The transcriptionally active regions in the genome of Bacillus subtilis

Molecular Microbiology

Volumn 73, Issue 6, 2009, Pages 1043-1057

  Rasmussen, Simon ^a   Nielsen, Henrik Bjørn ^a   Jarmer, Hanne ^a  

^a TECHNICAL UNIVERSITY OF DENMARK   (Denmark)

Author keywords

[No Author keywords available]

Indexed keywords

ARGININE; CARRIER PROTEIN;

3' UNTRANSLATED REGION; ARTICLE; BACILLUS SUBTILIS; BACTERIAL GENETICS; BACTERIAL GROWTH; CONTROLLED STUDY; GENE EXPRESSION; GENETIC TRANSCRIPTION; GENOME; HOUSEKEEPING GENE; NONHUMAN; PRIORITY JOURNAL; PROTEIN SECONDARY STRUCTURE;

BACILLUS SUBTILIS; BASE SEQUENCE; CULTURE MEDIA; GENE EXPRESSION PROFILING; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; NUCLEIC ACID CONFORMATION; RNA, ANTISENSE; RNA, UNTRANSLATED; TRANSCRIPTION, GENETIC;

BACILLUS SUBTILIS;

EID: 70350159135     PISSN: 0950382X     EISSN: 13652958     Source Type: Journal    
DOI: 10.1111/j.1365-2958.2009.06830.x     Document Type: Article

References (78)

