| [1] | Baldus JM, Green BD, Youngman P, Moran CP (1994) Phosphorylation of transcription factor Spo0A stimulates transcription from the spoIIG promoter by enhancing binding to weak 0A boxes. J Bacteriol 176: 296–306.
|
| [2] | Ben-Yehuda S, Rudner DZ, Losick R (2003) RacA, a bacterial protein that anchors chromosomes to the cell poles. Science 299: 532–536.
|
| [3] | Bonsen PP, Spudich JA, Nelson DL, Kornberg A (1969) Biochemical studies of bacterial sporulation and germination. XII. A sulfonic acid as a major sulfur compound of spores. J Bacteriol 98: 62–68.
|
| [4] | Britton RA, Eichenberger P, Gonzalez-Pastor JE, Fawcett P, Monson R, et al. (2002) Genome-wide analysis of the stationary-phase sigma factor (sigma-H) regulon of . J Bacteriol 184: 4881–4890.
|
| [5] | Brown PO, Botstein D (1999) Exploring the new world of the genome with DNA microarrays. Nat Genet 21: (Suppl 1)33–37.
|
| [6] | Chada VG, Sanstad EA, Wang R, Driks A (2003) Morphogenesis of Bacillus spore surfaces. J Bacteriol 185: 6255–6261.
|
| [7] | Conlon EM, Eichenberger P, Liu JS (2004) Determining and analyzing differentially expressed genes from cDNA microarray experiments with complementary designs. J Multivariate Anal 90: 1–18.
|
| [8] | Cutting S, Mandelstam J (1986) The nucleotide sequence and the transcription during sporulation of the gerE gene of . J Gen Microbiol 132: 3013–3024.
|
| [9] | Cutting S, Panzer S, Losick R (1989) Regulatory studies on the promoter for a gene governing synthesis and assembly of the spore coat in . J Mol Biol 207: 393–404.
|
| [10] | Cutting S, Oke V, Driks A, Losick R, Lu S, et al. (1990) A forespore checkpoint for mother cell gene expression during development in . Cell 62: 239–250.
|
| [11] | Cutting S, Driks A, Schmidt R, Kunkel B, Losick R (1991a) Forespore-specific transcription of a gene in the signal transduction pathway that governs Pro-sigma K processing in . Genes Dev 5: 456–466.
|
| [12] | Cutting S, Roels S, Losick R (1991b) Sporulation operon spoIVF and the characterization of mutations that uncouple mother-cell from forespore gene expression in . J Mol Biol 221: 1237–1256.
|
| [13] | Cutting S, Zheng LB, Losick R (1991c) Gene encoding two alkali-soluble components of the spore coat from . J Bacteriol 173: 2915–2919.
|
| [14] | Driks A (2002) Proteins of the spore coat and coat. In: Sonenshein AL, Hoch JA, Losick R, editors. Bacillus subtilis and its closest relatives: From genes to cells. Washington (DC): American Society for Microbiology. pp. 527–536.
|
| [15] | Driks A, Roels S, Beall B, Moran CP, Losick R (1994) Subcellular localization of proteins involved in the assembly of the spore coat of . Genes Dev 8: 234–244.
|
| [16] | Eichenberger P, Fawcett P, Losick R (2001) A three-protein inhibitor of polar septation during sporulation in . Mol Microbiol 42: 1147–1162.
|
| [17] | Eichenberger P, Jensen ST, Conlon EM, van Ooij C, Silvaggi J, et al. (2003) The sigmaE regulon and the identification of additional sporulation genes in . J Mol Biol 327: 945–972.
|
| [18] | Errington J (2003) Regulation of endospore formation in . Nat Rev Microbiol 1: 117–126.
|
| [19] | Fawcett P, Eichenberger P, Losick R, Youngman P (2000) The transcriptional profile of early to middle sporulation in . Proc Natl Acad Sci U S A 97: 8063–8068.
|
| [20] | Feucht A, Evans L, Errington J (2003) Identification of sporulation genes by genome-wide analysis of the sigmaE regulon of . Microbiology 149: 3023–3034.
|
| [21] | Foulger D, Errington J (1991) Sequential activation of dual promoters by different sigma factors maintains spoVJ expression during successive developmental stages of . Mol Microbiol 5: 1363–1373.
