Divergence of the SigB regulon and pathogenesis of the Bacillus cereus sensu lato group

BMC Genomics

Volumn 13, Issue 1, 2012, Pages

  Scott II, Edgar ^a   Dyer, David W ^a  

^a UNIVERSITY OF OKLAHOMA COLLEGE OF MEDICINE   (United States)

Author keywords

Generalized stress response; Microbial evolution; SigB sigma factor

Indexed keywords

ARTICLE; BACILLUS; BACILLUS ANTHRACIS; BACILLUS CEREUS; BACILLUS CYTOTOXICUS; BACILLUS MYCOIDES; BACILLUS PSEUDOMYCOIDES; BACILLUS WEIHENSTEPHANENSIS; BACTERIAL GENOME; COMPUTER MODEL; CONTROLLED STUDY; GENE STRUCTURE; GENETIC VARIABILITY; HORIZONTAL GENE TRANSFER; LISTERIA; NONHUMAN; NUCLEOTIDE SEQUENCE; PATHOGENICITY; PROMOTER REGION; REGULON; SIGB REGULON; STAPHYLOCOCCUS; STRESS; TRANSCRIPTION REGULATION;

BACILLUS; BACTERIAL PROTEINS; BINDING SITES; EVOLUTION, MOLECULAR; GENE TRANSFER, HORIZONTAL; GENOME, BACTERIAL; MULTIGENE FAMILY; PHYLOGENY; REGULON; SIGMA FACTOR;

BACILLUS ANTHRACIS; BACILLUS CEREUS; BACILLUS MYCOIDES; BACILLUS PSEUDOMYCOIDES; BACILLUS THURINGIENSIS; BACILLUS WEIHENSTEPHANENSIS; LISTERIA; STAPHYLOCOCCUS;

EID: 84867652597     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-13-564     Document Type: Article

References (100)