1. Altschul, S.F., Gish, W., Miller, W., Myers, E.W., and Lipman, DJ. (1990) Basic local alignment search tool. J Mol Biol 215: 403-410.
2. Anagnostopoulos, C, and Spizizen, J. (1961) Requirements for transformation in Bacillus subtilis. J Bacteriol 81: 741-746.
3. Ando, Y., Asan, S., Suzuma, S., Yamane, K., and Nakamura, K. (2002) Expression of a small RNA, BS203 RNA, from the yocl-yocJ intergenic region of the Bacillus subtilis genome. FEMS Microbiol Lett 207: 29-33. (Pubitemid 34214801)
4. Auchtung, J.M., Lee, CA., and Grossman, A.D. (2006) Modulation of the ComA-dependent quorum response in Bacillus subtilis by multiple Rap proteins and Phr peptides. J Bacterid 188: 5273-5285.
5. Barbe, V., Cruveiller, S., Kunst, F., Lenoble, P., Meu rice, G., Sekowska, A., et al. (2009) From a consortium sequence to a unified sequence: the Bacillus subtilis 168 reference genome a decade later. Microbiology 155: 1758-1775.
6. Bertone, P., Stole, V., Royce, T.E., Rozowsky, J.S., Urban, A.E., Zhu, X., et al . (2004) Global identification of human transcribed sequences with genome tiling arrays. Science 306: 2242-2246.
7. Burguière, P., Auger, S., Hullo, M.F., Danchin, A., and MartinVerstraete, I. (2004) Three different systems participate in L-cystine uptake in Bacillus subtilis. J Bacteriol 186: 4875-4884.
8. Burkholder, P.R., and Giles, N.H. (1947) Induced biochemical mutations in Bacillus subtilis. Am J Bot 34: 345-348.
9. Cervantes, C, Ji, G., Ramirez, J., and Silver, S. (1994) Resistance to arsenic compounds in microorganisms. FEMS Microbiol Rev 15: 355-367.
10. Cohn, F. (1872) Untersuchungen über Bakterien. Beitr Bid Pflanzen 1: 127-224.
11. Cohn, F. (1876) Untersuchungen über Bakterien, IV. Beiträge zur Biologie der Bacillen. Beitr Biol Pflanzen 2: 249-277.
12. Conn, HJ. (1930) The identity of Bacillus subtilis. J Infed Dis 46: 341-350.
13. David, L., Huber, W., Granovskaia, M., Toedling, J., Palm, CJ., Bofkin, L., et al. (2006) A high-resolution map of transcription in the yeast genome. Proc Nati Acad Sd USA 103: 5320-5325.
14. DeLisa, M.P., Tullman, D., and Georgiou, G. (2003) Folding quality control in the export of proteins by the bacterial twin-arginine translocation pathway. Proc Natl Acad Sd USA 100: 6115-6120. (Pubitemid 36576940)
15. Deutscher, J., Galinier, A., and Martin-Verstraete, I. (2002) Carbohydrate uptake and metabolism. In Bacillus subtilis and its closest relatives. Sonenshein, A.L., Hoch, J.A., and Losick, R. (eds). Washington, DC: American Society for Microbiology, pp. 129-150.
16. Dubey, A.K., Baker, CS., Suzuki, K., Jones, A.D., Pandit, P., Romeo, T., and Babitzke, P. (2003) CsrA regulates translation of the Escherichia coli carbon starvation gene, cstA, by blocking ribosome access to the cstA transcript. J Bacteriol 185: 4450-4460. (Pubitemid 36890492)
17. Ehrenberg, CG. (1835) Dritter Beitrag zur Erkenntniss grosser Organisation in der Richtung des kleinsten Raumes. In Physikalische Abhandlungen der Koeniglichen Akademie der Wissenschaften zu Berlin aus den Jahren 1833-1835, pp. 145-336.
18. Eiamphungpom, W., and Helmann, J.D. (2009) Extracytoplasmic function sigma factors regulate expression of the Bacillus subtilis yabE gene via a cis-acting antisense RNA. J Bacteriol 191: 1101-1105.
19. Fillinger, S., Boschi-Muller, S., Azza, S., Dervyn, E., Branlant, G., and Aymerieh, S. (2000) Two glyceraldehyde-3phosphate dehydrogenases with opposite physiological roles in a nonphotosynthetic bacterium. J Biol Chem 275: 14031-14037. (Pubitemid 30339676)
20. Gaballa, A., Antelmann, H., Aguilar, C, Khakh, S.K., KyungBok, S., Smaldone, G.T., and Helmann, J.D. (2008) The Bacillus subtilis iron-sparing response is mediated by a Fur-regulated small RNA and three small basic proteins. Proc Natl Acad Sci USA 105: 11927-11932.
