"Tsvetanova B, Wilson AC, Bongiorni C, Chiang C, Hoch JA, Perego M: Opposing effects of histidine phosphorylation regulate the AtxA virulence transcription factor in Bacillus anthracis. Mol Microbiol. 2007, 63: 644-655.","journal-title":"Mol Microbiol"},{"key":"5953_CR21","doi-asserted-by":"publisher","first-page":"4437","DOI":"10.1128\/IAI.00716-09","volume":"77","author":"W van Schaik","year":"2009","unstructured":"van Schaik W, Chateau A, Dillies MA, Coppee JY, Sonenshein AL, Fouet A: The global regulator CodY regulates toxin gene expression in Bacillus anthracis and is required for full virulence. Infect Immun. 2009, 77: 4437-4445. 10.1128\/IAI.00716-09.","journal-title":"Infect Immun"},{"key":"5953_CR22","doi-asserted-by":"publisher","first-page":"4445","DOI":"10.1096\/fj.11-188912","volume":"25","author":"A Chateau","year":"2011","unstructured":"Chateau A, van Schaik W, Six A, Aucher W, Fouet A: CodY regulation is required for full virulence and heme iron acquisition in Bacillus anthracis. FASEB J. 2011, 25: 4445-4456. 10.1096\/fj.11-188912.","journal-title":"FASEB J"},{"key":"5953_CR23","doi-asserted-by":"publisher","first-page":"634","DOI":"10.1111\/j.1365-2958.2011.07843.x","volume":"82","author":"TG Hammerstrom","year":"2011","unstructured":"Hammerstrom TG, Roh J, Nikonowicz EP, Koehler TM: Bacillus anthracis virulence regulator AtxA: oligomeric state, function, and CO(2) -signaling. Mol Microbiol. 2011, 82: 634-647. 10.1111\/j.1365-2958.2011.07843.x.","journal-title":"Mol Microbiol"},{"key":"5953_CR24","doi-asserted-by":"publisher","first-page":"249","DOI":"10.1016\/j.resmic.2010.03.003","volume":"161","author":"M Bertin","year":"2010","unstructured":"Bertin M, Chateau A, Fouet A: Full expression of Bacillus anthracis toxin gene in the presence of bicarbonate requires a 2.7-kb-long atxA mRNA that contains a terminator structure. Res Microbiol. 2010, 161: 249-259. 10.1016\/j.resmic.2010.03.003.","journal-title":"Res Microbiol"},{"key":"5953_CR25","doi-asserted-by":"publisher","first-page":"307","DOI":"10.1128\/JB.186.2.307-315.2004","volume":"186","author":"M Drysdale","year":"2004","unstructured":"Drysdale M, Bourgogne A, Hilsenbeck SG, Koehler TM: atxA controls Bacillus anthracis capsule synthesis via acpA and a newly discovered regulator, acpB. J Bacteriol. 2004, 186: 307-315. 10.1128\/JB.186.2.307-315.2004.","journal-title":"J Bacteriol"},{"key":"5953_CR26","doi-asserted-by":"publisher","first-page":"619","DOI":"10.1078\/1438-4221-00306","volume":"293","author":"T Mignot","year":"2004","unstructured":"Mignot T, Couture-Tosi E, Mesnage S, Mock M, Fouet A: In vivo Bacillus anthracis gene expression requires PagR as an intermediate effector of the AtxA signalling cascade. Int J Med Microbiol. 2004, 293: 619-624. 10.1078\/1438-4221-00306.","journal-title":"Int J Med Microbiol"},{"key":"5953_CR27","doi-asserted-by":"publisher","first-page":"2736","DOI":"10.1128\/IAI.71.5.2736-2743.2003","volume":"71","author":"A Bourgogne","year":"2003","unstructured":"Bourgogne A, Drysdale M, Hilsenbeck SG, Peterson SN, Koehler TM: Global effects of virulence gene regulators in a Bacillus anthracis strain with both virulence plasmids. Infect Immun. 2003, 71: 2736-2743. 10.1128\/IAI.71.5.2736-2743.2003.","journal-title":"Infect Immun"},{"key":"5953_CR28","doi-asserted-by":"publisher","first-page":"3203","DOI":"10.1128\/JB.00122-09","volume":"191","author":"KD Passalacqua","year":"2009","unstructured":"Passalacqua KD, Varadarajan A, Ondov BD, Okou DT, Zwick ME, Bergman NH: The structure and complexity of a bacterial transcriptome. J Bacteriol. 