1. Rooney AP, Price NP, Ehrhardt C, Swezey JL, Bannan JD. Phylogeny and molecular taxonomy of the Bacillus subtilis species complex and description of Bacillus subtilis subsp. inaquosorum subsp. nov. Int J Syst Evol Microbiol 2009, 59(Pt 10):2429-2436.
2. Hadjifrangiskou M, Chen Y, Koehler TM. The alternative sigma factor sigmaH is required for toxin gene expression by Bacillus anthracis. J Bacteriol 2007, 189(5):1874-1883. 10.1128/JB.01333-06, 1855707, 17189374.
3. Koehler TM. Bacillus anthracis physiology and genetics. Mol Aspects Med 2009, 30(6):386-396. 10.1016/j.mam.2009.07.004, 2784286, 19654018.
4. Lapidus A, Goltsman E, Auger S, Galleron N, Segurens B, Dossat C, Land ML, Broussolle V, Brillard J, Guinebretiere MH, et al. Extending the Bacillus cereus group genomics to putative food-borne pathogens of different toxicity. Chem Biol Interact 2008, 171(2):236-249. 10.1016/j.cbi.2007.03.003, 17434157.
5. Soufiane B, Cote JC. Discrimination among Bacillus thuringiensis H serotypes, serovars and strains based on 16S rRNA, gyrB and aroE gene sequence analyses. Antonie Van Leeuwenhoek 2009, 95(1):33-45. 10.1007/s10482-008-9285-4, 18839329.
6. Helgason E, Okstad OA, Caugant DA, Johansen HA, Fouet A, Mock M, Hegna I, Kolsto AB. Bacillus anthracis, Bacillus cereus, and Bacillus thuringiensis-one species on the basis of genetic evidence. Appl Environ Microbiol 2000, 66(6):2627-2630. 10.1128/AEM.66.6.2627-2630.2000, 110590, 10831447.
7. Schmidt TR, Scott EJ, Dyer DW. Whole-genome phylogenies of the family Bacillaceae and expansion of the sigma factor gene family in the Bacillus cereus species-group. BMC Genomics 2011, 12:430. 10.1186/1471-2164-12-430, 3171730, 21864360.
8. Tourasse NJ, Helgason E, Klevan A, Sylvestre P, Moya M, Haustant M, Okstad OA, Fouet A, Mock M, Kolsto AB. Extended and global phylogenetic view of the Bacillus cereus group population by combination of MLST, AFLP, and MLEE genotyping data. Food Microbiol 2011, 28(2):236-244. 10.1016/j.fm.2010.06.014, 21315979.
9. Tourasse NJ, Helgason E, Okstad OA, Hegna IK, Kolsto AB. The Bacillus cereus group: novel aspects of population structure and genome dynamics. J Appl Microbiol 2006, 101(3):579-593. 10.1111/j.1365-2672.2006.03087.x, 16907808.
10. Tourasse NJ, Kolsto AB. SuperCAT: a supertree database for combined and integrative multilocus sequence typing analysis of the Bacillus cereus group of bacteria (including B. cereus, B. anthracis and B. thuringiensis). Nucleic Acids Res 2008, 36(Database issue):D461-D468. 2238978, 17982177.
11. Hoffmaster AR, Novak RT, Marston CK, Gee JE, Helsel L, Pruckler JM, Wilkins PP. Genetic diversity of clinical isolates of Bacillus cereus using multilocus sequence typing. BMC Microbiol 2008, 8:191. 10.1186/1471-2180-8-191, 2585095, 18990211.
12. Auger S, Galleron N, Bidnenko E, Ehrlich SD, Lapidus A, Sorokin A. The genetically remote pathogenic strain NVH391-98 of the Bacillus cereus group is representative of a cluster of thermophilic strains. Appl Environ Microbiol 2008, 74(4):1276-1280. 10.1128/AEM.02242-07, 2258573, 18156332.
13. Stenfors Arnesen LP, Fagerlund A, Granum PE. From soil to gut: Bacillus cereus and its food poisoning toxins. FEMS Microbiol Rev 2008, 32(4):579-606. 10.1111/j.1574-6976.2008.00112.x, 18422617.
14. Moyer AL, Ramadan RT, Novosad BD, Astley R, Callegan MC. Bacillus cereus-induced permeability of the blood-ocular barrier during experimental endophthalmitis. Invest Ophthalmol Vis Sci 2009, 50(8):3783-3793. 10.1167/iovs.08-3051, 2880527, 19264886.
15. Latsios G, Petrogiannopoulos C, Hartzoulakis G, Kondili L, Bethimouti K, Zaharof A. Liver abscess due to Bacillus cereus: a case report. Clin Microbiol Infect 2003, 9(12):1234-1237. 10.1111/j.1469-0691.2003.00795.x, 14686990.