|
| [22] | Frandsen N, Stragier P (1995) Identification and characterization of the Bacillus subtilis spoIIP locus. J Bacteriol 177: 716–722.
|
| [23] | Frohman MA (1994) On beyond classic RACE (rapid amplification of cDNA ends). PCR Methods Appl 4: S40–S58.
|
| [24] | Fujita M, Losick R (2002) An investigation into the compartmentalization of the sporulation transcription factor sigmaE in . Mol Microbiol 43: 27–38.
|
| [25] | Fujita M, Losick R (2003) The master regulator for entry into sporulation in becomes a cell-specific transcription factor after asymmetric division. Genes Dev 17: 1166–1174.
|
| [26] | Fujita M, Sadaie Y (1998) Promoter selectivity of the RNA polymerase sigmaA and sigmaH holoenzymes. J Biochem (Tokyo) 124: 89–97.
|
| [27] | Glaser P, Frangeul L, Buchrieser C, Rusniok C, Amend A, et al. (2001) Comparative genomics of Listeria species. Science 294: 849–852.
|
| [28] | Graham DE, Xu H, White RH (2002) Identification of coenzyme M biosynthetic phosphosulfolactate synthase: A new family of sulfonate-biosynthesizing enzymes. J Biol Chem 277: 13421–13429.
|
| [29] | Grundy FJ, Henkin TM (1998) The S box regulon: A new global transcription termination control system for methionine and cysteine biosynthesis genes in gram-positive bacteria. Mol Microbiol 30: 737–749.
|
| [30] | Guerout-Fleury AM, Frandsen N, Stragier P (1996) Plasmids for ectopic integration in . Gene 180: 57–61.
|
| [31] | Halberg R, Kroos L (1994) Sporulation regulatory protein SpoIIID from activates and represses transcription by both mother-cell-specific forms of RNA polymerase. J Mol Biol 243: 425–436.
|
| [32] | Harwood CR, Cutting SM (1990) Molecular biological methods for Bacillus. Chichester (United Kingdom): Wiley. 581 p.
|
| [33] | Helmann JD, Moran CP (2002) RNA polymerase and sigma factors. In: Sonenshein AL, Hoch JA, Losick R, editors. Bacillus subtilis and its closest relatives: From genes to cells. Washington (DC): American Society for Microbiology. pp. 289–312.
|
| [34] | Hofmeister AE, Londono-Vallejo A, Harry E, Stragier P, Losick R (1995) Extracellular signal protein triggering the proteolytic activation of a developmental transcription factor in . Cell 83: 219–226.
|
| [35] | Illing N, Errington J (1991) The spoIIIA operon of defines a new temporal class of mother-cell-specific sporulation genes under the control of the sigma E form of RNA polymerase. Mol Microbiol 5: 1927–1940.
|
| [36] | Itaya M, Kondo K, Tanaka T (1989) A neomycin resistance gene cassette selectable in a single copy state in the chromosome. Nucleic Acids Res 17: 4410.
|
| [37] | Ivanova N, Sorokin A, Anderson I, Galleron N, Candelon B, et al. (2003) Genome sequence of and comparative analysis with . Nature 423: 87–91.
|
| [38] | Jensen ST, Liu JS (2004) BioOptimizer: A Bayesian scoring function approach to motif discovery. Bioinformatics 20: 1557–1564.
|
| [39] | Jensen ST, Liu XS, Zhou Q, Liu JS (2004) Computational discovery of gene regulatory binding motifs: A Bayesian perspective. Stat Sci 19: 188–204.
|
| [40] | Karmazyn-Campelli C, Bonamy C, Savelli B, Stragier P (1989) Tandem genes encoding sigma-factors for consecutive steps of development in . Genes Dev 3: 150–157.
|
| [41] | Karow ML, Glaser P, Piggot PJ (1995) Identification of a gene, spoIIR that links the activation of sigma E to the transcriptional activity of sigma F during sporulation in . Proc Natl Acad Sci U S A 92: 2012–2016.
|
| [42] | Kroos L, Kunkel B, Losick R (1989) Switch protein alters specificity of RNA polymerase containing a compartment-specific sigma factor. Science 243: 526–529.
|
| [43] | Kunkel B, Kroos L, Poth H, Youngman P, Losick R (1989) Temporal and spatial control of the mother-cell regulatory gene spoIIID of . Genes Dev 3: 1735–1744.