2009, 191: 3203-3211. 10.1128\/JB.00122-09.","journal-title":"J Bacteriol"},{"key":"5953_CR29","doi-asserted-by":"publisher","first-page":"5134","DOI":"10.1128\/JB.00422-09","volume":"191","author":"AP Pomerantsev","year":"2009","unstructured":"Pomerantsev AP, Camp A, Leppla SH: A new minimal replicon of Bacillus anthracis plasmid pXO1. J Bacteriol. 2009, 191: 5134-5146. 10.1128\/JB.00422-09.","journal-title":"J Bacteriol"},{"key":"5953_CR30","doi-asserted-by":"publisher","first-page":"5175","DOI":"10.1128\/IAI.00719-07","volume":"75","author":"M Moayeri","year":"2007","unstructured":"Moayeri M, Wiggins JF, Leppla SH: Anthrax protective antigen cleavage and clearance from the blood of mice and rats. Infect Immun. 2007, 75: 5175-5184. 10.1128\/IAI.00719-07.","journal-title":"Infect Immun"},{"key":"5953_CR31","doi-asserted-by":"publisher","first-page":"1124","DOI":"10.1073\/pnas.98.3.1124","volume":"98","author":"K Virtaneva","year":"2001","unstructured":"Virtaneva K, Wright FA, Tanner SM, Yuan B, Lemon WJ, Caligiuri MA, Bloomfield CD, de la Chapelle A, Krahe R: Expression profiling reveals fundamental biological differences in acute myeloid leukemia with isolated trisomy 8 and normal cytogenetics. Proc Natl Acad Sci USA. 2001, 98: 1124-1129. 10.1073\/pnas.98.3.1124.","journal-title":"Proc Natl Acad Sci USA"},{"key":"5953_CR32","doi-asserted-by":"publisher","first-page":"621","DOI":"10.1038\/nmeth.1226","volume":"5","author":"A Mortazavi","year":"2008","unstructured":"Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B: Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods. 2008, 5: 621-628. 10.1038\/nmeth.1226.","journal-title":"Nat Methods"},{"key":"5953_CR33","doi-asserted-by":"publisher","first-page":"9546","DOI":"10.1073\/pnas.0914005107","volume":"107","author":"R Bourgon","year":"2010","unstructured":"Bourgon R, Gentleman R, Huber W: Independent filtering increases detection power for high-throughput experiments. Proc Natl Acad Sci USA. 2010, 107: 9546-9551. 10.1073\/pnas.0914005107.","journal-title":"Proc Natl Acad Sci USA"},{"key":"5953_CR34","doi-asserted-by":"publisher","first-page":"R106","DOI":"10.1186\/gb-2010-11-10-r106","volume":"11","author":"S Anders","year":"2010","unstructured":"Anders S, Huber W: Differential expression analysis for sequence count data. Genome Biol. 2010, 11: R106-10.1186\/gb-2010-11-10-r106.","journal-title":"Genome Biol"},{"key":"5953_CR35","doi-asserted-by":"crossref","first-page":"289","DOI":"10.1111\/j.2517-6161.1995.tb02031.x","volume":"57","author":"Y Benjamini","year":"1995","unstructured":"Benjamini Y, Hochberg Y: Controlling the false discovery rate: a practical and powerful approach to multiple testing. J R Stat Soc Ser B Methodol. 1995, 57: 289-300.","journal-title":"J R Stat Soc Ser B Methodol"},{"key":"5953_CR36","doi-asserted-by":"publisher","first-page":"3389","DOI":"10.1093\/nar\/25.17.3389","volume":"25","author":"SF Altschul","year":"1997","unstructured":"Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ: Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 1997, 25: 3389-3402. 10.1093\/nar\/25.17.3389.","journal-title":"Nucleic Acids Res"},{"key":"5953_CR37","doi-asserted-by":"publisher","first-page":"2947","DOI":"10.1093\/bioinformatics\/btm404","volume":"23","author":"MA Larkin","year":"2007","unstructured":"Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R, Thompson JD, Gibson TJ, Higgins DG: Clustal W and Clustal X version 2.0. Bioinformatics. 2007, 23: 2947-2948. 