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Chapter 21 : RNA Polymerase and Sigma Factors

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Abstract:

RNA polymerase (RNAP) acts at a critical juncture to link the genomic potential of an organism to the expression of this potential as RNA, protein, and ultimately catalytic, structural, and behavioral properties. Studies in revealed the importance of the conserved TG in the -16 promoter region, as subsequently found in the "extended -10" class of promoters. Regulation in often occurs by unexpected mechanisms, quite distinct from those operative with analogous regulons in . During endospore development, four new RNAP sigma factors appear, displacing one another and conferring on RNAP different specificities for the recognition of different classes of promoters. These sigma factors appear in the order σ, σ, σ and σ. The sequential appearance of each sigma factor determines the temporal pattern of gene transcription. The sigma factors also play a critical role in determining cell-type specific patterns of gene expression. ECF σ factors from many organisms often share a related set of properties. First, these regulators typically control functions related to the cell surface, including cell envelope structure, transport or synthesis of secreted secondary metabolites. Second, most ECF σ factors are transcribed as part of a positively autoregulated operon encoding the σ factor itself together with a specific anti-σ;. Third, promoters recognized by ECF- σ; factors often have a characteristic -35 region, but they tend to differ in the -10 element. Compared with factors controlling transcription initiation, proteins affecting the elongation and termination phases of transcription have received little attention in .

Citation: Helmann J, Moran C. 2002. RNA Polymerase and Sigma Factors, p 289-312. In Sonenshein A, Losick R, Hoch J (ed), and Its Closest Relatives. ASM Press, Washington, DC. doi: 10.1128/9781555817992.ch21

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Transcription Start Point
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Transcription Start Site
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Core Promoter
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Figures

Image of FIGURE 1
FIGURE 1

Structure of bacterial promoters. Promoter sites are defined with respect to the transcriptional start point (TSP). The core promoter elements include the −35 and −10 regions (or the −24, −12 elements for σ-dependent promoters) and include those sequences recognized directly by the corresponding a factor. The spacer length, but not the sequence, is also conserved. The upstream sequence region is also decidedly nonrandom and includes A-T-rich sequences that favor binding by the α subunits of RNAP. This region also contains the binding sites for many activators (and some repressors). The downstream sequence region is not well conserved, but it is clear that sequences within this region can greatly affect promoter strength and influence the efficiency of promoter escape.

Citation: Helmann J, Moran C. 2002. RNA Polymerase and Sigma Factors, p 289-312. In Sonenshein A, Losick R, Hoch J (ed), and Its Closest Relatives. ASM Press, Washington, DC. doi: 10.1128/9781555817992.ch21
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Image of FIGURE 2
FIGURE 2

Common mechanisms of transcriptional control in bacterial systems. The activity of RNA polymerase at promoter (P) sites responds to various signals (S) as mediated by regulatory proteins. Extracellular signals are often perceived by “two-component systems,” including a membrane-localized his-tidine protein kinase (HPK) together with a partner response regulator (RR). In this example, signal 1 (S1) activates the HPK to phosphorylate the cognate RR, which can then act either positively (→) or negatively (⊣) at the target promoter (P). Extracellular signals can also be perceived by membrane-bound anti-σ factors that inhibit the activity of σ factors of the extra-cytoplasmic function (ECF) subfamily. In this example, the cognate ECF σ factor activates recognition of promoter P. Intracellular signals (e.g., small molecules, peptides, or metabolites) can be perceived directly by either activator proteins (Act.) or repressor proteins (Rep.). In the examples shown, signal 3 (S3) inhibits an activator and S6 stimulates a repressor, both leading to decreased gene expression. In contrast, S4 stimulates an activator and S5 inhibits a repressor, both leading to increased gene expression. Signals may be perceived by direct binding to the activator or repressor or through a more complex signaling cascade. Alternative σ factors are formally analogous to activator proteins, and their activity is typically regulated by anti-σ factors which respond to chemical or morphological signals.

Citation: Helmann J, Moran C. 2002. RNA Polymerase and Sigma Factors, p 289-312. In Sonenshein A, Losick R, Hoch J (ed), and Its Closest Relatives. ASM Press, Washington, DC. doi: 10.1128/9781555817992.ch21
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Image of FIGURE 3
FIGURE 3

Structure of the σ operon and its regulation. Regulation of transcription involves at least seven characterized promoter elements, including promoters activated by σ, σ, and σ. Within the (primase) gene is another, antidirectional reading frame that may serve a regulatory role (see text for details).

Citation: Helmann J, Moran C. 2002. RNA Polymerase and Sigma Factors, p 289-312. In Sonenshein A, Losick R, Hoch J (ed), and Its Closest Relatives. ASM Press, Washington, DC. doi: 10.1128/9781555817992.ch21
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References

/content/book/10.1128/9781555817992.chap21
1. Abe, A.,, H. Koide,, T. Kohno,, and K. Watabe. 1995. A Bacillus subtilis spore coat polypeptide gene, cotS. Microbiology 141:14331442.
2. Achberger, E. C.,, M. D. Hilton,, and H. R. Whiteley. 1982. The effect of the delta subunit on the interaction of Bacillus subtilis RNA polymerase with bases in a SP82 early gene promoter. Nucleic Acids Res. 10:28932910.
3. Achberger, E. C.,, and H. R. Whiteley. 1981. The role of the delta peptide of the Bacillus subtilis RNA polymerase in promoter selection. J. Biol. Chem. 256:74247432.
4. Aiyar, S. E.,, R. L. Gourse,, and W. Ross. 1998. Upstream A-tracts increase bacterial promoter activity through interactions with the RNA polymerase alpha subunit. Proc. Natl. Acad. Sci. USA 95:1465214657.
5. Akbar, S.,, and C. W. Price. 1996. Isolation and characterization of csbB, a gene controlled by Bacillus subtilis general stress transcription factor σB. Gene 177:123128.
6. Allmansberger, R. 1997. Temporal regulation of sigD from Bacillus subtilis depends on a minor promoter in front of the gene. J. Bacteriol. 179:65316535.
7. Alper, S.,, L. Duncan,, and R. Losick. 1994. An adenosine nucleotide switch controlling the activity of a cell type-specific transcription factor in B. subtilis. Cell 77:195205.
8. Amaya, E. I.,, and P. J. Piggot. 2000. Personal communication.
9. Antelmann, H.,, J. Bernhardt,, R. Schmid,, H. Mach,, U. Volker,, and M. Hecker. 1997. First steps from a two-dimensional protein index towards a response-regulation map for Bacillus subtillis. Electrophoresis 18:14511463.
10. Antoniewski, C.,, B. Savelli,, and P. Stragier. 1990. The spoIIJ gene, which regulates early developmental steps in Bacillus subtilis, belongs to a class of environmentally responsive genes. J. Bacteriol. 172:8693.
11. Antson, A. A.,, E. J. Dodson,, G. Dodson,, R. B. Greaves,, X. Chen,, and P. Gollnick. 1999. Structure of the trp RNA-binding attenuation protein, TRAP, bound to RNA. Nature 401:235242.
12. Arigoni, F.,, A. M. Guerout-Fleury,, I. Barak,, and P. Stragier. 1999. The SpoIIE phosphatase, the sporulation septum and the establishment of forespore-specific transcription in Bacillus subtilis: a reassessment. Mol. Microbiol. 31:14071415.
13. Artsimovitch, I.,, V. Svetlov,, L. Anthony,, R. R. Burgess,, and R. Landick. 2000. RNA polymerases from Bacillus subtilis and Escherichia coli differ in recognition of regulatory signals in vitro. J. Bacteriol. 182:60276035.
14. Babitzke, P. 1997. Regulation of tryptophan biosynthesis: Trp-ing the TRAP or how Bacillus subtilis reinvented the wheel. Mol. Microbiol. 26:19.
15. Bagyan, I.,, L. Casillas-Martinez,, and P. Setlow. 1998. The katX gene, which codes for the catalase in spores of Bacillus subtilis, is a forespore-specific gene controlled by sigmaF, and KatX is essential for hydrogen peroxide resistance of the germinating spore. J. Bacteriol. 180:20572062.