16. Psiachou-Leonard E, Sidi V, Tsivitanidou M, Gompakis N, Koliouskas D, Roilides E. Brain abscesses resulting from Bacillus cereus and an Aspergillus-like mold. J Pediatr Hematol Oncol 2002, 24(7):569-571. 10.1097/00043426-200210000-00016, 12368698.
17. Steggles JR, Wang J, Ellar DJ. Discovery of Bacillus thuringiensis virulence genes using signature-tagged mutagenesis in an insect model of septicaemia. Curr Microbiol 2006, 53(4):303-310. 10.1007/s00284-006-0037-2, 16941243.
18. Fedhila S, Nel P, Lereclus D. The InhA2 metalloprotease of Bacillus thuringiensis strain 407 is required for pathogenicity in insects infected via the oral route. J Bacteriol 2002, 184(12):3296-3304. 10.1128/JB.184.12.3296-3304.2002, 135110, 12029046.
19. Wei JZ, Hale K, Carta L, Platzer E, Wong C, Fang SC, Aroian RV. Bacillus thuringiensis crystal proteins that target nematodes. Proc Natl Acad Sci USA 2003, 100(5):2760-2765. 10.1073/pnas.0538072100, 151414, 12598644.
20. Cappello M, Bungiro RD, Harrison LM, Bischof LJ, Griffitts JS, Barrows BD, Aroian RV. A purified Bacillus thuringiensis crystal protein with therapeutic activity against the hookworm parasite Ancylostoma ceylanicum. Proc Natl Acad Sci USA 2006, 103(41):15154-15159. 10.1073/pnas.0607002103, 1622792, 17005719.
21. Rae R, Riebesell M, Dinkelacker I, Wang Q, Herrmann M, Weller AM, Dieterich C, Sommer RJ. Isolation of naturally associated bacteria of necromenic Pristionchus nematodes and fitness consequences. J Exp Biol 2008, 211(Pt 12):1927-1936.
22. Gunawan S, Tufts DM, Bextine BR. Molecular identification of hemolymph-associated symbiotic bacteria in red imported fire ant larvae. Curr Microbiol 2008, 57(6):575-579. 10.1007/s00284-008-9245-2, 18795363.
23. Cardazzo B, Negrisolo E, Carraro L, Alberghini L, Patarnello T, Giaccone V. Multiple-locus sequence typing and analysis of toxin genes in Bacillus cereus food-borne isolates. Appl Environ Microbiol 2008, 74(3):850-860. 10.1128/AEM.01495-07, 2227710, 18083872.
24. Ko KS, Kim JW, Kim JM, Kim W, Chung SI, Kim IJ, Kook YH. Population structure of the Bacillus cereus group as determined by sequence analysis of six housekeeping genes and the plcR Gene. Infect Immun 2004, 72(9):5253-5261. 10.1128/IAI.72.9.5253-5261.2004, 517475, 15322020.
25. Aronson A. Sporulation and delta-endotoxin synthesis by Bacillus thuringiensis. Cell Mol Life Sci 2002, 59(3):417-425. 10.1007/s00018-002-8434-6, 11964120.
26. Rasko DA, Altherr MR, Han CS, Ravel J. Genomics of the Bacillus cereus group of organisms. FEMS Microbiol Rev 2005, 29(2):303-329.
27. Han CS, Xie G, Challacombe JF, Altherr MR, Bhotika SS, Brown N, Bruce D, Campbell CS, Campbell ML, Chen J, et al. Pathogenomic sequence analysis of Bacillus cereus and Bacillus thuringiensis isolates closely related to Bacillus anthracis. J Bacteriol 2006, 188(9):3382-3390. 10.1128/JB.188.9.3382-3390.2006, 1447445, 16621833.
28. 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(3):e4904. 10.1371/journal.pone.0004904, 2654142, 19295911.
29. Huynen MA, Bork P. Measuring genome evolution. Proc Natl Acad Sci USA 1998, 95(11):5849-5856. 10.1073/pnas.95.11.5849, 34486, 9600883.
30. Lozada-Chavez I, Angarica VE, Collado-Vides J, Contreras-Moreira B. The role of DNA-binding specificity in the evolution of bacterial regulatory networks. J Mol Biol 2008, 379(3):627-643. 10.1016/j.jmb.2008.04.008, 2491489, 18466918.
31. Lozada-Chavez I, Janga SC, Collado-Vides J. Bacterial regulatory networks are extremely flexible in evolution. Nucleic Acids Res 2006, 34(12):3434-3445. 10.1093/nar/gkl423, 1524901, 16840530.
32. Mittenhuber G. A phylogenomic study of the general stress response sigma factor sigmaB of Bacillus subtilis and its regulatory proteins. J Mol Microbiol Biotechnol 2002, 4(4):427-452.
33. Becker LA, Cetin MS, Hutkins RW, Benson AK. Identification of the gene encoding the alternative sigma factor sigmaB from Listeria monocytogenes and its role in osmotolerance. J Bacteriol 1998, 180(17):4547-4554. 107466, 9721294.