10.1093\/bioinformatics\/btm404.","journal-title":"Bioinformatics"},{"key":"5953_CR38","doi-asserted-by":"publisher","first-page":"D225","DOI":"10.1093\/nar\/gkq1189","volume":"39","author":"A Marchler-Bauer","year":"2011","unstructured":"Marchler-Bauer A, Lu S, Anderson JB, Chitsaz F, Derbyshire MK, DeWeese-Scott C, Fong JH, Geer LY, Geer RC, Gonzales NR, Gwadz M, Hurwitz DI, Jackson JD, Ke Z, Lanczycki CJ, Lu F, Marchler GH, Mullokandov M, Omelchenko MV, Robertson CL, Song JS, Thanki N, Yamashita RA, Zhang D, Zhang N, Zheng C, Bryant SH: CDD: a Conserved Domain Database for the functional annotation of proteins. Nucleic Acids Res. 2011, 39: D225-D229. 10.1093\/nar\/gkq1189.","journal-title":"Nucleic Acids Res"},{"key":"5953_CR39","doi-asserted-by":"publisher","first-page":"49","DOI":"10.1186\/1741-7007-8-49","volume":"8","author":"OR Homann","year":"2010","unstructured":"Homann OR, Johnson AD: MochiView: versatile software for genome browsing and DNA motif analysis. BMC Biol. 2010, 8: 49-10.1186\/1741-7007-8-49.","journal-title":"BMC Biol"},{"key":"5953_CR40","doi-asserted-by":"publisher","first-page":"167","DOI":"10.1007\/BF00818163","volume":"125","author":"IL Hofacker","year":"1994","unstructured":"Hofacker IL, Fontana W, Stadler PF, Bonhoeffer LS, Tacker M, Schuster P: Fast folding and comparison of RNA secondary structures. Monatshefte fur Chemie\/Chem Mon. 1994, 125: 167-188. 10.1007\/BF00818163.","journal-title":"Monatshefte fur Chemie\/Chem Mon"},{"key":"5953_CR41","doi-asserted-by":"publisher","first-page":"W149","DOI":"10.1093\/nar\/gkr467","volume":"39","author":"F Eggenhofer","year":"2011","unstructured":"Eggenhofer F, Tafer H, Stadler PF, Hofacker IL: RNApredator: fast accessibility-based prediction of sRNA targets. Nucleic Acids Res. 2011, 39: W149-W154. 10.1093\/nar\/gkr467.","journal-title":"Nucleic Acids Res"},{"key":"5953_CR42","doi-asserted-by":"publisher","first-page":"e22705","DOI":"10.1371\/journal.pone.0022705","volume":"6","author":"X Ying","year":"2011","unstructured":"Ying X, Cao Y, Wu J, Liu Q, Cha L, Li W: sTarPicker: a method for efficient prediction of bacterial sRNA targets based on a two-step model for hybridization. PLoS ONE. 2011, 6: e22705-10.1371\/journal.pone.0022705.","journal-title":"PLoS ONE"},{"key":"5953_CR43","doi-asserted-by":"publisher","first-page":"387","DOI":"10.1016\/j.micinf.2011.11.009","volume":"14","author":"I Sastalla","year":"2011","unstructured":"Sastalla I, Leppla SH: Occurrence, recognition, and reversion of spontaneous, sporulation-deficient Bacillus anthracis mutants that arise during laboratory culture. Microbes Infect. 2011, 14: 387-391.","journal-title":"Microbes Infect"},{"key":"5953_CR44","doi-asserted-by":"publisher","first-page":"504","DOI":"10.1111\/j.1365-2958.2008.06169.x","volume":"68","author":"JW Kern","year":"2008","unstructured":"Kern JW, Schneewind O: BslA, a pXO1-encoded adhesin of Bacillus anthracis. Mol Microbiol. 2008, 68: 504-515. 10.1111\/j.1365-2958.2008.06169.x.","journal-title":"Mol Microbiol"},{"key":"5953_CR45","doi-asserted-by":"publisher","first-page":"7165","DOI":"10.1128\/JB.00903-09","volume":"191","author":"CM Ebrahimi","year":"2009","unstructured":"Ebrahimi CM, Kern JW, Sheen TR, Ebrahimi-Fardooee MA, van Sorge NM, Schneewind O, Doran KS: Penetration of the blood-brain barrier by Bacillus anthracis requires the pXO1-encoded BslA protein. J Bacteriol. 2009, 191: 7165-7173. 10.1128\/JB.00903-09.","journal-title":"J Bacteriol"},{"key":"5953_CR46","doi-asserted-by":"publisher","first-page":"324","DOI":"10.1111\/j.1365-2958.2009.06958.x","volume":"75","author":"J Kern","year":"2010","unstructured":"Kern J, Schneewind O: BslA, the S-layer adhesin of B. anthracis, is a virulence factor for anthrax pathogenesis. Mol Microbiol. 