16. Bagyan, I.,, J. Hobot,, and S. Cutting. 1996. A compartmentalized regulator of developmental gene expression in Bacillus subtilis. J. Bacteriol. 178:45004507.
17. Bagyan, I.,, M. Noback,, S. Bron,, M. Paidhungat,, and P. Setlow. 1998. Characterization of yhcN, a new forespore-specific gene of Bacillus subtilis. Gene 212:179188.
18. Bagyan, I.,, B. Setlow,, and P. Setlow. 1998. New small, acid-soluble proteins unique to spores of Bacillus subtilis: identification of the coding genes and regulation and function of two of these genes. J. Bacteriol. 180:67046712.
19. Baldus, J. M.,, B. D. Green,, P. Youngman,, and C. P. Moran, Jr. 1994. Phosphorylation of Bacillus subtilis transcription factor SpoOA stimulates transcription from the spoIIG promoter by enhancing binding to weak OA boxes. J. Bacteriol. 176:296306.
20. Banner, C. D.,, C. P. Moran, Jr.,, and R. Losick. 1983. Deletion analysis of a complex promoter for a developmen-tally regulated gene from Bacillus subtilis. J. Mol. Biol. 168:351365.
21. Barrios, H.,, B. Valderrama,, and E. Morett. 1999. Compilation and analysis of sigma(54)-dependent promoter sequences. Nucleic Acids Res. 27:43054313.
22. Beall, B.,, A. Driks,, R. Losick,, and C. P. Moran, Jr. 1993. Cloning and characterization of a gene required for assembly of the Bacillus subtilis spore coat. J. Bacteriol. 175:17051716.
23. Beall, B.,, and C. P. Moran, Jr. 1994. Cloning and characterization of spoVR, a gene from Bacillus subtilis involved in spore cortex formation. J. Bacteriol. 176:20032012.>
24. Belitsky, B. R.,, and A. L. Sonenshein. 1999. An enhancer element located downstream of the major glutamate dehydrogenase gene of Bacillus subtilis. Proc. Natl. Acad. Sci. USA 96:1029010295.
25. Belitsky, B. R.,, and A. L. Sonenshein. 1998. Role and regulation of Bacillus subtilis glutamate dehydrogenase genes. J. Bacteriol. 180:62986305.
26. Bernhardt, J.,, U. Volker,, A. Volker,, H. Antelmann,, R. Schmid,, H. Mach,, and M. Hecker. 1997. Specific and general stress proteins in Bacillus subtilis—a two-dimensional protein electrophoresis study. Microbiology 143:9991017.
27. Bird, T. H.,, J. K. Grimsley,, J. A. Hoch,, and G. B. Spiegelman. 1996. The Bacillus subtilis response regulator SpoOA stimulates transcription of the spoIIG operon through modification of RNA polymerase promoter complexes. J. Mol. Biol. 256:436448.
28. Bird, T. H.,, J. K. Grimsley,, J. A. Hoch,, and G. B. Spiegelman. 1993. Phosphorylation of SpoOA activates its stimulation of in vitro transcription from the Bacillus subtilis spoIIG operon. Mol. Microbiol. 9:741749.
29. Boor, K. J.,, M. L. Duncan,, and C. W. Price. 1995. Genetic and transcriptional organization of the region encoding the beta subunit of Bacillus subtilis RNA polymerase. J. Biol. Chem. 270:2032920336.
30. Bourne, N.,, P. C. FitzJames,, and A. I. Aronson. 1991. Structural and germination defects of Bacillus subtilis spores with altered contents of a spore coat protein. J. Bacteriol. 173:66186625.
31. Bown, J. A.,, K. A. Barne,, S. D. Minchin,, and S. J. W. Busby,. 1997. Extended -10 promoters, p. 4152. In F. Eckstein, and D. M. J. Lilley (ed.), Nucleic Acids and Molecular Biology, vol. 11. Springer-Verlag, Berlin, Germany.
32. Boylan, S. A.,, A. R. Redfield,, and C. W. Price. 1993. Transcription factor sigma B of Bacillus subtilis controls a large stationary-phase regulon. J. Bacteriol. 175:39573963.
33. Boylan, S. A.,, M. D. Thomas,, and C. W. Price. 1991. Genetic method to identify regulons controlled by nonessential elements: isolation of a gene dependent on alternate transcription factor sigma B of Bacillus subtilis. J. Bacteriol. 173:78567866.
34. Bryan, E. M.,, B. W. Beall,, and C. P. Moran, Jr. 1996. A sigma E dependent operon subject to catabolite repression during sporulation in Bacillus subtilis. J. Bacteriol. 178:47784786.
35. Bsat, N.,, A. Herbig,, L. Casillas-Martinez,, P. Setlow,, and J. D. Helmann. 1998. Bacillus subtilis contains multiple Fur homologues: identification of the iron uptake (Fur) and peroxide regulon (PerR) repressors. Mol. Microbiol. 29:189198.
36. Buchanan, C. E.,, and M. L. Ling. 1992. Isolation and sequence analysis of dacB, which encodes a sporulation-specific penicillin-binding protein in Bacillus subtilis. J. Bacteriol. 174:17171725.
37. Buckner, C. M. Schyns,, and C. P. Moran, Jr. 1998. A region in the Bacillus subtilis transcription factor SpoOA that is important for spoIIG promoter activation. J. Bacteriol. 180:35783583.
38. Buttner, M. Personal communication.
39. Cabrera-Hernandez, A.,, J. L. Sanchez-Salas,, M. Paidhungat,, and P. Setlow. 1999. Regulation of four genes encoding small, acid-soluble spore proteins in Bacillus subtilis. Gene 232:110.
40. Cabrera-Hernandez, A.,, and P. Setlow. 2000. Analysis of the regulation and function of five genes encoding small, acid-soluble spore proteins of Bacillus subtilis. Gene 248:169181.
41. Calogero, S.,, R. Gardan,, P. Glaser,, J. Schweizer,, G. Rapoport,, and M. Debarbouille. 1994. RocR, a novel regulatory protein controlling arginine utilization in Bacillus subtilis, belongs to the NtrC/NifA family of transcriptional activators. J. Bacteriol. 176:12341241.
42. Cao, M.,, and J. D. Helmann. Unpublished data.
43. Caramori, T.,, D. Barilla,, C. Nessi,, L. Sacchi,, and A. Galizzi. 1996. Role of FlgM in sigma D-dependent gene expression in Bacillus subtilis. J. Bacteriol. 178:31133118.
44. Carter, H. L., III,, and C. P. Moran, Jr. 1986. New RNA polymerase sigma factor under spoO control in Bacillus subtilis. Proc. Natl. Acad. Sci. USA 83:94389442.
45. Carter, H. L., III,, K. M. Tatti,, and C. P. Moran, Jr. 1990. Cloning of a promoter used by sigma H RNA polymerase in Bacillus subtilis. Gene 96:101105.
46. Carter, H. L., III,, L. F. Wang,, R. H. Doi,, and C. P. Moran, Jr. 1988. rpoD operon promoter used by sigma H-RNA polymerase in Bacillus subtilis. J. Bacteriol. 170: 16171621.
47. Cervin, M. A.,, R. J. Lewis,, J. A. Brannigan,, and G. B. Spiegelman. 1998. The Bacillus subtilis regulator SinR inhibits spoIIG promoter transcription in vitro without displacing RNA polymerase. Nucleic Acids Res. 26:38063812.
48. Chen, L.,, and J. D. Helmann. 1995. Bacillus subtilis MrgA is a Dps (PexB) homologue: evidence for metalloregulation of an oxidative stress gene. Mol. Microbiol. 18:295300.
49. Chen, L.,, and J. D. Helmann. 1994. The Bacillus subtilis sigma D-dependent operon encoding the flagellar proteins FliD, FliS, and FliT. J. Bacteriol. 176:30933101.
