Compilation and Analysis of Bacillus Subtilis Sigma A-dependent Promoter Sequences: Evidence for Extended Contact Between RNA Polymerase and Upstream Promoter DNA

Overview

Journal Nucleic Acids Res

Publisher Oxford University Press

Specialty Biochemistry

Date 1995 Jul 11

PMID 7630711

Citations 183

Authors

J D Helmann

Affiliations

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Abstract

Sequence analysis of 236 promoters recognized by the Bacillus subtilis sigma A-RNA polymerase reveals an extended promoter structure. The most highly conserved bases include the -35 and -10 hexanucleotide core elements and a TG dinucleotide 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 A2- and T2-rich sequences in the upstream promoter region (-36 to -70) which are phased with the DNA helix: An 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 alpha subunits of the polymerase core bind DNA and that the promoter may wrap around RNA polymerase.

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References

Glaser P, Kunst F, Arnaud M, Coudart M, Gonzales W, Hullo M . Bacillus subtilis genome project: cloning and sequencing of the 97 kb region from 325 degrees to 333 degrees. Mol Microbiol. 1993; 10(2):371-84. View

Sorokin A, Zumstein E, Azevedo V, Ehrlich S, Serror P . The organization of the Bacillus subtilis 168 chromosome region between the spoVA and serA genetic loci, based on sequence data. Mol Microbiol. 1993; 10(2):385-95. DOI: 10.1111/j.1365-2958.1993.tb02670.x. View

Benson D, Boguski M, Lipman D, Ostell J . GenBank. Nucleic Acids Res. 1994; 22(17):3441-4. PMC: 308298. DOI: 10.1093/nar/22.17.3441. View

Burns H, Minchin S . Thermal energy requirement for strand separation during transcription initiation: the effect of supercoiling and extended protein DNA contacts. Nucleic Acids Res. 1994; 22(19):3840-5. PMC: 308378. DOI: 10.1093/nar/22.19.3840. View

Matern H, Klein J, Henrich B, PLAPP R . Determination and comparison of Lactobacillus delbrueckii ssp. lactis DSM7290 promoter sequences. FEMS Microbiol Lett. 1994; 122(1-2):121-8. DOI: 10.1111/j.1574-6968.1994.tb07154.x. View

Riethdorf S, Volker U, Gerth U, Winkler A, Engelmann S, Hecker M . Cloning, nucleotide sequence, and expression of the Bacillus subtilis lon gene. J Bacteriol. 1994; 176(21):6518-27. PMC: 197005. DOI: 10.1128/jb.176.21.6518-6527.1994. View

Popham D, Setlow P . Cloning, nucleotide sequence, mutagenesis, and mapping of the Bacillus subtilis pbpD gene, which codes for penicillin-binding protein 4. J Bacteriol. 1994; 176(23):7197-205. PMC: 197107. DOI: 10.1128/jb.176.23.7197-7205.1994. View

Hahn J, Inamine G, Kozlov Y, Dubnau D . Characterization of comE, a late competence operon of Bacillus subtilis required for the binding and uptake of transforming DNA. Mol Microbiol. 1993; 10(1):99-111. DOI: 10.1111/j.1365-2958.1993.tb00907.x. View

Koide A, Hoch J . Identification of a second oligopeptide transport system in Bacillus subtilis and determination of its role in sporulation. Mol Microbiol. 1994; 13(3):417-26. DOI: 10.1111/j.1365-2958.1994.tb00436.x. View

10.

Okada M, Matsuzaki H, Shibuya I, Matsumoto K . Cloning, sequencing, and expression in Escherichia coli of the Bacillus subtilis gene for phosphatidylserine synthase. J Bacteriol. 1994; 176(24):7456-61. PMC: 197200. DOI: 10.1128/jb.176.24.7456-7461.1994. View

11.

Wise A, PRICE C . Four additional genes in the sigB operon of Bacillus subtilis that control activity of the general stress factor sigma B in response to environmental signals. J Bacteriol. 1995; 177(1):123-33. PMC: 176564. DOI: 10.1128/jb.177.1.123-133.1995. View

12.

Ledeaux J, Grossman A . Isolation and characterization of kinC, a gene that encodes a sensor kinase homologous to the sporulation sensor kinases KinA and KinB in Bacillus subtilis. J Bacteriol. 1995; 177(1):166-75. PMC: 176569. DOI: 10.1128/jb.177.1.166-175.1995. View

13.

Nakano M, Yang F, Hardin P, Zuber P . Nitrogen regulation of nasA and the nasB operon, which encode genes required for nitrate assimilation in Bacillus subtilis. J Bacteriol. 1995; 177(3):573-9. PMC: 176630. DOI: 10.1128/jb.177.3.573-579.1995. View

14.

Strauch M, Ayazifar M . Bent DNA is found in some, but not all, regions recognized by the Bacillus subtilis AbrB protein. Mol Gen Genet. 1995; 246(6):756-60. DOI: 10.1007/BF00290723. View

15.

Fredrick K, Caramori T, Chen Y, Galizzi A, Helmann J . 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 U S A. 1995; 92(7):2582-6. PMC: 42262. DOI: 10.1073/pnas.92.7.2582. View

16.

van Sinderen D, Kiewiet R, Venema G . Differential expression of two closely related deoxyribonuclease genes, nucA and nucB, in Bacillus subtilis. Mol Microbiol. 1995; 15(2):213-23. DOI: 10.1111/j.1365-2958.1995.tb02236.x. View

17.

Lavigne M, Herbert M, Kolb A, Buc H . Upstream curved sequences influence the initiation of transcription at the Escherichia coli galactose operon. J Mol Biol. 1992; 224(2):293-306. DOI: 10.1016/0022-2836(92)90995-v. View

18.

Stragier P . Developmental regulation of transcription of the Bacillus subtilis ftsAZ operon. J Mol Biol. 1992; 224(4):967-79. DOI: 10.1016/0022-2836(92)90463-t. View

19.

Holmberg C, RUTBERG B . Expression of the gene encoding glycerol-3-phosphate dehydrogenase (glpD) in Bacillus subtilis is controlled by antitermination. Mol Microbiol. 1991; 5(12):2891-900. DOI: 10.1111/j.1365-2958.1991.tb01849.x. View

20.

Green C, Vold B . A cluster of nine tRNA genes between ribosomal gene operons in Bacillus subtilis. J Bacteriol. 1992; 174(10):3147-51. PMC: 205980. DOI: 10.1128/jb.174.10.3147-3151.1992. View