34. Becker LA, Evans SN, Hutkins RW, Benson AK. Role of sigma(B) in adaptation of Listeria monocytogenes to growth at low temperature. J Bacteriol 2000, 182(24):7083-7087. 10.1128/JB.182.24.7083-7087.2000, 94839, 11092874.
35. Begley M, Hill C, Ross RP. Tolerance of Listeria monocytogenes to cell envelope-acting antimicrobial agents is dependent on SigB. Appl Environ Microbiol 2006, 72(3):2231-2234. 10.1128/AEM.72.3.2231-2234.2006, 1393204, 16517678.
36. Kazmierczak MJ, Mithoe SC, Boor KJ, Wiedmann M. Listeria monocytogenes sigma B regulates stress response and virulence functions. J Bacteriol 2003, 185(19):5722-5734. 10.1128/JB.185.19.5722-5734.2003, 193959, 13129943.
37. Pintens V, Massonet C, Merckx R, Vandecasteele S, Peetermans WE, Knobloch JK, Van Eldere J. The role of sigmaB in persistence of Staphylococcus epidermidis foreign body infection. Microbiology 2008, 154(Pt 9):2827-2836.
38. Oliver HF, Orsi RH, Wiedmann M, Boor KJ. Listeria monocytogenes {sigma}B has a small core regulon and a conserved role in virulence but makes differential contributions to stress tolerance across a diverse collection of strains. Appl Environ Microbiol 2010, 76(13):4216-4232. 10.1128/AEM.00031-10, 2897421, 20453120.
39. Inose Y, Takeshita SL, Hidaka T, Higashide M, Maruyama A, Hayashi H, Morikawa K, Ohta T. Genetic characterization of the natural SigB variants found in clinical isolates of Staphylococcus aureus. J Gen Appl Microbiol 2006, 52(5):259-271. 10.2323/jgam.52.259, 17310069.
40. Singh VK, Schmidt JL, Jayaswal RK, Wilkinson BJ. Impact of sigB mutation on Staphylococcus aureus oxacillin and vancomycin resistance varies with parental background and method of assessment. Int J Antimicrob Agents 2003, 21(3):256-261. 10.1016/S0924-8579(02)00359-X, 12636988.
41. Guinebretiere MH, Auger S, Galleron N, Contzen M, De Sarrau B, De Buyser ML, Lamberet G, Fagerlund A, Granum PE, Lereclus D, et al. Bacillus cytotoxicus sp. nov. is a new thermotolerant species of the Bacillus cereus group occasionally associated with food poisoning. Int J Syst Evol Microbiol 2012, [Epub Feb. 17].
42. Novichkov PS, Wolf YI, Dubchak I, Koonin EV. Trends in prokaryotic evolution revealed by comparison of closely related bacterial and archaeal genomes. J Bacteriol 2009, 191(1):65-73. 10.1128/JB.01237-08, 2612427, 18978059.
43. Rambukkana A. M. leprae genome sequence. Trends Microbiol 2001, 9(4):157.
44. van Schaik W, van der Voort M, Molenaar D, Moezelaar R, de Vos WM, Abee T. Identification of the sigmaB regulon of Bacillus cereus and conservation of sigmaB-regulated genes in low-GC-content gram-positive bacteria. J Bacteriol 2007, 189(12):4384-4390. 10.1128/JB.00313-07, 1913364, 17416654.
45. van Schaik W, Zwietering MH, de Vos WM, Abee T. Identification of sigmaB-dependent genes in Bacillus cereus by proteome and in vitro transcription analysis. J Bacteriol 2004, 186(13):4100-4109. 10.1128/JB.186.13.4100-4109.2004, 421595, 15205411.
46. Sorokin V, Severinov K, Gelfand MS. Systematic prediction of control proteins and their DNA binding sites. Nucleic Acids Res 2009, 37(2):441-451. 2632904, 19056824.
47. Sierro N, Makita Y, de Hoon M, Nakai K. DBTBS: a database of transcriptional regulation in Bacillus subtilis containing upstream intergenic conservation information. Nucleic Acids Res 2008, 36(Database issue):D93-96. 2247474, 17962296.
48. Nannapaneni P, Hertwig F, Depke M, Hecker M, Mader U, Volker U, Steil L, van Hijum SA. Defining the structure of the general stress regulon of Bacillus subtilis using targeted microarray analysis and random forest classification. Microbiology 2012, 158(Pt 3):696-707.