|
| [44] | Kunkel B, Losick R, Stragier P (1990) The gene for the development transcription factor sigma K is generated by excision of a dispensable DNA element containing a sporulation recombinase gene. Genes Dev 4: 525–535.
|
| [45] | Kuroda A, Asami Y, Sekiguchi J (1993) Molecular cloning of a sporulation-specific cell wall hydrolase gene of . J Bacteriol 175: 6260–6268.
|
| [46] | Kuwana R, Kasahara Y, Fujibayashi M, Takamatsu H, Ogasawara N, et al. (2002) Proteomics characterization of novel spore proteins of . Microbiology 148: 3971–3982.
|
| [47] | Kuwana R, Yamamura S, Ikejiri H, Kobayashi K, Ogasawara N, et al. (2003) Bacillus subtilis spoVIF (yjcC) gene, involved in coat assembly and spore resistance. Microbiology 149: 3011–3021.
|
| [48] | LaBell TL, Trempy JE, Haldenwang WG (1987) Sporulation-specific sigma factor sigma 29 of is synthesized from a precursor protein, P31. Proc Natl Acad Sci U S A 84: 1784–1788.
|
| [49] | Lai EM, Phadke ND, Kachman MT, Giorno R, Vazquez S, et al. (2003) Proteomic analysis of the spore coats of and . J Bacteriol 185: 1443–1454.
|
| [50] | Li Z, Piggot PJ (2001) Development of a two-part transcription probe to determine the completeness of temporal and spatial compartmentalization of gene expression during bacterial development. Proc Natl Acad Sci U S A 98: 12538–12543.
|
| [51] | Liu X, Brutlag DL, Liu JS (2001) BioProspector: Discovering conserved DNA motifs in upstream regulatory regions of co-expressed genes. Pac Symp Biocomput 6: 127–138.
|
| [52] | Liu XS, Brutlag DL, Liu JS (2002) An algorithm for finding protein–DNA binding sites with applications to chromatin-immunoprecipitation microarray experiments. Nat Biotechnol 20: 835–839.
|
| [53] | Londono-Vallejo JA, Stragier P (1995) Cell–cell signaling pathway activating a developmental transcription factor in . Genes Dev 9: 503–508.
|
| [54] | Lopez-Diaz I, Clarke S, Mandelstam J (1986) spoIID operon of : Cloning and sequence. J Gen Microbiol 132: 341–354.
|
| [55] | Lu S, Kroos L (1994) Overproducing the mother cell sigma factor precursor, Pro-sigma K, uncouples sigma K-dependent gene expression from dependence on intercompartmental communication. J Bacteriol 176: 3936–3943.
|
| [56] | Lu S, Halberg R, Kroos L (1990) Processing of the mother-cell sigma factor, sigma K, may depend on events occurring in the forespore during development. Proc Natl Acad Sci U S A 87: 9722–9726.
|
| [57] | Mangan S, Alon U (2003) Structure and function of the feed-forward loop network motif. Proc Natl Acad Sci U S A 100: 11980–11985.
|
| [58] | Mangan S, Zaslaver A, Alon U (2003) The coherent feedforward loop serves as a sign-sensitive delay element in transcription networks. J Mol Biol 334: 197–204.
|
| [59] | Mekjian KR, Bryan EM, Beall BW, Moran CP (1999) Regulation of hexuronate utilization in . J Bacteriol 181: 426–433.
|
| [60] | Miller JH (1972) Experiments in molecular genetics. Cold Spring Harbor (New York): Cold Spring Harbor Laboratory Press. 466 p.
|
| [61] | Milo R, Shen-Orr S, Itzkovitz S, Kashtan N, Chklovskii D, et al. (2002) Network motifs: Simple building blocks of complex networks. Science 298: 824–827.
|
| [62] | Molle V, Fujita M, Jensen ST, Eichenberger P, Gonzalez-Pastor JE, et al. (2003a) The Spo0A regulon of . Mol Microbiol 50: 1683–1701.
|
| [63] | Molle V, Nakaura Y, Shivers RP, Yamaguchi H, Losick R, et al. (2003b) Additional targets of the global regulator CodY identified by chromatin immunoprecipitation and genome-wide transcript analysis. J Bacteriol 185: 1911–1922.
