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.
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A. Maghnouj, T. F. de Sousa Cabral, V. Stalon, and C. Vander Wauven The arcABDC Gene Cluster, Encoding the Arginine Deiminase Pathway of Bacillus licheniformis, and Its Activation by the Arginine Repressor ArgR J. Bacteriol., December 15, 1998; 180(24): 6468 - 6475. [Abstract] [Full Text]
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S. E. Aiyar, R. L. Gourse, and W. Ross Upstream A-tracts increase bacterial promoter activity through interactions with the RNA polymerase alpha subunit PNAS, December 8, 1998; 95(25): 14652 - 14657. [Abstract] [Full Text] [PDF]
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W. Ross, S. E. Aiyar, J. Salomon, and R. L. Gourse Escherichia coli Promoters with UP Elements of Different Strengths: Modular Structure of Bacterial Promoters J. Bacteriol., October 15, 1998; 180(20): 5375 - 5383. [Abstract] [Full Text]
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S. T. Estrem, T. Gaal, W. Ross, and R. L. Gourse Identification of an UP element consensus sequence for bacterial promoters PNAS, August 18, 1998; 95(17): 9761 - 9766. [Abstract] [Full Text] [PDF]
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Z. Eichenbaum, M. J. Federle, D. Marra, W. M. de Vos, O. P. Kuipers, M. Kleerebezem, and J. R. Scott Use of the Lactococcal nisA Promoter To Regulate Gene Expression in Gram-Positive Bacteria: Comparison of Induction Level and Promoter Strength Appl. Envir. Microbiol., August 1, 1998; 64(8): 2763 - 2769. [Abstract] [Full Text]
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M. D. Bashyam and A. K. Tyagi Identification and Analysis of "Extended -10" Promoters from Mycobacteria J. Bacteriol., May 1, 1998; 180(9): 2568 - 2573. [Abstract] [Full Text]
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J. P. Brandner and L. Kroos Identification of the Omega 4400 Regulatory Region, a Developmental Promoter of Myxococcus xanthus J. Bacteriol., April 15, 1998; 180(8): 1995 - 2004. [Abstract] [Full Text]
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C. Scharf, S. Riethdorf, H. Ernst, S. Engelmann, U. Völker, and M. Hecker Thioredoxin Is an Essential Protein Induced by Multiple Stresses in Bacillus subtilis J. Bacteriol., April 1, 1998; 180(7): 1869 - 1877. [Abstract] [Full Text]
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M. M. S. M. Wösten, M. Boeve, M. G. A. Koot, A. C. van Nuenen, and B. A. M. van der Zeijst Identification of Campylobacter jejuni Promoter Sequences J. Bacteriol., February 1, 1998; 180(3): 594 - 599. [Abstract] [Full Text]
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 C.A. GROSS, C. CHAN, A. DOMBROSKI, T. GRUBER, M. SHARP, J. TUPY, and B. YOUNG The Functional and Regulatory Roles of Sigma Factors in Transcription Cold Spring Harb Symp Quant Biol, January 1, 1998; 63(0): 141 - 156. [Abstract] [PDF]
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K. Fredrick and J. D. Helmann RNA polymerase sigma factor determines start-site selection but is not required for upstream promoter element activation on heteroduplex (bubble) templates PNAS, May 13, 1997; 94(10): 4982 - 4987. [Abstract] [Full Text] [PDF]
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