50. Chen, N. Y.,, S. Q. Jiang,, D. A. Klein,, and H. Paulus. 1993. Organization and nucleotide sequence of the Bacillus subtilis diaminopimelate operon, a cluster of genes encoding the first three enzymes of diaminopimelate synthesis and dipicolinate synthase. J. Biol. Chem. 268:94489465.
51. Chen, Y. F.,, and J. D. Helmann. 1997. DNA-melting at the Bacillus subtilis flagellin promoter nucleates near -10 and expands unidirectionally. J. Mol. Biol. 267:4759.
52. Chen, Y. F.,, and J. D. Helmann. 1992. Restoration of motility to an Escherichia coli fliA flagellar mutant by a Bacillus subtilis sigma factor. Proc. Natl. Acad. Sci. USA 89:51235127.
53. Chibazakura, T.,, F. Kawamura,, and H. Takahashi. 1991. Differential regulation of spoOA transcription in Bacillus subtilis: glucose represses promoter switching at the initiation of sporulation. J. Bacteriol. 173:26252632.
54. Corfe, B. M.,, A. Moir,, D. Popham,, and P. Setlow. 1994. Analysis of the expression and regulation of the gerB spore germination operon of Bacillus subtilis 168. Microbiology 140:30793083.
55. Coulombe, B.,, and Z. F. Burton. 1999. DNA bending and wrapping around RNA polymerase: a “revolutionary” model describing transcriptional mechanisms. Microbiol. Mol. Biol. Rev. 63:457478.
56. Cramer, P.,, D. A. Bushnell,, J. Fu,, A. L. Gnatt,, B. Maier-Davis,, N. E. Thompson,, R. R. Burgess,, A. M. Edwards,, P. R. David,, and R. D. Romberg. 2000. Architecture of RNA polymerase II and implications for the transcription mechanism. Science 288:640649.
57. Cutting, S.,, A. Driks,, R. Schmidt,, B. Kunkel,, and R. Losick. 1991. Forespore-specific transcription of a gene in the signal transduction pathway that governs Pro-sigma K processing in Bacillus subtilis. Genes Dev. 5:456466.
58. Cutting, S.,, V. Oke,, A. Driks,, R. Losick,, S. Lu,, and L. Kroos. 1990. A forespore checkpoint for mother cell gene expression during development in B. subtilis. Cell 62:239250.
59. Cutting, S.,, S. Panzer,, and R. Losick. 1989. Regulatory studies on the promoter for a gene governing synthesis and assembly of the spore coat in Bacillus subtilis. J. Mol. Biol. 2O7:393404.
60. Cutting, S.,, S. Roels,, and R. Losick. 1991. Sporulation operon spoIVF and the characterization of mutations that uncouple mother-cell from forespore gene expression in Bacillus subtilis. J. Mol. Biol. 221:12371256.
61. Cutting, S.,, L. B. Zheng,, and R. Losick. 1991. Gene encoding two alkali-soluble components of the spore coat from Bacillus subtilis. J. Bacteriol. 173:29152919.
62. Daniel, R. A.,, S. Drake,, C. E. Buchanan,, R. Scholle,, and J. Errington. 1994. The Bacillus subtilis spoVD gene encodes a mother-cell specific penicillin-binding protein required for spore morphogenesis. J. Mol. Biol. 235:209220.
63. Daniel, R. A.,, and J. Errington. 1993. Cloning, DNA sequence, functional analysis and transcriptional regulation of the genes encoding dipicolinic acid synthetase required for sporulation in Bacillus subtilis. J. Mol. Biol. 232:468483.
64. Daniels, D.,, P. Zuber,, and R. Losick. 1990. Two amino acids in an RNA polymerase sigma factor involved in the recognition of adjacent base pairs in the -10 region of a cognate promoter. Proc. Natl. Acad. Sci. USA 87:80758079.
65. Debarbouille, M.,, R. Gardan,, M. Arnaud,, and G. Rapoport. 1999. Role of bkdR, a transcriptional activator of the sigL-dependent isoleucine and valine degradation pathway in Bacillus subtilis. J. Bacteriol. 181:20592066.
66. Debarbouille, M.,, I. Martin-Verstraete,, F. Kunst,, and G. Rapoport. 1991. The Bacillus subtilis sigL gene encodes an equivalent of sigma 54 from gram-negative bacteria. Proc. Natl. Acad. Sci. USA 88:90929096.
67. Decatur, A.,, and R. Losick. 1996. Identification of additional genes under the control of the transcription factor sigma F of Bacillus subtilis. J. Bacteriol. 178:50395041.
68. Decatur, A.,, M. T. McMurry,, B. N. Kunkel,, and R. Losick. 1997. Translation of the mRNA for the sporulation gene spoIIID of Bacillus subtilis is dependent upon translation of a small upstream open reading frame. J. Bacteriol. 179:13241328.
69. deHaseth, P. L.,, M. L. Zupancic,, and M. T. Record, Jr. 1998. RNA polymerase-promoter interactions: the comings and goings of RNA polymerase. J. Bacteriol. 180:30193025.
70. Diederich, B.,, K. M. Tatti,, C. H. Jones,, B. Beall,, and C. P. Moran, Jr. 1992. Genetic suppression analysis of sigma E interaction with three promoters in sporulating Bacillus subtilis. Gene 121:6369.
71. Dobinson, K. F.,, and G. B. Spiegelman. 1987. Effect of the delta subunit of Bacillus subtilis RNA polymerase on initiation of RNA synthesis at two bacteriophage phi 29 promoters. Biochemistry 26:82068213.
72. Doi, R. H., 1982. RNA polymerase of Bacillus subtilis, p. 71108. In D. A. Dubnau (ed.), The Molecular Biology of the Bacilli, vol. 1. Academic Press, New York, N.Y..
73. Drzewiecki, K.,, C. Eymann,, G. Mittenhuber,, and M. Hecker. 1998. The yvyD gene of Bacillus subtilis is under dual control of sigmaB and sigmaH. J. Bacteriol. 180:66746680.
74. Duncan, L.,, S. Alper,, F. Arigoni,, R. Losick,, and P. Stragier. 1995. Activation of cell-specific transcription by a serine phosphatase at the site of asymmetric division. Science 270:641644.
75. Duncan, L.,, S. Alper,, and R. Losick. 1996. SpoIIAA governs the release of the cell-type specific transcription factor sigma F from its anti-sigma factor SpoIIAB. J. Mol. Biol. 260:147164.
76. Duncan, L.,, and R. Losick. 1993. SpoIIAB is an anti-sigma factot that binds to and inhibits transcription by regulatory protein sigma F from Bacillus subtilis. Proc. Natl. Acad. Sci. USA 90:23252329.
77. Estacio, W.,, S. S. Anna-Arriola,, M. Adedipe,, and L. M. Marquez-Magana. 1998. Dual promoters are responsible for transcription initiation of the fla/che operon in Bacillus subtilis. J. Bacteriol. 180:35483555.
78. Estrem, S. T.,, W. Ross,, T. Gaal,, Z. W. Chen,, W. Niu,, R. H. Ebright,, and R. L. Gourse. 1999. Bacterial promoter architecture: subsite structure of UP elements and interactions with the carboxy-terminal domain of the RNA polymerase alpha subunit. Genes Dev. 13:21342147.
79. Fajardo-Cavazos, P.,, F. Tovar-Rojo,, and P. Setlow. 1991. Effect of promoter mutations and upstream deletions on the expression of genes coding for small, acid-soluble spore proteins of Bacillus subtilis. J. Bacteriol. 173:20112016.
80. Feavers, I. M.,, J. Foulkes,, B. Setlow,, D. Sun,, W. Nicholson,, P. Setlow,, and A. Moir. 1990. The regulation of transcription of the gerA spore germination operon of Bacillus subtilis. Mol. Microbiol. 4:275282.
81. Feavers, I. M.,, V. Price,, and A. Moir. 1988. The regulation of the fumarase (citG) gene of Bacillus subtilis 168. Mol. Gen. Genet. 211:465471.