49. Schulthess B, Bloes DA, Francois P, Girard M, Schrenzel J, Bischoff M, Berger-Bachi B. The sigmaB-dependent yabJ-spoVG operon is involved in the regulation of extracellular nuclease, lipase, and protease expression in Staphylococcus aureus. J Bacteriol 2011, 193(18):4954-4962. 10.1128/JB.05362-11, 3165683, 21725011.
50. Hu Y, Oliver HF, Raengpradub S, Palmer ME, Orsi RH, Wiedmann M, Boor KJ. Transcriptomic and phenotypic analyses suggest a network between the transcriptional regulators HrcA and sigmaB in Listeria monocytogenes. Appl Environ Microbiol 2007, 73(24):7981-7991. 10.1128/AEM.01281-07, 2168140, 17965207.
51. Hu Y, Raengpradub S, Schwab U, Loss C, Orsi RH, Wiedmann M, Boor KJ. Phenotypic and transcriptomic analyses demonstrate interactions between the transcriptional regulators CtsR and Sigma B in Listeria monocytogenes. Appl Environ Microbiol 2007, 73(24):7967-7980. 10.1128/AEM.01085-07, 2168136, 17933929.
52. McGann P, Wiedmann M, Boor KJ. The alternative sigma factor sigma B and the virulence gene regulator PrfA both regulate transcription of Listeria monocytogenes internalins. Appl Environ Microbiol 2007, 73(9):2919-2930. 10.1128/AEM.02664-06, 1892873, 17337550.
53. Callegan MC, Kane ST, Cochran DC, Gilmore MS, Gominet M, Lereclus D. Relationship of plcR-regulated factors to Bacillus endophthalmitis virulence. Infect Immun 2003, 71(6):3116-3124. 10.1128/IAI.71.6.3116-3124.2003, 155772, 12761089.
54. Lopez CS, Heras H, Garda H, Ruzal S, Sanchez-Rivas C, Rivas E. Biochemical and biophysical studies of Bacillus subtilis envelopes under hyperosmotic stress. Int J Food Microbiol 2000, 55(1-3):137-142.
55. Kontinen VP, Helander IM, Tokuda H. The secG deletion mutation of Escherichia coli is suppressed by expression of a novel regulatory gene of Bacillus subtilis. FEBS Lett 1996, 389(3):281-284. 10.1016/0014-5793(96)00602-3, 8766716.
56. Mikhaleva NI, Golovastov VV, Zolov SN, Bogdanov MV, Dowhan W, Nesmeyanova MA. Depletion of phosphatidylethanolamine affects secretion of Escherichia coli alkaline phosphatase and its transcriptional expression. FEBS Lett 2001, 493(2-3):85-90.
57. Lopez CS, Alice AF, Heras H, Rivas EA, Sanchez-Rivas C. Role of anionic phospholipids in the adaptation of Bacillus subtilis to high salinity. Microbiology 2006, 152(Pt 3):605-616.
58. Kanemasa Y, Takatsu T, Sasai K, Kojima I, Hayashi H. The salt-resistance mechanism of Staphylococcus aureus examined by salt-sensitive mutants. Acta Med Okayama 1976, 30(4):271-276.
59. Ivanisevic R, Milic M, Ajdic D, Rakonjac J, Savic DJ. Nucleotide sequence, mutational analysis, transcriptional start site, and product analysis of nov, the gene which affects Escherichia coli K-12 resistance to the gyrase inhibitor novobiocin. J Bacteriol 1995, 177(7):1766-1771. 176804, 7896699.
60. Clark DP, Beard JP. Altered phospholipid composition in mutants of Escherichia coli sensitive or resistant to organic solvents. J Gen Microbiol 1979, 113(2):267-274. 10.1099/00221287-113-2-267, 92527.
61. Peleg AY, Miyakis S, Ward DV, Earl AM, Rubio A, Cameron DR, Pillai S, Moellering RC, Eliopoulos GM. Whole genome characterization of the mechanisms of daptomycin resistance in clinical and laboratory derived isolates of Staphylococcus aureus. PLoS One 2012, 7(1):e28316. 10.1371/journal.pone.0028316, 3253072, 22238576.
62. Palmer KL, Daniel A, Hardy C, Silverman J, Gilmore MS. Genetic basis for daptomycin resistance in enterococci. Antimicrob Agents Chemother 2011, 55(7):3345-3356. 10.1128/AAC.00207-11, 3122436, 21502617.
63. Galvez A, Valdivia E, Martinez M, Maqueda M. Effect of peptide AS-48 on Enterococcus faecalis subsp. liquefaciens S-47. Antimicrob Agents Chemother 1989, 33(5):641-645. 10.1128/AAC.33.5.641, 172505, 2473710.
64. Mukhopadhyay K, Whitmire W, Xiong YQ, Molden J, Jones T, Peschel A, Staubitz P, Adler-Moore J, McNamara PJ, Proctor RA, et al. In vitro susceptibility of Staphylococcus aureus to thrombin-induced platelet microbicidal protein-1 (tPMP-1) is influenced by cell membrane phospholipid composition and asymmetry. Microbiology 2007, 153(Pt 4):1187-1197.
