Nucleic Acids Research, 1995, Vol. 23, No. 13 2351-2360
© 1995
SURVEY AND SUMMARY |
Compilation and analysus of Bacillus Subtilis 
A-dependent promoter sequences: evidence for extended contact between RNA polymerse and upstream promoter DNA
Section of Microbiology, Cornell University Ithaca, NY 14853–8101, USA
Received March 3, 1995. Accepted May 24, 1995.
Sequence analysis of 236 promoters recognized by the Bacillus subtilis 
ARNA polymerase reveals an extended promoter structure. The most highly conserved bases include the –35 and –10 hexanucleotide core elements and a TG dlnucleotide at position –15,–14. In addition, several weakly conserved A and T residues are present upstream of the –35 region. Analysis of dinucleotide composition reveals A 2and T2-rich sequences in the upstream promoter region (–36 to –70) which are phased with the DNA helix: A,, tracts are common near –43, –54 and –65; Tn tracts predominate at the intervening positions. When compared with larger regions of the genome, upstream promoter regions have an excess of An and Tn sequences for n > 4. These data indicate that an RNA polymerase binding site affects DNA sequence as far upstream as –70. This sequence conservation is discussed in light of recent evidence that the a subunits of the polymerase core bind DNA and that the promoter may wrap around RNA polymerase.
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  C. Paige, S. D. Reid, P. C. Hanna, and A. Claiborne The Type III Pantothenate Kinase Encoded by coaX Is Essential for Growth of Bacillus anthracis J. Bacteriol., September 15, 2008; 190(18): 6271 - 6275. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
K. Nagorska, K. Hinc, M. A. Strauch, and M. Obuchowski Influence of the {sigma}B Stress Factor and yxaB, the Gene for a Putative Exopolysaccharide Synthase under {sigma}B Control, on Biofilm Formation J. Bacteriol., May 15, 2008; 190(10): 3546 - 3556. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 M. Leibig, B. Krismer, M. Kolb, A. Friede, F. Gotz, and R. Bertram Marker Removal in Staphylococci via Cre Recombinase and Different lox Sites Appl. Envir. Microbiol., March 1, 2008; 74(5): 1316 - 1323. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 J. Bursy, A. J. Pierik, N. Pica, and E. Bremer Osmotically Induced Synthesis of the Compatible Solute Hydroxyectoine Is Mediated by an Evolutionarily Conserved Ectoine Hydroxylase J. Biol. Chem., October 26, 2007; 282(43): 31147 - 31155. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 T. D. Schoep and K. Gregg Isolation and characterization of putative Pseudobutyrivibrio ruminis promoters Microbiology, September 1, 2007; 153(9): 3071 - 3080. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. Romero, E. Merino, F. Bolivar, G. Gosset, and A. Martinez Metabolic Engineering of Bacillus subtilis for Ethanol Production: Lactate Dehydrogenase Plays a Key Role in Fermentative Metabolism Appl. Envir. Microbiol., August 15, 2007; 73(16): 5190 - 5198. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 M. Haenni, P. Moreillon, and V. Lazarevic Promoter and Transcription Analysis of Penicillin-Binding Protein Genes in Streptococcus gordonii Antimicrob. Agents Chemother., August 1, 2007; 51(8): 2774 - 2783. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. Chen, M. Bagdasarian, M. G. Kaufman, A. K. Bates, and E. D. Walker Mutational Analysis of the ompA Promoter from Flavobacterium johnsoniae J. Bacteriol., July 15, 2007; 189(14): 5108 - 5118. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. M. Fung, R. M. Morris, L. Adrian, and S. H. Zinder Expression of Reductive Dehalogenase Genes in Dehalococcoides ethenogenes Strain 195 Growing on Tetrachloroethene, Trichloroethene, or 2,3-Dichlorophenol Appl. Envir. Microbiol., July 15, 2007; 73(14): 4439 - 4445. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J.-H. Shin and C. W. Price The SsrA-SmpB Ribosome Rescue System Is Important for Growth of Bacillus subtilis at Low and High Temperatures J. Bacteriol., May 15, 2007; 189(10): 3729 - 3737. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. Muramatsu and Y. Hihara Coordinated High-Light Response of Genes Encoding Subunits of Photosystem I Is Achieved by AT-Rich Upstream Sequences in the Cyanobacterium Synechocystis sp. Strain PCC 6803 J. Bacteriol., April 1, 2007; 189(7): 2750 - 2758. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J.