21. Gaidenko, T.A., Kim, T.J., Weigel, A.L., Brody, M.S., and Price, CW. (2006) The blue-light receptor YtvA acts in the environmental stress signaling pathway of Bacillus subtilis. J Bacteriol188: 6387-6395.
22. Gardan, R., Rapoport, G., and Débarbouille, M. (1995) Expression of the rocDEF operon involved in arginine catabolism in Bacillus subtilis. J MoI Biol 249: 843-856.
23. Gollnick, P., Babitzke, P., Anteon, A., and Yanofsky, C (2005) Complexity in regulation of tryptophan biosynthesis in Bacillus subtilis. Annu Rev Genet 39: 47-68.
24. Gruber, A.R., Lorenz, R., Bernhart, S.H., Neuböck, R., and Hofacker, I.L. (2008) The Vienna RNA Web suite. Nucleic Acids Res 36: W70-W74.
25. Grundy, F.J., and Henkin, T.M. (1998) The S box regulon: a new global transcription termination control system for methionine and cysteine biosynthesis genes in Grampositive bacteria. Mol Microbiol 30: 737-774.
26. Haldenwang, W.G. (1995) The sigma factors of Bacillus subtilis. Microbiol Mol Biol Rev 59: 1-30.
27. Hallin, P.F., and Ussery, D.W. (2004) CBS Genome Atlas Database: a dynamic storage for bioinformatic results and sequence data. Bioinformatics 20: 3682-3686.
28. Helmann, J.D., Wu, M.F., Kobel, P.A., Gamo, F.J., Wilson, M., Morshedi, M.M., et al. (2001) Global transcriptional response of Bacillus subtilis to heat shock. J Bacteriol 183: 7318-7328. (Pubitemid 33121866)
29. Hoon, M J.L., Makita, Y., Nakai, K., and Miyano, S. (2005) Prediction of transcriptional terminators in Bacillus subtilis and related species. PLoS Comput Biol 1: 12-222.
30. Huang, J.M., La Ragione, R.M., Nunez, A., and Cutting, S.M. (2008) lmmunostimulatory activity of Bacillus spores. FEMS Immunol Med Microbiol 53: 195-203. (Pubitemid 351832187)
31. Huber, W., Toedling, J., and Steinmetz, L.M. (2006) Transcript mapping with high-density oligonucleotide tiling arrays. Bioinformatics 22: 1963-1970. (Pubitemid 44283008)
32. Jarmer, H., Larsen, T.S., Krogh, A., Saxild, H.H., Brunak, S., and Knudsen, S. (2001) Sigma A recognition sites in the Bacillus subtilis genome. Microbiology 147: 2417-2424. (Pubitemid 32899238)
33. Jerga, A., Lu, Y.J., Schujman, G.E., de Mendoza, D., and Rock, CO. (2007) Identification of a soluble diacylglycerol kinase required for lipoteichoic acid production in Bacillus subtilis. J Biol Chem 282: 21738-21745. (Pubitemid 47195761)
34. Jongbloed, J.D.H., Grieger, U., Antelmann, H., Hecker, M., Nijland, R., Bran, S., and van Dijl, J.M. (2004) Two minimal Tat translocases in Bacillus. Mol Microbiol 54: 1319-1325.
35. Kanehisa, M., Araki, M., Goto, S., Hattori, M., Hirakawa, M., Itoh, M., et al. (2008) KEGG for linking genomes to life and the environment. Nucleic Acids Res 36: D480-D484. (Pubitemid 351149770)
36. Kawano, M., Reynolds, A.A., Miranda-Rios, J., and Storz, G. (2005) Detection of 5'- and 3'-UTR-derived small RNAs and cis-encoded antisense RNAs in Escheridiia coli. Nucleic Acids Res 33: 1040-1050.
37. Kent, W.J. (2002) BLAT - the BLAST-like alignment tool. Genome Res 12: 656-664.
38. Kingsford, C.L., Ayabule, K., and Salzberg, S.L. (2007) Rapid, accurate, computational discovery of Rho- independent transcription terminators illuminates their relationship to DNA uptake. Genome Biol 8: R22.
39. Krogh, S., O'Reailly, M., Nolan, N., and Devine, K.M. (1996) The phage-like element PBSX and part of the skin element, which are resident at different locations on the Bacillus subtilis chromosome are highly homologous. Microbiology 142: 2031-2040. (Pubitemid 26288075)
40. Kunst, F., Ogasawara, N., Moszer, I., Albertini, A.M., Alloni, G., Azevedo, V., et al. (1997) The complete genome sequence of the Gram-positive bacterium Bacillus subtilis. Nature 390: 249-256.