82. Foulger, D.,, and J. Errington. 1991. Sequential activation of dual promoters by different sigma factors maintains spoVJ expression during successive developmental stages of Bacillus subtilis. Mol. Microbiol. 5:13631373.
83. Frandsen, N.,, and P. Stragier. 1995. Identification and characterization of the Bacillus subtilis spoIIP locus. J. Bacteriol. 177:716722.
84. Fredrick, K.,, T. Caramori,, Y. F. Chen,, A. Galizzi,, and J. D. Helmann. 1995. Promoter architecture in the flagellar regulon of Bacillus subtilis: high-level expression of flagellin by the sigma D RNA polymerase requires an upstream promoter element. Proc. Natl. Acad. Sci. USA 92:25822586.
85. Fredrick, K.,, and J. D. Helmann. 1996. FlgM is a primary regulator of sigmaD activity, and its absence restores motility to a sinR mutant. J. Bacteriol. 178:70107013.
86. Fredrick, K. L.,, and J. D. Helmann. 1994. Dual chemotaxis signaling pathways in Bacillus subtilis: a sigma D-dependent gene encodes a novel protein with both CheW and CheY homologous domains. J. Bacteriol. 176:27272735.
87. Fujita, M. 1999. Identification of new sigma K-dependent promoters using an in vitro transcription system derived from Bacillus subtilis. Gene 237:4552.
88. Gardan, R.,, G. Rapoport,, and M. Debarbouille. 1995. Expression of the rocDEF operon involved in arginine catabolism in Bacillus subtilis. J. Mol. Biol. 249:843856.
89. Gardan, R.,, G. Rapoport,, and M. Debarbouille. 1997. Role of the transcriptional activator RocR in the arginine-degradation pathway of Bacillus subtilis. Mol. Microbiol. 24:825837.
90. Ge, Y.,, I. G. Old,, I. S. Girons,, and N. W. Charon. 1997. The flgK motility operon of Borrelia burgdorferi is initiated by a sigma 70-like promoter. Microbiology 143:16811690.
91. Ge, Y.,, I. G. Old,, I. Saint Girons,, and N. W. Charon. 1997. Molecular characterization of a large Borrelia burgdorferi motility operon which is initiated by a consensus sigma70 promoter. J. Bacteriol. 179:22892299.
92. Gholamhoseinian, A.,, Z. Shen,, J. J. Wu,, and P. Piggot. 1992. Regulation of transcription of the cell division gene ftsA during sporulation of Bacillus subtilis. J. Bacteriol. 174:46474656.
93. Gilman, M. Z.,, J. S. Glenn,, V. L. Singer,, and M. J. Chamberlin. 1984. Isolation of sigma-28-specific promoters from Bacillus subtilis DNA. Gene 32:1120.
94. Gomez, M.,, and S. M. Cutting. 1997. BofC encodes a putative forespore regulator of the Bacillus subtilis sigma K checkpoint. Microbiology 143:157170.
95. Gomez, M.,, and S. M. Cutting. 1996. Expression of the Bacillus subtilis spolVB gene is under dual sigma F/sigma G control. Microbiology 142:34533457.
96. Gonzy-Treboul, G.,, C. Karmazyn-Campelli,, and P. Stragier. 1992. Developmental regulation of transcription of the Bacillus subtilis ftsAZ operon. J. Mol. Biol. 224:967979.
97. Greene, E. A.,, and G. B. Spiegelman. 1996. The SpoOA protein of Bacillus subtilis inhibits transcription of the abrB gene without preventing binding of the polymerase to the promoter. J. Biol. Chem. 271:1145511461.
98. Haldenwang, W. G. 1995. The sigma factors of Bacillus subtilis. Microbiol Rev. 59:130.
99. Haldenwang, W. G.,, N. Lang,, and R. Losick. 1981. A sporulation-induced sigma-like regulatory protein from B. subtilis. Cell 23:615624.
100. Haldenwang, W. G.,, and R. Losick. 1980. Novel RNA polymerase sigma factor from Bacillus subtilis. Proc. Natl. Acad. Sci. USA 77:70007004.
101. Han, W. D.,, S. Kawamoto,, Y. Hosoya,, M. Fujita,, Y. Sadaie,, K. Suzuki,, Y. Ohashi,, F. Kawamura,, and K. Ochi. 1998. A novel sporulation-control gene (spoOM) of Bacillus subtilis with a sigmaH-regulated promoter. Gene 217:3140.
102. Hancock, R. E.,, and D. S. Chappie. 1999. Peptide antibiotics. Antimicrob. Agents Chemother. 43:13171323.
103. Hanlon, D. W.,, and G. W. Ordal. 1994. Cloning and characterization of genes encoding methyl-accepting chemotaxis proteins in Bacillus subtilis. J. Biol. Chem. 269:1403814046.
104. Hanlon, D. W.,, M. M. Rosario,, G. W. Ordal,, G. Venema,, and D. Van Sinderen. 1994. Identification of TlpC, a novel 62 kDa MCP-like protein from Bacillus subtilis. Microbiology 140:18471854.
105. Hecker, M.,, W. Schumann,, and U. Volker. 1996. Heat-shock and general stress response in Bacillus subtilis. Mol. Microbiol. 19:417428.
106. Helmann, J. D. 1991. Alternative sigma factors and the regulation of flagellar gene expression. Mol. Microbiol. 5:28752882.
107. Helmann, J. D. 1999. Anti-sigma factors. Curr. Opin. Microbiol. 2:135141.
108. Helmann, J. D. 1995. Compilation and analysis of Bacillus subtilis sigma A-dependent promoter sequences: evidence for extended contact between RNA polymerase and upstream promoter DNA. Nucleic Acids Res. 23:23512360.
109. Helmann, J. D.,, and M. J. Chamberlin. 1987. DNA sequence analysis suggests that expression of flagellar and chemotaxis genes in Escherichia coli and Salmonella typhimurium is controlled by an alternative sigma factor. Proc. Natl. Acad. Sci. USA 84:64226424.
110. Helmann, J. D.,, L. M. Marquez,, and M. J. Chamberlin. 1988. Cloning, sequencing, and disruption of the Bacillus subtilis sigma 28 gene. J. Bacteriol. 170:15681574.
111. Henkin, T. M. 1996. Control of transcription termination in prokaryotes. Annu. Rev. Genet. 30:3557.
112. Henkin, T. M. 1994. tRNA-directed transcription antitermination. Mol. Microbiol. 13:381387.
113. Henkin, T. M.,, and A. L. Sonenshein. 1987. Mutations of the Escherichia coli lacUV5 promoter resulting in increased expression in Bacillus subtilis. Mol. Gen. Genet. 209:467474.
114. Henriques, A. O.,, B. W. Beall,, and C. P. Moran, Jr. 1997. CotM of Bacillus subtilis, a member of the alpha-crystallin family of stress proteins, is induced during development and participates in spore outer coat formation. J. Bacteriol. 179:18871897.
115. Henriques, A. O.,, B. W. Beall,, K. Roland,, and C. P. Moran, Jr. 1995. Characterization of cotJ, a sigma E-controlled operon affecting the polypeptide composition of the coat of Bacillus subtilis spores. J. Bacteriol. 177:33943406.
116. Henriques, A. O.,, E. M. Bryan,, B. W. Beall,, and C. P. Moran, Jr. 1997. csel5, cse60, and csk22 are new members of mother-cell-specific sporulation regulons in Bacillus subtilis. J. Bacteriol. 179:389398.
117. Hofmeister, A. E.,, A. Londono-Vallejo,, E. Harry,, P. Stragier,, and R. Losick. 1995. Extracellular signal protein triggering the proteolytic activation of a developmental transcription factor in B. subtilis. Cell 83:219226.
118. Horsburgh, M. J.,, and A. Moir. 1999. Sigma M, an ECF RNA polymerase sigma factor of Bacillus subtilis 168, is essential for growth and survival in high concentrations of salt. Mol. Microbiol. 32:4150.
119. Huang, M.,, F. B. Oppermann-Sanio,, and A. Steinbuchel. 1999. Biochemical and molecular characterization of the Bacillus subtilis acetoin catabolic pathway. J. Bacteriol. 181:38373841.