-S. Lin and G.-C. Shaw Regulation of the kduID operon of Bacillus subtilis by the KdgR repressor and the ccpA gene: identification of two KdgR-binding sites within the kdgR-kduI intergenic region Microbiology, March 1, 2007; 153(3): 701 - 710. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. Bizzini, P. Majcherczyk, S. Beggah-Moller, B. Soldo, J. M. Entenza, M. Gaillard, P. Moreillon, and V. Lazarevic Effects of {alpha}-phosphoglucomutase deficiency on cell wall properties and fitness in Streptococcus gordonii Microbiology, February 1, 2007; 153(2): 490 - 498. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. Shulami, G. Zaide, G. Zolotnitsky, Y. Langut, G. Feld, A. L. Sonenshein, and Y. Shoham A Two-Component System Regulates the Expression of an ABC Transporter for Xylo-Oligosaccharides in Geobacillus stearothermophilus Appl. Envir. Microbiol., February 1, 2007; 73(3): 874 - 884. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
L. Shen, X. Feng, Y. Yuan, X. Luo, T. P. Hatch, K. T. Hughes, J. S. Liu, and Y.-x. Zhang Selective Promoter Recognition by Chlamydial {sigma}28 Holoenzyme J. Bacteriol., November 1, 2006; 188(21): 7364 - 7377. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. Schmitz, A. Hoffmann, C. Szekat, B. Rudd, and G. Bierbaum The Lantibiotic Mersacidin Is an Autoinducing Peptide Appl. Envir. Microbiol., November 1, 2006; 72(11): 7270 - 7277. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 N. Agarwal and A. K. Tyagi Mycobacterial transcriptional signals: requirements for recognition by RNA polymerase and optimal transcriptional activity Nucleic Acids Res., September 10, 2006; 34(15): 4245 - 4257. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
T. A. Gaidenko, T.-J. Kim, A. L. Weigel, M. S. Brody, and C. W. Price The Blue-Light Receptor YtvA Acts in the Environmental Stress Signaling Pathway of Bacillus subtilis. J. Bacteriol., September 1, 2006; 188(17): 6387 - 6395. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. M. Zalieckas, L. V. Wray Jr., and S. H. Fisher Cross-Regulation of the Bacillus subtilis glnRA and tnrA Genes Provides Evidence for DNA Binding Site Discrimination by GlnR and TnrA. J. Bacteriol., April 1, 2006; 188(7): 2578 - 2585. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
R. Seepersaud, R. H. V. Needham, C. S. Kim, and A. L. Jones Abundance of the {delta} Subunit of RNA Polymerase Is Linked to the Virulence of Streptococcus agalactiae J. Bacteriol., March 15, 2006; 188(6): 2096 - 2105. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. A. Ramirez-Romero, I. Masulis, M. A. Cevallos, V. Gonzalez, and G. Davila The Rhizobium etli {sigma}70 (SigA) factor recognizes a lax consensus promoter Nucleic Acids Res., March 9, 2006; 34(5): 1470 - 1480. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. M. Silvaggi, J. B. Perkins, and R. Losick Genes for Small, Noncoding RNAs under Sporulation Control in Bacillus subtilis J. Bacteriol., January 15, 2006; 188(2): 532 - 541. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
N. Mani, B. Dupuy, and A. L. Sonenshein Isolation of RNA Polymerase from Clostridium difficile and Characterization of Glutamate Dehydrogenase and rRNA Gene Promoters In Vitro and In Vivo J. Bacteriol., January 1, 2006; 188(1): 96 - 102. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. M. Silvaggi, J. B. Perkins, and R. Losick Small Untranslated RNA Antitoxin in Bacillus subtilis J. Bacteriol., October 1, 2005; 187(19): 6641 - 6650. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
G. Real, S. M. Pinto, G. Schyns, T. Costa, A. O. Henriques, and C. P. Moran Jr. A Gene Encoding a Holin-Like Protein Involved in Spore Morphogenesis and Spore Germination in Bacillus subtilis J. Bacteriol., September 15, 2005; 187(18): 6443 - 6453. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
T. Tanaka, H. Ishida, and T. Maehara Characterization of the Replication Region of Plasmid pLS32 from the Natto Strain of Bacillus subtilis J. Bacteriol., July 1, 2005; 187(13): 4315 - 4326. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 M. Gupta and J. S. Liu De novo cis-regulatory module elicitation for eukaryotic genomes PNAS, May 17, 2005; 102(20): 7079 - 7084. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