|
| [64] | Moqtaderi Z, Struhl K (2004) Genome-wide occupancy profile of the RNA polymerase III machinery in reveals loci with incomplete transcription complexes. Mol Cell Biol 24: 4118–4127.
|
| [65] | Nicholson WL, Setlow P (1990) Sporulation, germination and outgrowth. In: Harwood CR, Cutting SM, editors. Molecular biological methods for Bacillus. Chichester (United Kingdom): Wiley. pp. 391–450.
|
| [66] | Nolling J, Breton G, Omelchenko MV, Makarova KS, Zeng Q, et al. (2001) Genome sequence and comparative analysis of the solvent-producing bacterium . J Bacteriol 183: 4823–4838.
|
| [67] | Nugroho FA, Yamamoto H, Kobayashi Y, Sekiguchi J (1999) Characterization of a new sigma-K-dependent peptidoglycan hydrolase gene that plays a role in mother cell lysis. J Bacteriol 181: 6230–6237.
|
| [68] | Pan Q, Losick R, Rudner DZ (2003) A second PDZ-containing serine protease contributes to activation of the sporulation transcription factor sigmaK in . J Bacteriol 185: 6051–6056.
|
| [69] | Piggot PJ, Coote JG (1976) Genetic aspects of bacterial endospore formation. Bacteriol Rev 40: 908–962.
|
| [70] | Piggot PJ, Losick R (2002) Sporulation genes and intercompartmental regulation. In: Sonenshein AL, Hoch JA, Losick R, editors. Bacillus subtilis and its closest relatives: From genes to cells. Washington (DC): American Society for Microbiology. pp. 483–518.
|
| [71] | Price CW, Fawcett P, Ceremonie H, Su N, Murphy CK, et al. (2001) Genome-wide analysis of the general stress response in . Mol Microbiol 41: 757–774.
|
| [72] | Price KD, Losick R (1999) A four-dimensional view of assembly of a morphogenetic protein during sporulation in . J Bacteriol 181: 781–790.
|
| [73] | Read TD, Peterson SN, Tourasse N, Baillie LW, Paulsen IT, et al. (2003) The genome sequence of Ames and comparison to closely related bacteria. Nature 423: 81–86.
|
| [74] | Resnekov O, Alper S, Losick R (1996) Subcellular localization of proteins governing the proteolytic activation of a developmental transcription factor in . Genes Cells 1: 529–542.
|
| [75] | Ricca E, Cutting S, Losick R (1992) Characterization of bofA a gene involved in intercompartmental regulation of pro-sigma K processing during sporulation in . J Bacteriol 174: 3177–3184.
|
| [76] | Roels S, Driks A, Losick R (1992) Characterization of spoIVA a sporulation gene involved in coat morphogenesis in . J Bacteriol 174: 575–585.
|
| [77] | Rudner DZ, Losick R (2002) A sporulation membrane protein tethers the pro-sigmaK processing enzyme to its inhibitor and dictates its subcellular localization. Genes Dev 16: 1007–1018.
|
| [78] | Rudner DZ, Pan Q, Losick RM (2002) Evidence that subcellular localization of a bacterial membrane protein is achieved by diffusion and capture. Proc Natl Acad Sci U S A 99: 8701–8706.
|
| [79] | Satola SW, Baldus JM, Moran CP (1992) Binding of Spo0A stimulates spoIIG promoter activity in . J Bacteriol 174: 1448–1453.
|
| [80] | Schneider TD, Stephens RM (1990) Sequence logos: A new way to display consensus sequences. Nucleic Acids Res 18: 6097–6100.
|
| [81] | Setlow P (2003) Spore germination. Curr Opin Microbiol 6: 550–556.
|
| [82] | Shen-Orr SS, Milo R, Mangan S, Alon U (2002) Network motifs in the transcriptional regulation network of . Nat Genet 31: 64–68.
|
| [83] | Shimizu T, Ohtani K, Hirakawa H, Ohshima K, Yamashita A, et al. (2002) Complete genome sequence of Clostridium perfringens an anaerobic flesh-eater. Proc Natl Acad Sci U S A 99: 996–1001.
|
| [84] | Smith K, Youngman P (1993) Evidence that the spoIIM gene of is transcribed by RNA polymerase associated with sigma E. J Bacteriol 175: 3618–3627.