41. Larkin, M.A., Blackshields, G., Brown, N.P., Chenna, R., McGettigan, P.A., McWilliam, H., et al. (2007) ClustalW and ClustalX version 2. Bioinformatics 23: 2647-2648.
42. Lazarevic, V., DQsterhõft, A., Soldo, B., Hubert, H., Maeueμl, C, and Karamata, D. (1999) Nucleotide sequence of the Bacillus subtilis temperate bacteriophage SPßc2. Microbiology 145: 1055-1067. (Pubitemid 29231809)
43. Li, L., Wang, X., Stole, V., Li, X., Zhang, D., Su, N., et al. (2006) Genome-wide transcription analyses in rice using tiling microarrays. Nat Genet 38: 124-129. (Pubitemid 43011893)
44. Licht, A., Preis, S., and Brantl, S. (2005) Implication of CcpN in the regulation of a novel untranslated RNA (SR1) in B. subtilis. Mol Microbiol 58: 189-206. (Pubitemid 41415040)
45. Mãder, U., Henning, S., Hecker, M., and Homuth, G. (2004) Transcriptional organization and posttranscriptional regulation of the Bacillus subtilis branched-chain amino acid biosynthesis genes. J Bacteriol 186: 2240-2252. (Pubitemid 38451826)
46. Maillard, J., Spronk, C.A.E.M., Buchanan, G., Lyall, V., Richardson, DJ., Palmer, T., et al. (2007) Structural diversity in twin-arginine signal peptide-binding proteins. Proc Natl Acad Sei USA 104: 15641-15646. (Pubitemid 350035353)
47. Mazumder, B., Seshadri, V., and Fox, P.L. (2003) Translational control by the 3'-UTR: the ends specify the means. Trends Biochem Sei 28: 91-98. (Pubitemid 36165138)
48. Nagalakshmi, U., Wang, Z., Waern, K., Shou, C, Raha, D., Gerstein, M., and Snyder, M. (2008) The transcriptional landscape of the yeast genome defined by RNA sequencing. Science 320: 1344-1349. (Pubitemid 351929471)
49. Nicolas, P., Bize, L., Muri, F., Hoebeke, M., Rodolphe, F., Ehrlic, S.D., et al. (2002) Mining Bacillus subtilis chromosome heterogeneities using hidden Markov models. Nucleic Acids Res 30: 1418-1426. (Pubitemid 34679721)
50. Nielsen, P., and Krogh, A. (2005) Large-scale prokaryotic gene prediction and comparison to genome annotation. Bioinformatics 21: 4322-4329. (Pubitemid 41782921)
51. Ogura, M., Shimane, K., Asai, K., Ogasawara, N., and Tanaka, T. (2003) Binding of response regulator DegU to the aprE promoter is inhibited by RapG, which is counteracted by extracellular PhrG in Bacillus subtilis. Mol Microbiol 49: 1685-1697. (Pubitemid 37153525)
52. Ollinger, J., Song, K.B., Antelmann, H., Hecker, M., and Helmann, J.D. (2006) Role of the Fur regulon in iron transport in Bacillus subtilis. J Bacteriol 188: 3664-3673.
53. Oussenko, I.A., Abe, T., Ujiie, H., Muto, A., and Bechhofer, D.H. (2005) Participation of 3'- to 5'-exoribonucleases in the turnover of Bacillus subtilis mRNA. J Bacteriol 187: 2758-2767. (Pubitemid 40490380)
54. Perocchi, F., Xu, Z., Clauder-Münster, S., and Steinmetz, L.M. (2007) Antisense artifacts in transcriptome microarray experimente are resolved by actinomycin D. Nucleic Acids Res 35: 1-7. (Pubitemid 350111636)
55. Ratushna, V.G., Weller, J.W., and Gibas, CJ. (2005) Secondary structure in the target as a confounding factor in synthetic oligomer microarray design. BMC Genomics 6: 31.
56. Reppas, N.B., Wade, J.T., Church, G.M., and Struhl, K. (2006) The transition between transcriptional initiation and elongation in E. coli is highly variable and often rate limiting. Mol Cell 24: 747-757.
57. Saito, S., Kakeshita, H., and Nakamura, K. (2009) Novel small RNA-encoding genes in the intergenic regions of Bacillus subtilis. Gene 428: 2-8.
58. Shivers, R.P., and Sonenshein, A.L. (2005) Bacillus subtilis UvB operon: an intersection of global régulons. Mol Microbiol 56: 1549-1559.