K. Streker, C. Freiberg, H. Labischinski, J. Hacker, and K. Ohlsen Staphylococcus aureus NfrA (SA0367) Is a Flavin Mononucleotide-Dependent NADPH Oxidase Involved in Oxidative Stress Response J. Bacteriol., April 1, 2005; 187(7): 2249 - 2256. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. Kamionka, R. Bertram, and W. Hillen Tetracycline-Dependent Conditional Gene Knockout in Bacillus subtilis Appl. Envir. Microbiol., February 1, 2005; 71(2): 728 - 733. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
K. B. Arnvig, B. Gopal, K. G. Papavinasasundaram, R. A. Cox, and M. J. Colston The mechanism of upstream activation in the rrnB operon of Mycobacterium smegmatis is different from the Escherichia coli paradigm Microbiology, February 1, 2005; 151(2): 467 - 473. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
W. Ross and R. L. Gourse Sequence-independent upstream DNA-{alpha}CTD interactions strongly stimulate Escherichia coli RNA polymerase-lacUV5 promoter association PNAS, January 11, 2005; 102(2): 291 - 296. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
G. Amati, P. Bisicchia, and A. Galizzi DegU-P Represses Expression of the Motility fla-che Operon in Bacillus subtilis J. Bacteriol., September 15, 2004; 186(18): 6003 - 6014. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
P. Joseph, A. Guiseppi, A. Sorokin, and F. Denizot Characterization of the Bacillus subtilis YxdJ response regulator as the inducer of expression for the cognate ABC transporter YxdLM Microbiology, August 1, 2004; 150(8): 2609 - 2617. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
F. Lorquet, P. Goffin, L. Muscariello, J.-B. Baudry, V. Ladero, M. Sacco, M. Kleerebezem, and P. Hols Characterization and Functional Analysis of the poxB Gene, Which Encodes Pyruvate Oxidase in Lactobacillus plantarum J. Bacteriol., June 15, 2004; 186(12): 3749 - 3759. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. Liu, M. Tolstorukov, V. Zhurkin, S. Garges, and S. Adhya A mutant spacer sequence between -35 and -10 elements makes the Plac promoter hyperactive and cAMP receptor protein-independent PNAS, May 4, 2004; 101(18): 6911 - 6916. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
W. J. J. Meijer and M. Salas Relevance of UP elements for three strong Bacillus subtilis phage {phi}29 promoters Nucleic Acids Res., February 18, 2004; 32(3): 1166 - 1176. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
K. A. Susanna, A. F. van der Werff, C. D. den Hengst, B. Calles, M. Salas, G. Venema, L. W. Hamoen, and O. P. Kuipers Mechanism of Transcription Activation at the comG Promoter by the Competence Transcription Factor ComK of Bacillus subtilis J. Bacteriol., February 15, 2004; 186(4): 1120 - 1128. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
O. Uziel, I. Borovok, R. Schreiber, G. Cohen, and Y. Aharonowitz Transcriptional Regulation of the Staphylococcus aureus Thioredoxin and Thioredoxin Reductase Genes in Response to Oxygen and Disulfide Stress J. Bacteriol., January 15, 2004; 186(2): 326 - 334. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
D. B. Hicks, Z. Wang, Y. Wei, R. Kent, A. A. Guffanti, H. Banciu, D. H. Bechhofer, and T. A. Krulwich A tenth atp gene and the conserved atpI gene of a Bacillus atp operon have a role in Mg2+ uptake PNAS, September 2, 2003; 100(18): 10213 - 10218. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. E. Mitchell, D. Zheng, S. J. W. Busby, and S. D. Minchin Identification and analysis of 'extended -10' promoters in Escherichia coli Nucleic Acids Res., August 15, 2003; 31(16): 4689 - 4695. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
D. A. Schofield, C. Westwater, B. D. Hoel, P. A. Werner, J. S. Norris, and M. G. Schmidt Development of a Thermally Regulated Broad-Spectrum Promoter System for Use in Pathogenic Gram-Positive Species Appl. Envir. Microbiol., June 1, 2003; 69(6): 3385 - 3392. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
C. S. Schaumburg and M. Tan Mutational analysis of the Chlamydia trachomatis dnaK promoter defines the optimal -35 promoter element Nucleic Acids Res., January 15, 2003; 31(2): 551 - 555. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
B. Soldo, V. Lazarevic, and D. Karamata tagO is involved in the synthesis of all anionic cell-wall polymers in Bacillus subtilis 168 Microbiology, July 1, 2002; 148(7): 2079 - 2087. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. Fuangthong, A. F. Herbig, N. Bsat, and J. D. Helmann Regulation of the Bacillus subtilis fur and perR Genes by PerR: Not All Members of the PerR Regulon Are Peroxide Inducible J. Bacteriol., June 15, 2002; 184(12): 3276 - 3286. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