120. Huang, X.,, A. Decatur,, A. Sorokin,, and J. D. Helmann. 1997. The Bacillus subtilis sigma(X) protein is an extracytoplasmic function sigma factor contributing to survival at high temperature. J. Bacteriol. 179:29152921.
121. Huang, X.,, K. L. Fredrick,, and J. D. Helmann. 1998. Promoter recognition by Bacillus subtilis sigmaW: autoregulation and partial overlap with the sigmaX regulon. J. Bacteriol. 180:37653770.
122. Huang, X.,, A. Gaballa,, M. Cao,, and J. D. Helmann. 1999. Identification of target promoters for the Bacillus subtilis extracytoplasmic function sigma factor, sigma W. Mol. Microbiol. 31:361371.
123. Huang, X.,, and J. D. Helmann. 1998. Identification of target promoters for the Bacillus subtilis sigma X factor using a consensus-directed search. J. Mol. Biol. 279:165173.
124. Hughes, K. T.,, K. L. Gillen,, M. J. Semon,, and J. E. Karlinksy. 1993. Sensing structural intermediates in bacterial flagellar assembly by export of a negative regulator. Science 262:12771280.
125. Ichikawa, H.,, R. Halberg,, and L. Kroos. 1999. Negative regulation by the Bacillus subtilis GerE protein. J. Biol. Chem. 274:83228327.
126. Ming, N.,, and J. Errington. 1991. The spoIIIA operon of Bacillus subtilis defines a new temporal class of mother-cell-specific sporulation genes under the control of the sigma E form of RNA polymerase. Mol. Microbiol. 5:19271940.
127. Ingham, C. J.,, J. Dennis,, and P. A. Furneaux. 1999. Autogenous regulation of transcription termination factor Rho and the requirement for Nus factors in Bacillus subtilis. Mol. Microbiol. 31:651663.
128. Ireton, K.,, and A. D. Grossman. 1992. Interactions among mutations that cause altered timing of gene expression during sporulation in Bacillus subtilis. J. Bacteriol. 174:31853195.
129. Ishikawa, S.,, K. Yamane,, and J. Sekiguchi. 1998. Regulation and characterization of a newly deduced cell wall hydrolase gene (cwlJ) which affects germination of Bacillus subtilis spores. J. Bacteriol. 180:13751380.
130. Jaacks, K. J.,, J. Healy,, R. Losick,, and A. D. Grossman. 1989. Identification and characterization of genes controlled by the sporulation-regulatory gene spoOH in Bacillus subtilis. J. Bacteriol. 171:41214129.
131. Jonas, R. M.,, E. A. Weaver,, T. J. Kenney,, C. P. Moran, Jr.,, and W. G. Haldenwang. 1988. The Bacillus subtilis spoIIG operon encodes both sigma E and a gene necessary for sigma E activation. J. Bacteriol. 170:507511.
132. Jones, C. H.,, and C. P. Moran, Jr. 1992. Mutant sigma factor blocks transition between promoter binding and initiation of transcription. Proc. Natl. Acad. Sci. USA 89:19581962.
133. Ju, J.,, T. Luo,, and W. G. Haldenwang. 1997. Bacillus subtilis Pro-sigmaE fusion protein localizes to the forespore septum and fails to be processed when synthesized in the forespore. J. Bacteriol. 179:48884893.
134. Juang, Y. L.,, and J. D. Helmann. 1994. The delta subunit of Bacillus subtilis RNA polymerase. An allosteric effector of the initiation and core-recycling phases of transcription. J. Mol. Biol. 239:114.
135. Juang, Y. L.,, and J. D. Helmann. 1995. Pathway of promoter melting by Bacillus subtilis RNA polymerase at a stable RNA promoter: effects of temperature, delta protein, and sigma factor mutations. Biochemistry 34:84658473.
136. Juang, Y. L.,, and J. D. Helmann. 1994. A promoter melting region in the primary sigma factor of Bacillus subtilis. Identification of functionally important aromatic amino acids. J. Mol. Biol. 235:14701488.
137. Karow, M. L.,, P. Glaser,, and P. J. Piggot. 1995. Identification of a gene, spoIIR, that links the activation of sigma E to the transcriptional activity of sigma F during sporulation in Bacillus subtilis. Proc. Natl. Acad. Sci. USA 92:20122016.
138. Keilty, S.,, and M. Rosenberg. 1987. Constitutive function of a positively regulated promoter reveals new sequences essential for activity. J. Biol. Chem. 262:63896395.
139. Kellner, E. M.,, A. Decatur,, and C. P. Moran, Jr. 1996. Two-stage regulation of an anti-sigma factor determines developmental fate during bacterial endospore formation. Mol. Microbiol. 21:913924.
140. Kemp, E. H.,, R. L. Sammons,, A. Moir,, D. Sun,, and P. Setlow. 1991. Analysis of transcriptional control of the gerD spore germination gene of Bacillus subtilis 168. J. Bacteriol. 173:46464652.
141. Kenney, T. J.,, P. A. Kirchman,, and C. P. Moran, Jr. 1988. Gene encoding sigma E is transcribed from a sigma A-like promoter in Bacillus subtilis. J. Bacteriol. 170:30583064.
142. Kenney, T. J.,, and C. P. Moran, Jr. 1987. Organization and regulation of an operon that encodes a sporulation-essential sigma factor in Bacillus subtilis. J. Bacteriol. 169:33293339.
143. Kenney, T. J.,, K. York,, P. Youngman,, and C. P. Moran, Jr. 1989. Genetic evidence that RNA polymerase associated with sigma A factor uses a sporulation-specific promoter in Bacillus subtilis. Proc. Natl. Acad. Sci USA 86:91099113.
144. Kiel, J. A.,, J. M. Boels,, G. Beldman,, and G. Venema. 1994. Glycogen in Bacillus subtilis: molecular characterization of an operon encoding enzymes involved in glycogen biosynthesis and degradation. Mol. Microbiol. 11:203218.
145. Kirchman, P. A.,, H. DeGrazia,, E. M. Kellner,, and C. P. Moran, Jr. 1993. Forespore-specific disappearance of the sigma-factor antagonist SpoIIAB: implications for its role in determination of cell fate in Bacillus subtilis. Mol. Microbiol. 8:663671.
146. Klose, K. E.,, and J. J. Mekalanos. 1998. Differential regulation of multiple flagellins in Vibrio cholerae. J. Bacteriol. 180:303316.
147. Kodama, T.,, H. Takamatsu,, K. Asai,, K. Kobayashi,, N. Ogasawara,, and K. Watabe. 1999. The Bacillus subtilis yaaH gene is transcribed by SigE RNA polymerase during sporulation, and its product is involved in germination of spores. J. Bacteriol. 181:45844591.
148. Kroos, L.,, B. Zhang,, H. Ichikawa,, and Y. T. Yu. 1999. Control of sigma factor activity during Bacillus subtilis sporulation. Mol. Microbiol. 31:12851294.
149. Kunkel, B.,, K. Sandman,, S. Panzer,, P. Youngman,, and R. Losick. 1988. The promoter for a sporulation gene in the spoIVC locus of Bacillus subtilis and its use in studies of temporal and spatial control of gene expression. J. Bacteriol. 170:35133522.
150. Kunst, F., et al. 1997. The complete genome sequence of the gram-positive bacterium Bacillus subtilis. Nature 390:249256.
151. Kuroda, A.,, Y. Asami,, and J. Sekiguchi. 1993. Molecular cloning of a sporulation-specific cell wall hydrolase gene of Bacillus subtilis. J. Bacteriol. 175:62606268.
152. Kutsukake, K. 1994. Excretion of the anti-sigma factor through a flagellar substructure couples flagellar gene expression with flagellar assembly in Salmonella typhimurium. Mol. Gen. Genet. 243:605612.