2010, 75: 324-332. 10.1111\/j.1365-2958.2009.06958.x.","journal-title":"Mol Microbiol"},{"key":"5953_CR47","doi-asserted-by":"publisher","first-page":"2099","DOI":"10.1128\/AEM.02066-08","volume":"75","author":"I Sastalla","year":"2009","unstructured":"Sastalla I, Chim K, Cheung GY, Pomerantsev AP, Leppla SH: Codon-optimized fluorescent proteins designed for expression in low GC Gram-positive bacteria. Appl Environ Microbiol. 2009, 75: 2099-2110. 10.1128\/AEM.02066-08.","journal-title":"Appl Environ Microbiol"},{"key":"5953_CR48","doi-asserted-by":"publisher","first-page":"2501","DOI":"10.1099\/mic.0.2007\/016162-0","volume":"154","author":"M Hadjifrangiskou","year":"2008","unstructured":"Hadjifrangiskou M, Koehler TM: Intrinsic curvature associated with the coordinately regulated anthrax toxin gene promoters. Microbiology. 2008, 154: 2501-2512. 10.1099\/mic.0.2007\/016162-0.","journal-title":"Microbiology"},{"key":"5953_CR49","doi-asserted-by":"crossref","first-page":"4485","DOI":"10.1128\/JB.181.15.4485-4492.1999","volume":"181","author":"AR Hoffmaster","year":"1999","unstructured":"Hoffmaster AR, Koehler TM: Autogenous regulation of the Bacillus anthracis pag operon. J Bacteriol. 1999, 181: 4485-4492.","journal-title":"J Bacteriol"},{"key":"5953_CR50","first-page":"a003798","volume":"3","author":"S Gottesman","year":"2010","unstructured":"Gottesman S, Storz G: Bacterial small RNA regulators: versatile roles and rapidly evolving variations. Cold Spring Harb Perspect Biol. 2010, 3: a003798-","journal-title":"Cold Spring Harb Perspect Biol"},{"key":"5953_CR51","doi-asserted-by":"publisher","first-page":"e10986","DOI":"10.1371\/journal.pone.0010986","volume":"5","author":"SR Klee","year":"2010","unstructured":"Klee SR, Brzuszkiewicz EB, Nattermann H, Bruggemann H, Dupke S, Wollherr A, Franz T, Pauli G, Appel B, Liebl W, Couacy-Hymann E, Boesch C, Meyer FD, Leendertz FH, Ellerbrok H, Gottschalk G, Grunow R, Liesegang H: The genome of a Bacillus isolate causing anthrax in chimpanzees combines chromosomal properties of B. cereus with B. anthracis virulence plasmids. PLoS ONE. 2010, 5: e10986-10.1371\/journal.pone.0010986.","journal-title":"PLoS ONE"},{"key":"5953_CR52","doi-asserted-by":"publisher","first-page":"8449","DOI":"10.1073\/pnas.0402414101","volume":"101","author":"AR Hoffmaster","year":"2004","unstructured":"Hoffmaster AR, Ravel J, Rasko DA, Chapman GD, Chute MD, Marston CK, De BK, Sacchi CT, Fitzgerald C, Mayer LW, Maiden MC, Priest FG, Barker M, Jiang L, Cer RZ, Rilstone J, Peterson SN, Weyant RS, Galloway DR, Read TD, Popovic T, Fraser CM: Identification of anthrax toxin genes in a Bacillus cereus associated with an illness resembling inhalation anthrax. Proc Natl Acad Sci USA. 2004, 101: 8449-8454. 10.1073\/pnas.0402414101.","journal-title":"Proc Natl Acad Sci USA"},{"key":"5953_CR53","doi-asserted-by":"publisher","first-page":"3352","DOI":"10.1128\/JCM.00561-06","volume":"44","author":"AR Hoffmaster","year":"2006","unstructured":"Hoffmaster AR, Hill KK, Gee JE, Marston CK, De BK, Popovic T, Sue D, Wilkins PP, Avashia SB, Drumgoole R, Helma CH, Ticknor LO, Okinaka RT, Jackson PJ: Characterization of Bacillus cereus isolates associated with fatal pneumonias: strains are closely related to Bacillus anthracis and harbor B. anthracis virulence genes. J Clin Microbiol. 2006, 44: 3352-3360. 