T. Hao, D. Biran, G. J. Velicer, and L. Kroos Identification of the {Omega}4514 Regulatory Region, a Developmental Promoter of Myxococcus xanthus That Is Transcribed In Vitro by the Major Vegetative RNA Polymerase J. Bacteriol., June 15, 2002; 184(12): 3348 - 3359. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. H. Fisher and L. V. Wray Jr. Bacillus subtilis 168 Contains Two Differentially Regulated Genes Encoding L-Asparaginase J. Bacteriol., April 15, 2002; 184(8): 2148 - 2154. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. U. Kuhlmann and E. Bremer Osmotically Regulated Synthesis of the Compatible Solute Ectoine in Bacillus pasteurii and Related Bacillus spp. Appl. Envir. Microbiol., February 1, 2002; 68(2): 772 - 783. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
T. Hoffmann, A. Schutz, M. Brosius, A. Volker, U. Volker, and E. Bremer High-Salinity-Induced Iron Limitation in Bacillus subtilis J. Bacteriol., February 1, 2002; 184(3): 718 - 727. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
I. Moszer, L. M. Jones, S. Moreira, C. Fabry, and A. Danchin SubtiList: the reference database for the Bacillus subtilis genome Nucleic Acids Res., January 1, 2002; 30(1): 62 - 65. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. H. Godsey, N. N. Baranova, A. A. Neyfakh, and R. G. Brennan Crystal Structure of MtaN, a Global Multidrug Transporter Gene Activator J. Biol. Chem., December 7, 2001; 276(50): 47178 - 47184. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
H. Jarmer, T. S. Larsen, A. Krogh, H. H. Saxild, S. Brunak, and S. Knudsen Sigma A recognition sites in the Bacillus subtilis genome Microbiology, September 1, 2001; 147(9): 2417 - 2424. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 W. J. J. Meijer, J. A. Horcajadas, and M. Salas {phi}29 Family of Phages Microbiol. Mol. Biol. Rev., June 1, 2001; 65(2): 261 - 287. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
V. Burrus, C. Bontemps, B. Decaris, and G. Guédon Characterization of a Novel Type II Restriction-Modification System, Sth368I, Encoded by the Integrative Element ICESt1 of Streptococcus thermophilus CNRZ368 Appl. Envir. Microbiol., April 1, 2001; 67(4): 1522 - 1528. [Abstract] [Full Text]
|
|
|
|
|
|
S. M. Doree and M. H. Mulks Identification of an Actinobacillus pleuropneumoniae Consensus Promoter Structure J. Bacteriol., March 15, 2001; 183(6): 1983 - 1989. [Abstract] [Full Text]
|
|
|
|
|
|
T. Ishii, K.-i. Yoshida, G. Terai, Y. Fujita, and K. Nakai DBTBS: a database of Bacillus subtilis promoters and transcription factors Nucleic Acids Res., January 1, 2001; 29(1): 278 - 280. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
I. Artsimovitch, V. Svetlov, L. Anthony, R. R. Burgess, and R. Landick RNA Polymerases from Bacillus subtilis and Escherichia coli Differ in Recognition of Regulatory Signals In Vitro J. Bacteriol., November 1, 2000; 182(21): 6027 - 6035. [Abstract] [Full Text]
|
|
|
|
|
|
N. Goupil-Feuillerat, G. Corthier, J.-J. Godon, S. D. Ehrlich, and P. Renault Transcriptional and Translational Regulation of alpha -Acetolactate Decarboxylase of Lactococcus lactis subsp. lactis J. Bacteriol., October 1, 2000; 182(19): 5399 - 5408. [Abstract] [Full Text]
|
|
|
|
|
|
S. Derzelle, B. Hallet, K. P. Francis, T. Ferain, J. Delcour, and P. Hols Changes in cspL, cspP, and cspC mRNA Abundance as a Function of Cold Shock and Growth Phase in Lactobacillus plantarum J. Bacteriol., September 15, 2000; 182(18): 5105 - 5113. [Abstract] [Full Text]
|
|
|
|
|
|
C. Moch, O. Schrögel, and R. Allmansberger Transcription of the nfrA-ywcH Operon from Bacillus subtilis Is Specifically Induced in Response to Heat J. Bacteriol., August 15, 2000; 182(16): 4384 - 4393. [Abstract] [Full Text]
|
|
|
|
|
|
G. Venema Expression of the Neutral Protease Gene from a Thermophilic Bacillus sp. BT1 Strain in Bacillus subtilis and Its Natural Host: Identification of a Functional Promoter J. Bacteriol., July 15, 2000; 182(14): 4104 - 4107. [Abstract] [Full Text]
|
|
|
|
|
|
T. Burr, J. Mitchell, A. Kolb, S. Minchin, and S. Busby DNA sequence elements located immediately upstream of the -10 hexamer in Escherichia coli promoters: a systematic study Nucleic Acids Res., May 1, 2000; 28(9): 1864 - 1 |