153. LaBell, T. L.,, J. E. Trempy,, and W. G. Haldenwang. 1987. Sporulation-specific sigma factor sigma 29 of Bacillus subtilis is synthesized from a precursor protein, P31. Proc. Natl. Acad. Sci. USA 84:17841788.
154. Lampe, M.,, C. Binnie,, R. Schmidt,, and R. Losick. 1988. Cloned gene encoding the delta subunit of Bacillus subtilis RNA polymerase. Gene 67:1319.
155. Lazarevic, V.,, P. Margot,, B. Soldo,, and D. Karamata. 1992. Sequencing and analysis of the Bacillus subtilis lyt-RABC divergon: a regulatory unit encompassing the structural genes of the N-acetylmuramoyl-L-alanine amidase and its modifier. J. Gen. Microbiol. 138:19491961.
156. Lee, S.,, and C. W. Price. 1993. The minCD locus of Bacillus subtilis lacks the minE determinant that provides topological specificity to cell division. Mol. Microbiol. 7:601610.
157. Levin, P. A.,, N. Fan,, E. Ricca,, A. Driks,, R. Losick,, and S. Cutting. 1993. An unusually small gene required for sporulation by Bacillus subtilis. Mol. Microbiol. 9:761771.
158. Li, X.,, L. Lindahl,, Y. Sha,, and J. M. Zengel. 1997. Analysis of the Bacillus subtilis S10 ribosomal protein gene cluster identifies two promoters that may be responsible for transcription of the entire 15-kilobase S10-spc-alpha cluster. J. Bacteriol. 179:70467054.
159. Liu, J.,, W. M. Cosby,, and P. Zuber. 1999. Role of Lon and ClpX in the post-translational regulation of a sigma subunit of RNA polymerase required for cellular differentiation in Bacillus subtilis. Mol. Microbiol. 33:415428.
160. Liu, J.,, and P. Zuber. 1998. A molecular switch controlling competence and motility: competence regulatory factors ComS, MecA, and ComK control sigmaD-dependent gene expression in Bacillus subtilis. J. Bacteriol. 180:42434251.
161. Lonetto, M. A.,, K. L. Brown,, K. E. Rudd,, and M. J. Buttner. 1994. Analysis of the Streptomyces coelicolor sigE gene reveals the existence of a subfamily of eubacterial σ factors involved in the regulation of extracytoplasmic functions. Proc. Natl. Acad. Sci. USA 91:75737577.
162. Lopez de Saro, F. J.,, A. Y. Woody,, and J. D. Helmann. 1995. Structural analysis of the Bacillus subtilis delta factor: a protein polyanion which displaces RNA from RNA polymerase. J. Mol. Biol. 252:189202.
163. Lopez de Saro, F. J.,, N. Yoshikawa,, and J. D. Helmann. 1999. Expression, abundance, and RNA polymerase binding properties of the delta factor of Bacillus subtilis. J. Biol. Chem. 274:1595315958.
164. Lopez-Diaz, I.,, S. Clarke,, and J. Mandelstam. 1986. spoIID operon of Bacillus subtilis: cloning and sequence. J. Gen. Microbiol. 132:341354.
165. Losick, R.,, and P. Stragier. 1992. Crisscross regulation of cell-type-specific gene expression during development in B. subtilis. Nature 355:601604.
166. Lu, S.,, S. Cutting,, and L. Kroos. 1995. Sporulation protein SpoIVFB from Bacillus subtilis enhances processing of the sigma factor precursor Pro-sigma K in the absence of other sporulation gene products. J. Bacteriol. 177:10821085.
167. Magnin, T.,, M. Lord,, and M. D. Yudkin. 1997. Contribution of partner switching and SpoIIAA cycling to regulation of sigmaF activity in sporulating Bacillus subtilis. J. Bacteriol. 179:39223927.
168. Manganelli, R.,, E. Dubnau,, S. Tyagi,, F. R. Kramer,, and I. Smith. 1999. Differential expression of 10 sigma factor genes in Mycobacterium tuberculosis. Mol. Microbiol. 31:715724.
169. Margot, P.,, C. Mauel,, and D. Karamata. 1994- The gene of the N-acetylglucosaminidase, a Bacillus subtilis 168 cell wall hydrolase not involved in vegetative cell autolysis. Mol. Microbiol. 12:535545.
170. Margot, P.,, M. Pagni,, and D. Karamata. 1999. Bacillus subtilis 168 gene lytF encodes a gamma-D-glutamatemeso-diaminopimelate muropeptidase expressed by the alternative vegetative sigma factor, sigmaD. Microbiology 145:5765.
171. Marquez, L. M.,, J. D. Helmann,, E. Ferrari,, H. M. Parker,, G. W. Ordal,, and M. J. Chamberlin. 1990. Studies of sigma D-dependent functions in Bacillus subtilis. J. Bacteriol. 172:34353443.
172. Matsumoto, K.,, M. Okada,, Y. Horikoshi,, H. Matsuzaki,, T. Kishi,, M. Itaya,, and I. Shibuya. 1998. Cloning, sequencing, and disruption of the Bacillus subtilis psd gene coding for phosphatidylserine decarboxylase. J. Bacteriol. 180:100106.
173. McAllister, C. F.,, and E. C. Achberger. 1988. Effect of polyadenine-containing curved DNA on promoter utilization in Bacillus subtilis. J. Biol. Chem. 263:1174311749.
174. McDonnell, G. E.,, H. Wood,, K. M. Devine,, and D. J. McConnell. 1994. Genetic control of bacterial suicide: regulation of the induction of PBSX in Bacillus subtilis. J. Bacteriol. 176:58205830.
175. Mekjian, K. R.,, E. M. Bryan,, B. W. Beall,, and C. P. Moran, Jr. 1999. Regulation of hexuronate utilization in Bacillus subtilis. J. Bacteriol. 181:426433.
176. Mencia, M.,, M. Monsalve,, F. Rojo,, and M. Salas. 1998. Substitution of the C-terminal domain of the Escherichia coli RNA polymerase alpha subunit by that from Bacillus subtilis makes the enzyme responsive to a Bacillus subtilis transcriptional activator. J. Mol. Biol. 275:177185.
177. Mencia, M.,, M. Monsalve,, F. Rojo,, and M. Salas. 1996. Transcription activation by phage phi29 protein p4 is mediated by interaction with the alpha subunit of Bacillus subtilis RNA polymerase. Proc. Natl. Acad. Sci. USA 93:66166620.
178. Metzger, R.,, D. P. Brown,, P. Grealish,, M. J. Staver,, J. Versalovic,, J. R. Lupski,, and L. Katz. 1994. Characterization of the macromolecular synthesis (MMS) operon from Listeria monocytogenes. Gene 151:161166.
179. Min, K. T.,, C. M. Hilditch,, B. Diederich,, J. Errington,, and M. D. Yudkin. 1993. Sigma F, the first compartment-specific transcription factor of B. subtilis, is regulated by an anti-sigma factor that is also a protein kinase. Cell 74:735742.
180. Mirel, D. B.,, and M. J. Chamberlin. 1989. The Bacillus subtilis flagellin gene (hag) is transcribed by the sigma 28 form of RNA polymerase. J. Bacteriol. 171:30953101.
181. Mirel, D. B.,, W. F. Estacio,, M. Mathieu,, E. Olmsted,, J. Ramirez,, and L. M. Marquez-Magana. 2000. Environmental regulation of Bacillus subtilis sigma(D)-dependent gene expression. J. Bacteriol. 182:30553062.
182. Mirel, D. B.,, P. Lauer,, and M. J. Chamberlin. 1994. Identification of flagellar synthesis regulatory and structural genes in a sigma D-dependent operon of Bacillus subtilis. J. Bacteriol. 176:44924500.
183. Mirel, D. B.,, V. M. Lustre,, and M. J. Chamberlin. 1992. An operon of Bacillus subtilis motility genes transcribed by the sigma D form of RNA polymerase. J. Bacteriol. 174:41974204.
184. Missiakas, D.,, and S. Raina. 1998. The extracytoplasmic function sigma factors: role and regulation. Mol. Microbiol. 28:10591066.