10.1128\/JCM.00561-06.","journal-title":"J Clin Microbiol"},{"key":"5953_CR54","doi-asserted-by":"publisher","first-page":"100","DOI":"10.1016\/j.mib.2008.02.001","volume":"11","author":"A Srivatsan","year":"2008","unstructured":"Srivatsan A, Wang JD: Control of bacterial transcription, translation and replication by (p)ppGpp. Curr Opin Microbiol. 2008, 11: 100-105. 10.1016\/j.mib.2008.02.001.","journal-title":"Curr Opin Microbiol"},{"key":"5953_CR55","doi-asserted-by":"publisher","first-page":"55","DOI":"10.1038\/nrg1749","volume":"7","author":"DB Allison","year":"2006","unstructured":"Allison DB, Cui X, Page GP, Sabripour M: Microarray data analysis: from disarray to consolidation and consensus. Nat Rev Genet. 2006, 7: 55-65. 10.1038\/nrg1749.","journal-title":"Nat Rev Genet"},{"key":"5953_CR56","doi-asserted-by":"publisher","first-page":"e83","DOI":"10.1371\/journal.pbio.0060083","volume":"6","author":"EN Smith","year":"2008","unstructured":"Smith EN, Kruglyak L: Gene-environment interaction in yeast gene expression. PLoS Biol. 2008, 6: e83-10.1371\/journal.pbio.0060083.","journal-title":"PLoS Biol"},{"key":"5953_CR57","doi-asserted-by":"publisher","first-page":"72","DOI":"10.4161\/viru.1.2.10752","volume":"1","author":"MB Jones","year":"2010","unstructured":"Jones MB, Peterson SN, Benn R, Braisted JC, Jarrahi B, Shatzkes K, Ren D, Wood TK, Blaser MJ: Role of luxS in Bacillus anthracis growth and virulence factor expression. Virulence. 2010, 1: 72-83. 10.4161\/viru.1.2.10752.","journal-title":"Virulence"},{"key":"5953_CR58","doi-asserted-by":"publisher","first-page":"1268","DOI":"10.1126\/science.1176951","volume":"326","author":"M Guell","year":"2009","unstructured":"Guell M, van Noort V, Yus E, Chen WH, Leigh-Bell J, Michalodimitrakis K, Yamada T, Arumugam M, Doerks T, Kuhner S, Rode M, Suyama M, Schmidt S, Gavin AC, Bork P, Serrano L: Transcriptome complexity in a genome-reduced bacterium. Science. 2009, 326: 1268-1271. 10.1126\/science.1176951.","journal-title":"Science"},{"key":"5953_CR59","doi-asserted-by":"publisher","first-page":"185","DOI":"10.1038\/nrmicro2261","volume":"8","author":"SC Dillon","year":"2010","unstructured":"Dillon SC, Dorman CJ: Bacterial nucleoid-associated proteins, nucleoid structure and gene expression. Nat Rev Microbiol. 2010, 8: 185-195. 10.1038\/nrmicro2261.","journal-title":"Nat Rev Microbiol"},{"key":"5953_CR60","doi-asserted-by":"publisher","first-page":"4234","DOI":"10.1099\/mic.0.2007\/010355-0","volume":"153","author":"W van Schaik","year":"2007","unstructured":"van Schaik W, Prigent J, Fouet A: The stringent response of Bacillus anthracis contributes to sporulation but not to virulence. Microbiology. 2007, 153: 4234-4239. 10.1099\/mic.0.2007\/010355-0.","journal-title":"Microbiology"}],"container-title":["BMC Genomics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2164-15-229.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,5,25]],"date-time":"2024-05-25T09:41:57Z","timestamp":1716630117000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcgenomics.biomedcentral.com\/articles\/10.1186\/1471-2164-15-229"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2014,3,25]]},"references-count":60,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2014,12]]}},"alternative-id":["5953"],"URL":"https:\/\/doi.org\/10.1186\/1471-2164-15-229","relation":{},"ISSN":["1471-2164"],"issn-type":[{"value":"1471-2164","type":"electronic"}],"subject":[],"published":{"date-parts":[[2014,3,25]]},"assertion":[{"value":"9 July 2013","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"12 March 2014","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"25 March 2014","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}}],"article-number":"229"}}