|
| [85] | Smith K, Bayer ME, Youngman P (1993) Physical and functional characterization of the Bacillus subtilis spoIIM gene. J Bacteriol 175: 3607–3617.
|
| [86] | Smith MC, Czaplewski L, North AK, Baumberg S, Stockley PG (1989) Sequences required for regulation of arginine biosynthesis promoters are conserved between and . Mol Microbiol 3: 23–28.
|
| [87] | Smith TJ, Foster SJ (1995) Characterization of the involvement of two compensatory autolysins in mother cell lysis during sporulation of 168. J Bacteriol 177: 3855–3862.
|
| [88] | Sterlini JM, Mandelstam J (1969) Commitment to sporulation in and its relationship to development of actinomycin resistance. Biochem J 113: 29–37.
|
| [89] | Stevens CM, Errington J (1990) Differential gene expression during sporulation in Bacillus subtilis Structure and regulation of the spoIIID gene. Mol Microbiol 4: 543–551.
|
| [90] | Stevens CM, Daniel R, Illing N, Errington J (1992) Characterization of a sporulation gene, spoIVA involved in spore coat morphogenesis in . J Bacteriol 174: 586–594.
|
| [91] | Stragier P (2002) A gene odyssey: Exploring the genomes of endospore-forming bacteria. In: Sonenshein AL, Hoch JA, Losick R, editors. Bacillus subtilis and its closest relatives: From genes to cells. Washington (DC): American Society for Microbiology. pp. 519–526.
|
| [92] | Stragier P, Losick R (1996) Molecular genetics of sporulation in . Annu Rev Genet 30: 297–241.
|
| [93] | Stragier P, Bonamy C, Karmazyn-Campelli C (1988) Processing of a sporulation sigma factor in : How morphological structure could control gene expression. Cell 52: 697–704.
|
| [94] | Stragier P, Kunkel B, Kroos L, Losick R (1989) Chromosomal rearrangement generating a composite gene for a developmental transcription factor. Science 243: 507–512.
|
| [95] | Takamatsu H, Watabe K (2002) Assembly and genetics of spore protective structures. Cell Mol Life Sci 59: 434–444.
|
| [96] | Takami H, Takaki Y, Uchiyama I (2002) Genome sequence of isolated from the Iheya Ridge and its unexpected adaptive capabilities to extreme environments. Nucleic Acids Res 30: 3927–3935.
|
| [97] | Takami H, Nakasone K, Takaki Y, Maeno G, Sasaki R, et al. (2000) Complete genome sequence of the alkaliphilic bacterium and genomic sequence comparison with . Nucleic Acids Res 28: 4317–4331.
|
| [98] | Tatti KM, Jones CH, Moran CP (1991) Genetic evidence for interaction of sigma E with the spoIIID promoter in . J Bacteriol 173: 7828–7833.
|
| [99] | Tatti KM, Shuler MF, Moran CP (1995) Sequence-specific interactions between promoter DNA and the RNA polymerase sigma factor E. J Mol Biol 253: 8–16.
|
| [100] | van Ooij C, Eichenberger P, Losick R (2004) Dynamic patterns of subcellular protein localization during spore coat morphogenesis in . J Bacteriol 186: 4441–4448.
|
| [101] | Wach A (1996) PCR-synthesis of marker cassettes with long flanking homology regions for gene disruptions in . Yeast 12: 259–265.
|
| [102] | Wu LJ, Errington J (2000) Identification and characterization of a new prespore-specific regulatory gene, rsfA of . J Bacteriol 182: 418–424.
|
| [103] | Yoshida K, Fujita Y, Ehrlich SD (1999) Three asparagine synthetase genes of . J Bacteriol 181: 6081–6091.
|
| [104] | Zhang B, Daniel RA, Errington J, Kroos L (1997) SpoIIID protein binds to two sites in the spoVD promoter and represses transcription by sigmaE RNA polymerase. J Bacteriol 179: 972–975.
|
| [105] | Zheng L, Halberg R, Roels S, Ichikawa H, Kroos L, et al. (1992) Sporulation regulatory protein GerE from binds to and can activate or repress transcription from promoters for mother-cell-specific genes. J Mol Biol 226: 1037–1050.
|
| [106] | Zheng LB, Losick R (1990) Cascade regulation of spore coat gene expression in . J Mol Biol 212: 645–660.
|