185. Miyao, A.,, G. Theeragool,, M. Takeuchi,, and Y. Kobayashi. 1993. Bacillus subtilis spoVE gene is transcribed by sigma E-associated RNA polymerase. J. Bacteriol. 175:40814086.
186. Moch, C.,, O. Schrogel,, and R. Allmansberger. 1998. The sigmaD-dependent transcription of the ywcG gene from Bacillus subtilis is dependent on an excess of glucose and glutamate. Mol. Microbiol. 27:889898.
187. Moldover, B.,, P. J. Piggot,, and M. D. Yudkin. 1991. Identification of the promoter and the transcriptional start site of the spoVA operon of Bacillus subtilis and Bacillus licheniformis. J. Gen. Microbiol. 137:527531.
188. Monkgolsuk, S. Personal communication.
189. Monsalve, M.,, M. Mencia,, M. Salas,, and F. Rojo. 1996. Protein p4 represses phage phi 29 A2c promoter by interacting with the alpha subunit of Bacillus subtilis RNA polymerase. Proc. Natl. Acad. Sci. USA 93:89138918.
190. Mooney, R. A.,, I. Artsimovitch,, and R. Landick. 1998. Information processing by RNA polymerase: recognition of regulatory signals during RNA chain elongation. J. Bacteriol. 180:32653275.
191. Moran, C. P., Jr.,, N. Lang,, C. D. Banner,, W. G. Haldenwang,, and R. Losick. 1981. Promoter for a developmentally regulated gene in Bacillus subtilis. Cell 25:783791.
192. Moran, C. P., Jr.,, N. Lang,, S. F. LeGrice,, G. Lee,, M. Stephens,, A. L. Sonenshein,, J. Pero,, and R. Losick. 1982. Nucleotide sequences that signal the initiation of transcription and translation in Bacillus subtilis. Mol. Gen. Genet. 186:339346.
193. Moriyama, R.,, H. Fukuoka,, S. Miyata,, S. Kudoh,, A. Hattori,, S. Kozuka,, Y. Yasuda,, K. Tochikubo,, and S. Makino. 1999. Expression of a germination-specific amidase, SleB, of Bacilli in the forespore compartment of sporulating cells and its localization on the exterior side of the cortex in dormant spores. J. Bacteriol. 181:23732378.
194. Mukherjee, K.,, and D. Chatterji. 1997. Studies on the omega subunit of Escherichia coli RNA polymerase—its role in the recovery of denatured enzyme activity. Eur. J. Biochem. 247:884889.
195. Mukherjee, K.,, H. Nagai,, N. Shimamoto,, and D. Chatterii. 1999. GroEL is involved in activation of Escherichia coli RNA polymerase devoid of the omega subunit in vivo. Eur. J. Biochem. 266:228235.
196. Muller, J.,, S. Schiel,, G. W. Ordal,, and H. H. Saxild. 1997. Functional and genetic characterization of mcpC, which encodes a third methyl-accepting chemotaxis protein in Bacillus subtilis. Microbiology 143:32313240.
197. Naclerio, G.,, L. Baccigalupi,, R. Zilhao,, M. De Felice,, and E. Ricca. 1996. Bacillus subtilis spore coat assembly requires cotH gene expression. J. Bacteriol. 178:43754380.
198. Najafi, S. M.,, D. A. Harris,, and M. D. Yudkin. 1997. Properties of the phosphorylation reaction catalyzed by SpoIIAB that help to regulate sporulation of Bacillus subtilis. J. Bacteriol. 179:56285631.
199. Naryshkin, N.,, A. Revyakin,, Y. Kim,, V. Mekler,, and R. H. Ebright. 2000. Structural organization of the RNA polymerase-promoter open complex. Cell 101:601611.
200. Nicholas, R.,, and D. Gentry. Personal communication.
201. Nicholson, W. L.,, D. X. Sun,, B. Setlow,, and P. Setlow. 1989. Promoter specificity of sigma G-containing RNA polymerase from sporulating cells of Bacillus subtilis: identification of a group of forespore-specific promoters. J. Bacteriol. 171:27082718.
202. Novak, R.,, E. Charpentier,, J. S. Braun,, and E. Tuomanen. 2000. Signal transduction by a death signal peptide: uncovering the mechanism of bacterial killing by penicillin. Mol. Cell 5:4957.
203. Nudler, E. 1999. Transcription elongation: structural basis and mechanisms. J. Mol. Biol. 288:112.
204. Nugroho, F. A.,, H. Yamamoto,, Y. Kobayashi,, and J. Sekiguchi. 1999. Characterization of a new sigma-K-dependent peptidoglycan hydrolase gene that plays a role in Bacillus subtilis mother cell lysis. J. Bacteriol. 181:62306237.
205. Ogura, M.,, and T. Tanaka. 1996. Transcription of Bacillus subtilis degR is sigma D dependent and suppressed by multicopy proB through sigma D. J. Bacteriol. 178:216222.
206. Okada, M.,, H. Matsuzaki,, I. Shibuya,, and K. Mat-sumoto. 1994. Cloning, sequencing, and expression in Escherichia coli of the Bacillus subtilis gene for phos-phatidylserine synthase. J. Bacteriol. 176:74567461.
207. Pedersen, L. B.,, K. Ragkousi,, T. J. Cammett,, E. Melly,, A. Sekowska,, E. Schopick,, T. Murray,, and P. Setlow. 2000. Characterization of ywhE, which encodes a putative high-molecular-weight class A penicillin-binding protein in Bacillus subtilis. Gene 246:187196.
208. Pedraza-Reyes, M.,, F. Gutierrez-Corona,, and W. L. Nicholson. 1997. Spore photoproduct lyase operon (spIAB) regulation during Bacillus subtilis sporulation: modulation of splB-lacZ fusion expression by P1 promoter mutations and by an in-frame deletion of splA. Curr. Microbiol. 34:133137.
209. Perego, M.,, P. Glaser,, A. Minutello,, M. A. Strauch,, K. Leopold,, and W. Fischer. 1995. Incorporation of D-alanine into lipoteichoic acid and wall teichoic acid in Bacillus subtilis. Identification of genes and regulation. J. Biol. Chem. 270:1559815606.
210. Peschel, A.,, M. Otto,, R. W. Jack,, H. Kalbacher,, G. Jung,, and F. Gotz. 1999. Inactivation of the dlt operon in Staphylococcus aureus confers sensitivity to defensins, protegrins, and other antimicrobial peptides. J. Biol. Chem. 274:84058410.
211. Petersohn, A.,, H. Antelmann,, U. Gerth,, and M. Hecker. 1999. Identification and transcriptional analysis of new members of the sigmaB regulon in Bacillus subtilis. Microbiology 145:869880.
212. Petersohn, A.,, S. Engelmann,, P. Setlow,, and M. Hecker. 1999. The katX gene of Bacillus subtilis is under dual control of sigmaB and sigmaF. Mol. Gen. Genet. 262:173179.
213. Pogliano, K.,, A. E. Hofmeister,, and R. Losick. 1997. Disappearance of the sigma E transcription factor from the forespore and the SpoIIE phosphatase from the mother cell contributes to establishment of cell-specific gene expression during sporulation in Bacillus subtilis. J. Bacteriol. 179:33313341.
214. Popham, D. L.,, and P. Stragier. 1991. Cloning, characterization, and expression of the spoVB gene of Bacillus subtilis. J. Bacteriol. 173:79427949.
215. Predich, M.,, G. Nair,, and I. Smith. 1992. Bacillus subtilis early sporulation genes kinA, spoOF, and spoOA are transcribed by the RNA polymerase containing sigma H. J. Bacteriol. 174:27712778.
216. Price, C. W., 2000. Protective function and regulation of the general stress response in Bacillus subtilis and related gram-positive bacteria, p. 179197. In G. Storz, and R. Hengge-Aronis (ed.), Bacterial Stress Responses. ASM Press, Washington, D.C..
217. Price, C. W.,, M. A. Gitt,, and R. H. Doi. 1983. Isolation and physical mapping of the gene encoding the major sigma factor of Bacillus subtilis RNA polymerase. Proc. Natl. Acad. Sci. USA 80:40744078.