65. Kawai F, Shoda M, Harashima R, Sadaie Y, Hara H, Matsumoto K. Cardiolipin domains in Bacillus subtilis marburg membranes. J Bacteriol 2004, 186(5):1475-1483. 10.1128/JB.186.5.1475-1483.2004, 344405, 14973018.
66. Kaminski WE, Piehler A, Wenzel JJ. ABC A-subfamily transporters: structure, function and disease. Biochim Biophys Acta 2006, 1762(5):510-524. 10.1016/j.bbadis.2006.01.011, 16540294.
67. Malla S, Niraula NP, Liou K, Sohng JK. Self-resistance mechanism in Streptomyces peucetius: overexpression of drrA, drrB and drrC for doxorubicin enhancement. Microbiol Res 2010, 165(4):259-267. 10.1016/j.micres.2009.04.002, 19651502.
68. Podlesek Z, Comino A, Herzog-Velikonja B, Zgur-Bertok D, Komel R, Grabnar M. Bacillus licheniformis bacitracin-resistance ABC transporter: relationship to mammalian multidrug resistance. Mol Microbiol 1995, 16(5):969-976. 10.1111/j.1365-2958.1995.tb02322.x, 7476193.
69. Masure HR, Pearce BJ, Shio H, Spellerberg B. Membrane targeting of RecA during genetic transformation. Mol Microbiol 1998, 27(4):845-852. 10.1046/j.1365-2958.1998.00732.x, 9515709.
70. Kaimer C, Graumann PL. Bacillus subtilis CinA is a stationary phase-induced protein that localizes to the nucleoid and plays a minor role in competent cells. Arch Microbiol 2010, 192(7):549-557. 10.1007/s00203-010-0583-7, 20480359.
71. Au N, Kuester-Schoeck E, Mandava V, Bothwell LE, Canny SP, Chachu K, Colavito SA, Fuller SN, Groban ES, Hensley LA, et al. Genetic composition of the Bacillus subtilis SOS system. J Bacteriol 2005, 187(22):7655-7666. 10.1128/JB.187.22.7655-7666.2005, 1280312, 16267290.
72. Daniel RA, Harry EJ, Errington J. Role of penicillin-binding protein PBP 2B in assembly and functioning of the division machinery of Bacillus subtilis. Mol Microbiol 2000, 35(2):299-311. 10.1046/j.1365-2958.2000.01724.x, 10652091.
73. Errington J, Daniel RA, Scheffers DJ. Cytokinesis in bacteria. Microbiol Mol Biol Rev 2003, 67(1):52-65. table of contents, 10.1128/MMBR.67.1.52-65.2003, 150516, 12626683.
74. Hubscher J, Luthy L, Berger-Bachi B, Stutzmann Meier P. Phylogenetic distribution and membrane topology of the LytR-CpsA-Psr protein family. BMC Genomics 2008, 9:617. 10.1186/1471-2164-9-617, 2632651, 19099556.
75. Lazarevic V, Margot P, Soldo B, Karamata D. Sequencing and analysis of the Bacillus subtilis lytRABC divergon: a regulatory unit encompassing the structural genes of the N-acetylmuramoyl-L-alanine amidase and its modifier. J Gen Microbiol 1992, 138(9):1949-1961. 10.1099/00221287-138-9-1949, 1357079.
76. Johnsborg O, Havarstein LS. Pneumococcal LytR, a protein from the LytR-CpsA-Psr family, is essential for normal septum formation in Streptococcus pneumoniae. J Bacteriol 2009, 191(18):5859-5864. 10.1128/JB.00724-09, 2737952, 19581359.
77. Chatfield CH, Koo H, Quivey RG. The putative autolysin regulator LytR in Streptococcus mutans plays a role in cell division and is growth-phase regulated. Microbiology 2005, 151(Pt 2):625-631.
78. Hubscher J, McCallum N, Sifri CD, Majcherczyk PA, Entenza JM, Heusser R, Berger-Bachi B, Stutzmann Meier P. MsrR contributes to cell surface characteristics and virulence in Staphylococcus aureus. FEMS Microbiol Lett 2009, 295(2):251-260. 10.1111/j.1574-6968.2009.01603.x, 19459977.
79. Rossi J, Bischoff M, Wada A, Berger-Bachi B. MsrR, a putative cell envelope-associated element involved in Staphylococcus aureus sarA attenuation. Antimicrob Agents Chemother 2003, 47(8):2558-2564. 10.1128/AAC.47.8.2558-2564.2003, 166063, 12878519.
80. Kern J, Schneewind O. BslA, the S-layer adhesin of B. anthracis, is a virulence factor for anthrax pathogenesis. Mol Microbiol 2010, 75(2):324-332. 10.1111/j.1365-2958.2009.06958.x, 2828814, 19906175.
