Abstract
The LexA repressor from Escherichia coli induces DNA bending upon interaction with the two overlapping operators which regulate the transcription of the colicin A encoding gene caa. Both caa operators harbor T-tracts adjacent to their recognition motifs. These tracts have been suggested to be especially favorable for the promotion of LexA-induced DNA bending. Here we show that this is indeed the case, since disruption of the TTTT-tract adjacent to operator O1 by the replacement of the two central thymine bases by AA, GA or CG markedly reduces LexA-induced DNA bending. Simple A.T-richness in this position is thus not sufficient to promote full LexA-induced bending, albeit a TAAT sequence is always more efficient to promote bending than those sequences containing one or two C/G base pairs.
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- Bertrand-Burggraf E., Hurstel S., Daune M., Schnarr M. Promoter properties and negative regulation of the uvrA gene by the LexA repressor and its amino-terminal DNA binding domain. J Mol Biol. 1987 Jan 20;193(2):293–302. doi: 10.1016/0022-2836(87)90220-8. [DOI] [PubMed] [Google Scholar]
- Crothers D. M., Gartenberg M. R., Shrader T. E. DNA bending in protein-DNA complexes. Methods Enzymol. 1991;208:118–146. doi: 10.1016/0076-6879(91)08011-6. [DOI] [PubMed] [Google Scholar]
- Diekmann S. Temperature and salt dependence of the gel migration anomaly of curved DNA fragments. Nucleic Acids Res. 1987 Jan 12;15(1):247–265. doi: 10.1093/nar/15.1.247. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Dumoulin P., Oertel-Buchheit P., Granger-Schnarr M., Schnarr M. Orientation of the LexA DNA-binding motif on operator DNA as inferred from cysteine-mediated phenyl azide crosslinking. Proc Natl Acad Sci U S A. 1993 Mar 1;90(5):2030–2034. doi: 10.1073/pnas.90.5.2030. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Gartenberg M. R., Crothers D. M. DNA sequence determinants of CAP-induced bending and protein binding affinity. Nature. 1988 Jun 30;333(6176):824–829. doi: 10.1038/333824a0. [DOI] [PubMed] [Google Scholar]
- Granger-Schnarr M., Lloubes R., de Murcia G., Schnarr M. Specific protein-DNA complexes: immunodetection of the protein component after gel electrophoresis and Western blotting. Anal Biochem. 1988 Oct;174(1):235–238. doi: 10.1016/0003-2697(88)90540-4. [DOI] [PubMed] [Google Scholar]
- Hagerman P. J. Sequence-directed curvature of DNA. Annu Rev Biochem. 1990;59:755–781. doi: 10.1146/annurev.bi.59.070190.003543. [DOI] [PubMed] [Google Scholar]
- Heumann H., Ricchetti M., Werel W. DNA-dependent RNA polymerase of Escherichia coli induces bending or an increased flexibility of DNA by specific complex formation. EMBO J. 1988 Dec 20;7(13):4379–4381. doi: 10.1002/j.1460-2075.1988.tb03336.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Hurstel S., Granger-Schnarr M., Schnarr M. Contacts between the LexA repressor--or its DNA-binding domain--and the backbone of the recA operator DNA. EMBO J. 1988 Jan;7(1):269–275. doi: 10.1002/j.1460-2075.1988.tb02809.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Kleinschmidt C., Tovar K., Hillen W. Computer simulations and experimental studies of gel mobility patterns for weak and strong non-cooperative protein binding to two targets on the same DNA: application to binding of tet repressor variants to multiple and single tet operator sites. Nucleic Acids Res. 1991 Mar 11;19(5):1021–1028. doi: 10.1093/nar/19.5.1021. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Koo H. S., Wu H. M., Crothers D. M. DNA bending at adenine . thymine tracts. Nature. 1986 Apr 10;320(6062):501–506. doi: 10.1038/320501a0. [DOI] [PubMed] [Google Scholar]
- Lane D., Prentki P., Chandler M. Use of gel retardation to analyze protein-nucleic acid interactions. Microbiol Rev. 1992 Dec;56(4):509–528. doi: 10.1128/mr.56.4.509-528.1992. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Little J. W. Mechanism of specific LexA cleavage: autodigestion and the role of RecA coprotease. Biochimie. 1991 Apr;73(4):411–421. doi: 10.1016/0300-9084(91)90108-d. [DOI] [PubMed] [Google Scholar]
- Lloubes R., Baty D., Lazdunski C. The promoters of the genes for colicin production, release and immunity in the ColA plasmid: effects of convergent transcription and Lex A protein. Nucleic Acids Res. 1986 Mar 25;14(6):2621–2636. doi: 10.1093/nar/14.6.2621. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Lloubes R., Granger-Schnarr M., Lazdunski C., Schnarr M. Interaction of a regulatory protein with a DNA target containing two overlapping binding sites. J Biol Chem. 1991 Feb 5;266(4):2303–2312. [PubMed] [Google Scholar]
- Lloubès R., Granger-Schnarr M., Lazdunski C., Schnarr M. LexA repressor induces operator-dependent DNA bending. J Mol Biol. 1988 Dec 20;204(4):1049–1054. doi: 10.1016/0022-2836(88)90062-9. [DOI] [PubMed] [Google Scholar]
- Sayers J. R., Schmidt W., Eckstein F. 5'-3' exonucleases in phosphorothioate-based oligonucleotide-directed mutagenesis. Nucleic Acids Res. 1988 Feb 11;16(3):791–802. doi: 10.1093/nar/16.3.791. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Schmitz A., Galas D. J. The interaction of RNA polymerase and lac repressor with the lac control region. Nucleic Acids Res. 1979 Jan;6(1):111–137. doi: 10.1093/nar/6.1.111. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Schnarr M., Oertel-Buchheit P., Kazmaier M., Granger-Schnarr M. DNA binding properties of the LexA repressor. Biochimie. 1991 Apr;73(4):423–431. doi: 10.1016/0300-9084(91)90109-e. [DOI] [PubMed] [Google Scholar]
- Stark M. J. Multicopy expression vectors carrying the lac repressor gene for regulated high-level expression of genes in Escherichia coli. Gene. 1987;51(2-3):255–267. doi: 10.1016/0378-1119(87)90314-3. [DOI] [PubMed] [Google Scholar]
- Straney S. B., Crothers D. M. Lac repressor is a transient gene-activating protein. Cell. 1987 Dec 4;51(5):699–707. doi: 10.1016/0092-8674(87)90093-6. [DOI] [PubMed] [Google Scholar]
- Travers A. A. DNA conformation and protein binding. Annu Rev Biochem. 1989;58:427–452. doi: 10.1146/annurev.bi.58.070189.002235. [DOI] [PubMed] [Google Scholar]
- Wu H. M., Crothers D. M. The locus of sequence-directed and protein-induced DNA bending. Nature. 1984 Apr 5;308(5959):509–513. doi: 10.1038/308509a0. [DOI] [PubMed] [Google Scholar]