218. Puttikhunt, C.,, T. Nihira,, and Y. Yamada. 1995. Cloning, nucleotide sequence, and transcriptional analysis of the nusG gene of Streptomyces coelicolor A3(2), which encodes a putative transcriptional antiterminator. Mol. Gen. Genet. 247:118122.
219. Qi, F. X.,, and R. H. Doi. 1990. Localization of a second SigH promoter in the Bacillus subtilis sigA operon and regulation of dnaE expression by the promoter. J. Bacteriol. 172:56315636.
220. Qi, F. X.,, X. S. He,, and R. H. Doi. 1991. Localization of a new promoter, P5, in the sigA operon of Bacillus subtilis and its regulation in some spo mutant strains. J. Bacteriol. 173:70507054.
221. Qiu, J.,, and J. D. Helmann. 2001. The -10 region is a key promoter specificity determinant for the Bacillus subtilis extracytoplasmic-function sigma factors sigma (X) and sigma (W) J. Bacteriol. 183:19211927.
222. Qiu, J.,, and J. D. Helmann. Unpublished data.
223. Quirk, P. G.,, E. A. Dunkley, Jr.,, P. Lee,, and T. A. Krulwich. 1993. Identification of a putative Bacillus subtilis rho gene. J. Bacteriol. 175:647654.
224. Rashid, M. H.,, M. Mori,, and J. Sekiguchi. 1995. Glucosaminidase of Bacillus subtilis: cloning, regulation, primary structure and biochemical characterization. Microbiology 141:23912404.
225. Rather, P. N.,, R. E. Hay,, G. L. Ray,, W. G. Haldenwang,, and C. P. Moran, Jr. 1986. Nucleotide sequences that define promoters that are used by Bacillus subtilis sigma-29 RNA polymerase. J. Mol. Biol. 192:557565.
226. Rather, P. N.,, and C. P. Moran, Jr. 1988. Compartment-specific transcription in Bacillus subtilis: identification of the promoter for gdh. J. Bacteriol. 170:50865092.
227. Ray, G. L.,, and W. G. Haldenwang. 1986. Isolation of Bacillus subtilis genes transcribed in vitro and in vivo by a major sporulation-induced, DNA-dependent RNA polymerase. J. Bacteriol. 166:472478.
228. Resnekov, O.,, S. Alper,, and R. Losick. 1996. Subcellular localization of proteins governing the proteolytic activation of a developmental transcription factor in Bacillus subtilis. Genes Cells 1:529542.
229. Resnekov, O.,, A. Driks,, and R. Losick. 1995. Identification and characterization of sporulation gene spoVS from Bacillus subtilis. J. Bacteriol. 177:56285635.
230. Resnekov, O.,, and R. Losick. 1998. Negative regulation of the proteolytic activation of a developmental transcription factor in Bacillus subtilis. Proc. Natl. Acad. Sci. USA 95:31623167.
231. Ricca, E.,, S. Cutting,, and R. Losick. 1992. Characterization of bofA, a gene involved in intercompartmental regulation of pro-sigma K processing during sporulation in Bacillus subtilis. J. Bacteriol. 174:31773184.
232. Roels, S.,, A. Driks,, and R. Losick. 1992. Characterization of spoIVA, a sporulation gene involved in coat morphogenesis in Bacillus subtilis. J. Bacteriol. 174:575585.
233. Roels, S.,, and R. Losick. 1995. Adjacent and divergently oriented operons under the control of the sporulation regulatory protein GerE in Bacillus subtilis. J. Bacteriol. 177:62636275.
234. Rojo, F.,, M. Mencia,, M. Monsalve,, and M. Salas. 1998. Transcription activation and repression by interaction of a regulator with the alpha subunit of RNA polymerase: the model of phage phi 29 protein p4. Prog. Nucleic Acid Res. Mol. Biol. 60:2946.
235. Rojo, F.,, B. Nuez,, M. Mencia,, and M. Salas. 1993. The main early and late promoters of Bacillus subtilis phage phi 29 form unstable open complexes with sigma A-RNA polymerase that are stabilized by DNA supercoiling. Nucleic Acids Res. 21:935940.
236. Rong, J. C.,, and J. D. Helmann. 1994. Genetic and physiological studies of Bacillus subtilis sigma A mutants defective in promoter melting. J. Bacteriol. 176:52185224.
237. Rong, S.,, M. S. Rosenkrantz,, and A. L. Sonenshein. 1986. Transcriptional control of the Bacillus subtilis spoIID gene. J. Bacteriol. 165:771779.
238. Rosario, M. M.,, K. L. Fredrick,, G. W. Ordal,, and J. D. Helmann. 1994. Chemotaxis in Bacillus subtilis requires either of two functionally redundant CheW homo logs. J. Bacteriol. 176:27362739.
239. Ross, W.,, S. E. Aiyar,, J. Salomon,, and R. L. Gourse. 1998. Escherichia coli promoters with UP elements of different strengths: modular structure of bacterial promoters. J. Bacteriol. 180:53755383.
240. Ross, W.,, K. K. Gosink,, J. Salomon,, K. Igarashi,, C. Zou,, A. Ishihama,, K. Severinov,, and R. L. Gourse. 1993. A third recognition element in bacterial promoters: DNA binding by the alpha subunit of RNA polymerase. Science 262:14071413.
241. Sacco, M.,, E. Ricca,, R. Losick,, and S. Cutting. 1995. An additional GerE-controlled gene encoding an abundant spore coat protein from Bacillus subtilis. J. Bacteriol. 177:372377.
242. Sandman, K.,, L. Kroos,, S. Cutting,, P. Youngman,, and R. Losick. 1988. Identification of the promoter for a spore coat protein gene in Bacillus subtilis and studies on the regulation of its induction at a late stage of sporulation. J. Mol. Biol. 200:461473.
243. Satola, S.,, P. A. Kirchman,, and C. P. Moran, Jr. 1991. SpoOA binds to a promoter used by sigma A RNA polymerase during sporulation in Bacillus subtilis. Proc. Natl. Acad. Sci. USA 88:45334537.
244. Satola, S. W.,, J. M. Baldus,, and C. P. Moran, Jr. 1992. Binding of SpoOA stimulates spoIIG promoter activity in Bacillus subtilis. J. Bacteriol. 174:14481453.
245. Schmidt, R.,, P. Margolis,, L. Duncan,, R. Coppolecchia,, C. P. Moran, Jr.,, and R. Losick. 1990. Control of developmental transcription factor sigma F by sporulation regulatory proteins SpoIIAA and SpoIIAB in Bacillus subtilis. Proc. Natl. Acad. Sci USA 87:92219225.
246. Schuch, R.,, and P. J. Piggot. 1994. The dacF-spoIIA operon of Bacillus subtilis, encoding sigma F, is autoregu-lated. J. Bacteriol. 176:41044110.
247. Sekiguchi, J.,, K. Akeo,, H. Yamamoto,, F. K. Khasanov,, J. C. Alonso,, and A. Kuroda. 1995. Nucleotide sequence and regulation of a new putative cell wall hydrolase gene, cwlD, which affects germination in Bacillus subtilis. J. Bacteriol. 177:55825589.
248. Serrano, M.,, R. Fior,, C. P. Moran, Jr.,, and A. O. Henriques. Unpublished data.
249. Shcheptov, M.,, G. Chyu,, I. Bagyan,, and S. Cutting. 1997. Characterization of csgA, a new member of the forespore-expressed sigmaG-regulon from Bacillus subtilis. Gene 184:133140.
250. Siranosian, K. J.,, and A. D. Grossman. 1994. Activation of spoOA transcription by sigma H is necessary for sporulation but not for competence in Bacillus subtilis. J. Bacteriol. 176:38123815.
251. Smith, K.,, and P. Youngman. 1993. Evidence that the spoIIM gene of Bacillus subtilis is transcribed by RNA polymerase associated with sigma E. J. Bacteriol. 175:36183627.