81. Dong S, Chesnokova ON, Turnbough CL, Pritchard DG. Identification of the UDP-N-acetylglucosamine 4-epimerase involved in exosporium protein glycosylation in Bacillus anthracis. J Bacteriol 2009, 191(22):7094-7101. 10.1128/JB.01050-09, 2772498, 19749053.
82. Vetting MW, LP SC, Yu M, Hegd SS, Magnet S, Roderick SL, Blanchard JS. Structure and functions of the GNAT superfamily of acetyltransferases. Arch Biochem Biophys 2005, 433(1):212-226. 10.1016/j.abb.2004.09.003, 15581578.
83. Forsberg LS, Choudhury B, Leoff C, Marston CK, Hoffmaster AR, Saile E, Quinn CP, Kannenberg EL, Carlson RW. Secondary cell wall polysaccharides from Bacillus cereus strains G9241, 03BB87 and 03BB102 causing fatal pneumonia share similar glycosyl structures with the polysaccharides from Bacillus anthracis. Glycobiology 2011, 21(7):934-948. 10.1093/glycob/cwr026, 3110489, 21421577.
84. Steichen C, Chen P, Kearney JF, Turnbough CL. Identification of the immunodominant protein and other proteins of the Bacillus anthracis exosporium. J Bacteriol 2003, 185(6):1903-1910. 10.1128/JB.185.6.1903-1910.2003, 150129, 12618454.
85. Carr KA, Janes BK, Hanna PC. Role of the gerP operon in germination and outgrowth of Bacillus anthracis spores. PLoS One 2010, 5(2):e9128. 10.1371/journal.pone.0009128, 2817736, 20161744.
86. Frankel AE, Kuo SR, Dostal D, Watson L, Duesbery NS, Cheng CP, Cheng HJ, Leppla SH. Pathophysiology of anthrax. Front Biosci 2009, 14:4516-4524.
87. Klee SR, Brzuszkiewicz EB, Nattermann H, Bruggemann H, Dupke S, Wollherr A, Franz T, Pauli G, Appel B, Liebl W, et al. 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(7):e10986. 10.1371/journal.pone.0010986, 2901330, 20634886.
88. Guindon S, Delsuc F, Dufayard JF, Gascuel O. Estimating maximum likelihood phylogenies with PhyML. Methods Mol Biol 2009, 537:113-137. 10.1007/978-1-59745-251-9_6, 19378142.
89. Bateman A, Birney E, Durbin R, Eddy SR, Howe KL, Sonnhammer EL. The Pfam protein families database. Nucleic Acids Res 2000, 28:263-266. 10.1093/nar/28.1.263, 102420, 10592242.
90. Eddy SR. Accelerated Profile HMM Searches. PLoS Comput Biol 2011, 7(10):e1002195. 10.1371/journal.pcbi.1002195, 3197634, 22039361.
91. Sandelin A. Prediction of regulatory elements. Methods Mol Biol 2008, 453:233-244. 10.1007/978-1-60327-429-6_11, 18712306.
92. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol 1990, 215(3):403-410.
93. Bailey TL, Williams N, Misleh C, Li WW. MEME: discovering and analyzing DNA and protein sequence motifs. Nucleic Acids Res 2006, 34(Web Server issue):W369-373. 1538909, 16845028.
94. Eddy SR, Mitchison G, Durbin R. Maximum discrimination hidden Markov models of sequence consensus. J Comput Biol 1995, 2(1):9-23. 10.1089/cmb.1995.2.9, 7497123.
95. Picard R, Cook D. Cross-validation of Regression Models. J Am Stat Assoc 1984, 79(387):575-583.
96. Letondal C. A Web interface generator for molecular biology programs in Unix. Bioinformatics 2001, 17(1):73-82. 10.1093/bioinformatics/17.1.73, 11222264.
97. Li W, Godzik A. Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics 2006, 22(13):1658-1659. 10.1093/bioinformatics/btl158, 16731699.
98. Li G, Che D, Xu Y. A universal operon predictor for prokaryotic genomes. J Bioinform Comput Biol 2009, 7(1):19-38. 10.1142/S0219720009003984, 19226658.
99. Bergman NH, Passalacqua KD, Hanna PC, Qin ZS. Operon prediction for sequenced bacterial genomes without experimental information. Appl Environ Microbiol 2007, 73(3):846-854. 10.1128/AEM.01686-06, 1800777, 17122389.
100. Nicolas P, Mader U, Dervyn E, Rochat T, Leduc A, Pigeonneau N, Bidnenko E, Marchadier E, Hoebeke M, Aymerich S, et al. Condition-dependent transcriptome reveals high-level regulatory architecture in Bacillus subtilis. Science 2012, 335(6072):1103-1106. 10.1126/science.1206848, 22383849.