59. Sierro, N., Makita, Y., de Hoon, M., and Nakai, K. (2008) DBTBS: a database of transcriptional regulation in Bacillus subtilis containing upstream intergenic conservation information. Nucleic Acids Res 36: D93-D96. (Pubitemid 351149702)
60. Silvaggi, J.M., Perkins, J.B., and Losick, R. (2005) Small untranslated RNA antitoxin in Bacillus subtilis. J Bacteriol 187: 6641-6650.
61. Silvaggi, J.M., Perkins, J.B., and Losick, R. (2006) Genes for small, noncoding RNAs under sporulation control in Bacillus subtilis. J Bacteriol 188: 532-541.
62. Spizizen, J. (1958) Transformation of biochemically deficient strains of Bacillus subtilis by deoxyribonucleate. Proc Natl Acad Sci USA 44: 1072-1078.
63. Spizizen, J. (1984) Citation classic -Transformation of biochemically deficient strains of Bacillus subtilis by deoxyribonucleate. Curr Contents Life Sci 19: 15.
64. Steil, L., Serrano, M., Henriques, A.O., and Völker, U. (2005) Genome-wide analysis of temporally regulated and compartment-specific gene expression in sporulating cells of Bacillus subtilis. Microbiology 151: 339-420. (Pubitemid 40277744)
65. Suzuma, S., Asari, S., Bunai, K., Yoshino, K., Ando, Y., Kakeshita, H., et al. (2002) Identification and characterization of novel small RNAs in the aspS-yrvM intergenic region of the Bacillus subtilis genome. Microbiology 148: 2591-2598.
66. Swets, J.A. (1988) Measuring the accuracy of diagnostic systems. Science 240: 1285-1293.
67. Takemaru, K., Mizuno, M., Sato, T., Takeuchi, M., and Kobayashi, Y. (1995) Complete nucleotide sequence of a skin element excised by DNA rearrangement during sporulation in Bacillus subtilis. Microbiology 141: 323-327.
68. Teas, HJ. (1949) Mutants of Bacillus subtilis that require threonine or threonine plus methionine. J Bacteriol 59: 93-104.
69. Tjaden, B., Goodwin, S.S., Opdyke, J.A., Guillier, M., Fu, D.X., Gottesman, S., and Storz, G. (2006) Target prediction for small, noncoding RNAs in bacteria. Nucleic Adds Res 34: 2791-2802. (Pubitemid 43985640)
70. Tjaden, B., Saxena, R.M., Stolyar, S., Haynor, D.R., Kolker, E., and Rosenow, C (2002) Transcriptome analysis of Escherichia coli using high-density oligonucleotide probe arrays. Nucleic Acids Res 30: 3732-3738. (Pubitemid 35012445)
71. Vogel, J., and Wagner, E.G.H. (2007) Target identification of small noncoding RNAs in bacteria. CurrOpin Microbiol 10: 262-270. (Pubitemid 46963091)
72. Wang, L., Park, S., and Doi, R.H. (1999) A novel Bacillus subtilis gene, antE, temporally regulated and convergent to and overlapping dnaE. J Bacteriol 181: 353-356.
73. Wernersson, R., and Nielsen, H.B. (2005) OligoWiz 2.0 integrating sequence feature annotation into the design of microarray probes. Nucleic Acids Res 33: W611- W615.
74. Wood, H.E., Dawson, MT., Devine, K.M., and McConnell, DJ. (1990) Characterization of PBSX, a defective prophage of Bacillus subtilis. J Bacteriol 172: 2667-2674.
75. Xu, Z., Wei, W., Gagneur, J., Perocchi, F., Clauder-Münster, S., Camblon, J., et al. (2009) Bidirectional promoters generate pervasive transcription in yeast. Nature 457: 1033-1037.
76. Yakhnin, H., Pandi, P., Petty, TJ., Baker, CS., Romeo, T., and Babitzke, P. (2007) CrsA of Bacillus subtilis regulates translation initiation of the gene encoding the flagellin protein (hag) by blocking ribosome binding. Mol Microbiol 64: 1605-1620.
77. Zahler, S.A., Korman, R.Z., Rosenthal, R., and Hemphill H.E. (1977) Bacillus subtilis bacteriophage SPß: localization of the prophage attachment site and specialized transduction. J Bacteriol 129: 556-558.
78. Zeigler, D.R., Pragai, Z., Rodriguez, S., Chevreux, B., Muffler, A., Albert, T., et al. (2008) The origins of 168, W23, and other Bacillus subtilis legacy strains. J Bacteriol 190: 6983-6995.