Abstract
The repressor of phage 434 binds to six operator sites on the phage chromosome1–3. A comparison of the sequences of these 14-base-pair (bp) operator sites3 reveals a striking pattern: at five of the six sites, the symmetrically arrayed outer eight base pairs (four in each half-site) are identical and the remaining site differs at only one position (Fig. 1b). In contrast, the sequences of the inner four base pairs are highly variable. Crystallographic analysis of the represser–operator complex4 shows that at each half-site, the 'recognition α-helix' of the repressor is positioned in the major groove such that it could contact the outermost five base pairs, but not the innermost two (Fig. 1a). We show in this paper that the sequence of the central base pairs of the operator (two in each half-site) have a significant role in determining operator affinity for repressor, despite the evidence presented here and in the accompanying paper4 that these base pairs are not contacted by repressor. We also show that these central base pairs influence operator affinity for Cro, a second gene regulatory protein encoded by phage 434 (ref. 5). We discuss the likely structural basis for this evidently indirect, but sequence-dependent, effect of the central base pairs of the operator on its affinity for the two regulatory proteins.
This is a preview of subscription content, access via your institution
Access options
Subscribe to this journal
Receive 51 print issues and online access
$199.00 per year
only $3.90 per issue
Buy this article
- Purchase on Springer Link
- Instant access to full article PDF
Prices may be subject to local taxes which are calculated during checkout
Similar content being viewed by others
References
Johnson, A. D. et al. Nature 294, 217–223 (1981).
Wharton, R. P., Brown, E. L. & Ptashne, M. Cell 38, 361–369 (1984).
Wharton, R. P. thesis, Harvard Univ. (1985).
Anderson, J. E., Ptashne, M. & Harrison, S. C. Nature 326, 888–891 (1987).
Crosschedl, R. & Schwarz, E. Nucleic Acids Res. 6, 867–881 (1979).
Eliason, J. L., Weiss, M. A. & Ptashne, M. Proc. natn. Acad. Sci. U.S.A. 82, 2339–2343 (1984).
Pabo, C. O., Krovatin, W., Jeffrey, A. & Sauer, R. T. Nature 298, 441–443 (1982).
Sauer, R. T., Yocum, R. R., Doolittle, R. F., Lewis, M. & Pabo, C. O. Nature 298, 447–451 (1982).
Drew, H. R. & Travers, A. A. J. molec. Biol. 186, 773–790 (1985).
Satchwell, S. C., Drew, H. R. & Travers, A. A. J. molec. Biol. 191, 659–675 (1986).
Calladine, C. R. J. molec. Biol. 343–352 (1982).
Fratini, A. V., Kopka, M. L., Drew, H. R. & Dickerson, R. E. J. biol. Chem. 257, 14686–14707 (1982).
Anderson, J. E. thesis, Harvard Univ. (1984).
Ptashne, M. A Genetic Switch (Blackwell, Palo Alto, 1986).
Maniatis, T., Fritsch, E. F. & Sambrook, J. Molecular Cloning, a Laboratory Manual (Cold Spring Harbor Laboratory, New York, 1982).
Yannisch-Perron, C., Vieira, J. & Messing, J. Gene 33, 103–119 (1985).
Messing, J. Meth. Enzym. 101, 29–79 (1983).
Maxam, A. M. & Gilbert, W. Proc. natn. Acad. Sci. U.S.A. 74, 560–564 (1977).
Johnson, A. D., Meyer, B. J. & Ptashne, M. Proc. natn. Acad. Sci. U.S.A. 76, 5061–5065 (1979).
Zoller, M. J. & Smith, M. Nucleic Acids Res. 10, 6487–6500 (1982).
Anderson, J. A., Ptashne, M. & Harrison, S. C. Proc. natn. Acad. Sci. U.S.A. 81, 1307–1311 (1984).
Author information
Authors and Affiliations
Rights and permissions
About this article
Cite this article
Koudelka, G., Harrison, S. & Ptashne, M. Effect of non-contacted bases on the affinity of 434 operator for 434 repressor and Cro. Nature 326, 886–888 (1987). https://doi.org/10.1038/326886a0
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1038/326886a0
This article is cited by
-
An affinity-structure database of helix-turn-helix: DNA complexes with a universal coordinate system
BMC Bioinformatics (2015)
-
A single spacer nucleotide determines the specificities of two mRNA regulatory proteins
Nature Structural & Molecular Biology (2005)
-
Fine mapping of inherent flexibility variation along DNA molecules. Validation by atomic force microscopy (AFM) in buffer
Molecular Genetics and Genomics (2005)
-
Statistical analysis of DNA duplex structures in solution derived by high resolution NMR
Applied Magnetic Resonance (1994)
-
Extracting refined rules from knowledge-based neural networks
Machine Learning (1993)
Comments
By submitting a comment you agree to abide by our Terms and Community Guidelines. If you find something abusive or that does not comply with our terms or guidelines please flag it as inappropriate.