DOI: 10.1128/jb.180.8.2201-2211.1998. The <i>Bacillus subtilis</i> DinR Binding Site: Redefinition of the Consensus Sequence

The Bacillus subtilis DinR Binding Site: Redefinition of the Consensus Sequence

10.1128/jb.180.8.2201-2211.1998

Crossref journal-article

American Society for Microbiology

Journal of Bacteriology (235)

Abstract

ABSTRACT Recently, the DinR protein was established as the cellular repressor of the SOS response in the bacterium Bacillus subtilis . It is believed that DinR functions as the repressor by binding to a consensus sequence located in the promoter region of each SOS gene. The binding site for DinR is believed to be synonymous with the formerly identified Cheo box, a region of 12 bp displaying dyad symmetry (GAAC-N 4 -GTTC). Electrophoretic mobility shift assays revealed that highly purified DinR does bind to such sites located upstream of the dinA , dinB , dinC , and dinR genes. Furthermore, detailed mutational analysis of the B. subtilis recA operator indicates that some nucleotides are more important than others for maintaining efficient DinR binding. For example, nucleotide substitutions immediately 5′ and 3′ of the Cheo box as well as those in the N 4 region appear to affect DinR binding. This data, combined with computational analyses of potential binding sites in other gram-positive organisms, yields a new consensus (DinR box) of 5′-CGAACRNRYGTTYC-3′. DNA footprint analysis of the B. subtilis dinR and recA DinR boxes revealed that the DinR box is centrally located within a DNA region of 31 bp that is protected from hydroxyl radical cleavage in the presence of DinR. Furthermore, while DinR is predominantly monomeric in solution, it apparently binds to the DinR box in a dimeric state.

Bibliography

Winterling, K. W., Chafin, D., Hayes, J. J., Sun, J., Levine, A. S., Yasbin, R. E., & Woodgate, R. (1998). The Bacillus subtilis DinR Binding Site: Redefinition of the Consensus Sequence. Journal of Bacteriology, 180(8), 2201â2211.

Authors 7

Kevin W. Winterling (first)
David Chafin (additional)
Jeffery J. Hayes (additional)
Ji Sun (additional)
Arthur S. Levine (additional)
Ronald E. Yasbin (additional)
Roger Woodgate (additional)

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Dates

Type	When
Created	5 years, 8 months ago (Dec. 31, 2019, 11:32 a.m.)
Deposited	4 years, 1 month ago (July 29, 2021, 2:27 p.m.)
Indexed	1 year, 2 months ago (June 20, 2024, 9:55 a.m.)
Issued	27 years, 4 months ago (April 15, 1998)
Published	27 years, 4 months ago (April 15, 1998)
Published Print	27 years, 4 months ago (April 15, 1998)

Funders 0

None

BibTeX

@article{Winterling_1998, title={The Bacillus subtilis DinR Binding Site: Redefinition of the Consensus Sequence}, volume={180}, ISSN={1098-5530}, url={http://dx.doi.org/10.1128/jb.180.8.2201-2211.1998}, DOI={10.1128/jb.180.8.2201-2211.1998}, number={8}, journal={Journal of Bacteriology}, publisher={American Society for Microbiology}, author={Winterling, Kevin W. and Chafin, David and Hayes, Jeffery J. and Sun, Ji and Levine, Arthur S. and Yasbin, Ronald E. and Woodgate, Roger}, year={1998}, month=apr, pages={2201–2211} }

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  "abstract": "<jats:title>ABSTRACT</jats:title>\n          <jats:p>\n            Recently, the DinR protein was established as the cellular repressor of the SOS response in the bacterium\n            <jats:italic>Bacillus subtilis</jats:italic>\n            . It is believed that DinR functions as the repressor by binding to a consensus sequence located in the promoter region of each SOS gene. The binding site for DinR is believed to be synonymous with the formerly identified Cheo box, a region of 12 bp displaying dyad symmetry (GAAC-N\n            <jats:sub>4</jats:sub>\n            -GTTC). Electrophoretic mobility shift assays revealed that highly purified DinR does bind to such sites located upstream of the\n            <jats:italic>dinA</jats:italic>\n            ,\n            <jats:italic>dinB</jats:italic>\n            ,\n            <jats:italic>dinC</jats:italic>\n            , and\n            <jats:italic>dinR</jats:italic>\n            genes. Furthermore, detailed mutational analysis of the\n            <jats:italic>B. subtilis recA</jats:italic>\n            operator indicates that some nucleotides are more important than others for maintaining efficient DinR binding. For example, nucleotide substitutions immediately 5\u2032 and 3\u2032 of the Cheo box as well as those in the N\n            <jats:sub>4</jats:sub>\n            region appear to affect DinR binding. This data, combined with computational analyses of potential binding sites in other gram-positive organisms, yields a new consensus (DinR box) of 5\u2032-CGAACRNRYGTTYC-3\u2032. DNA footprint analysis of the\n            <jats:italic>B. subtilis dinR</jats:italic>\n            and\n            <jats:italic>recA</jats:italic>\n            DinR boxes revealed that the DinR box is centrally located within a DNA region of 31 bp that is protected from hydroxyl radical cleavage in the presence of DinR. Furthermore, while DinR is predominantly monomeric in solution, it apparently binds to the DinR box in a dimeric state.\n          </jats:p>",
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