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. 1988 Oct;120(2):319–327. doi: 10.1093/genetics/120.2.319

The Effects of Mutations in the Ant Promoter of Phage P22 Depend on Context

D Grana 1, T Gardella 1, M M Susskind 1
PMCID: PMC1203512  PMID: 3143618

Abstract

Recombination was used to construct 22 two- or three-way combinations of down- and up-mutations in P(ant), a strong, near-consensus promoter of phage P22. The relative strengths of these promoters in vivo were assayed by fusing them to an ant/lacZ gene fusion and measuring β-galactosidase levels produced by lysogens carrying the fusions on single-copy prophages. The results of these assays show that the magnitude of the effect of a promoter mutation can vary considerably when its context is changed by the presence of another mutation. In addition, as P(ant) approaches conformity with the consensus promoter sequence, the up-mutations decrease promoter strength, even though the same mutations increase promoter strength in the presence of a down-mutation. These context effects imply that individual consensus base pairs cannot be considered to contribute to promoter strength independently.

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Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Calos M. P. DNA sequence for a low-level promoter of the lac repressor gene and an 'up' promoter mutation. Nature. 1978 Aug 24;274(5673):762–765. doi: 10.1038/274762a0. [DOI] [PubMed] [Google Scholar]
  2. Carpousis A. J., Gralla J. D. Interaction of RNA polymerase with lacUV5 promoter DNA during mRNA initiation and elongation. Footprinting, methylation, and rifampicin-sensitivity changes accompanying transcription initiation. J Mol Biol. 1985 May 25;183(2):165–177. doi: 10.1016/0022-2836(85)90210-4. [DOI] [PubMed] [Google Scholar]
  3. Churchward G., Belin D., Nagamine Y. A pSC101-derived plasmid which shows no sequence homology to other commonly used cloning vectors. Gene. 1984 Nov;31(1-3):165–171. doi: 10.1016/0378-1119(84)90207-5. [DOI] [PubMed] [Google Scholar]
  4. Deuschle U., Kammerer W., Gentz R., Bujard H. Promoters of Escherichia coli: a hierarchy of in vivo strength indicates alternate structures. EMBO J. 1986 Nov;5(11):2987–2994. doi: 10.1002/j.1460-2075.1986.tb04596.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Graña D., Youderian P., Susskind M. M. Mutations that improve the ant promoter of Salmonella phage P22. Genetics. 1985 May;110(1):1–16. doi: 10.1093/genetics/110.1.1. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Harley C. B., Reynolds R. P. Analysis of E. coli promoter sequences. Nucleic Acids Res. 1987 Mar 11;15(5):2343–2361. doi: 10.1093/nar/15.5.2343. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Hawley D. K., McClure W. R. Compilation and analysis of Escherichia coli promoter DNA sequences. Nucleic Acids Res. 1983 Apr 25;11(8):2237–2255. doi: 10.1093/nar/11.8.2237. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Kammerer W., Deuschle U., Gentz R., Bujard H. Functional dissection of Escherichia coli promoters: information in the transcribed region is involved in late steps of the overall process. EMBO J. 1986 Nov;5(11):2995–3000. doi: 10.1002/j.1460-2075.1986.tb04597.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Leong J. M., Nunes-Düby S. E., Oser A. B., Lesser C. F., Youderian P., Susskind M. M., Landy A. Structural and regulatory divergence among site-specific recombination genes of lambdoid phage. J Mol Biol. 1986 Jun 20;189(4):603–616. doi: 10.1016/0022-2836(86)90491-2. [DOI] [PubMed] [Google Scholar]
  10. Mandecki W., Goldman R. A., Powell B. S., Caruthers M. H. lac Up-promoter mutants with increased homology to the consensus promoter sequence. J Bacteriol. 1985 Dec;164(3):1353–1355. doi: 10.1128/jb.164.3.1353-1355.1985. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Maxam A. M., Gilbert W. Sequencing end-labeled DNA with base-specific chemical cleavages. Methods Enzymol. 1980;65(1):499–560. doi: 10.1016/s0076-6879(80)65059-9. [DOI] [PubMed] [Google Scholar]
  12. McClure W. R. Mechanism and control of transcription initiation in prokaryotes. Annu Rev Biochem. 1985;54:171–204. doi: 10.1146/annurev.bi.54.070185.001131. [DOI] [PubMed] [Google Scholar]
  13. Mulligan M. E., Hawley D. K., Entriken R., McClure W. R. Escherichia coli promoter sequences predict in vitro RNA polymerase selectivity. Nucleic Acids Res. 1984 Jan 11;12(1 Pt 2):789–800. doi: 10.1093/nar/12.1part2.789. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Oka A., Sugisaki H., Takanami M. Nucleotide sequence of the kanamycin resistance transposon Tn903. J Mol Biol. 1981 Apr 5;147(2):217–226. doi: 10.1016/0022-2836(81)90438-1. [DOI] [PubMed] [Google Scholar]
  15. Sauer R. T., Krovatin W., DeAnda J., Youderian P., Susskind M. M. Primary structure of the immI immunity region of bacteriophage P22. J Mol Biol. 1983 Aug 25;168(4):699–713. doi: 10.1016/s0022-2836(83)80070-9. [DOI] [PubMed] [Google Scholar]
  16. Sauer R. T., Krovatin W., Poteete A. R., Berget P. B. Phage P22 tail protein: gene and amino acid sequence. Biochemistry. 1982 Nov 9;21(23):5811–5815. doi: 10.1021/bi00266a014. [DOI] [PubMed] [Google Scholar]
  17. Straney D. C., Crothers D. M. A stressed intermediate in the formation of stably initiated RNA chains at the Escherichia coli lac UV5 promoter. J Mol Biol. 1987 Jan 20;193(2):267–278. doi: 10.1016/0022-2836(87)90218-x. [DOI] [PubMed] [Google Scholar]
  18. Susskind M. M. A new gene of bacteriophage P22 which regulates synthesis of antirepressor. J Mol Biol. 1980 Apr 25;138(4):685–713. doi: 10.1016/0022-2836(80)90060-1. [DOI] [PubMed] [Google Scholar]
  19. Susskind M. M., Wright A., Botstein D. Superinfection exclusion by P22 prophage in lysogens of Salmonella typhimurium. II. Genetic evidence for two exclusion systems. Virology. 1971 Sep;45(3):638–652. doi: 10.1016/0042-6822(71)90178-4. [DOI] [PubMed] [Google Scholar]
  20. Szoke P. A., Allen T. L., deHaseth P. L. Promoter recognition by Escherichia coli RNA polymerase: effects of base substitutions in the -10 and -35 regions. Biochemistry. 1987 Sep 22;26(19):6188–6194. doi: 10.1021/bi00393a035. [DOI] [PubMed] [Google Scholar]
  21. Vershon A. K., Liao S. M., McClure W. R., Sauer R. T. Bacteriophage P22 Mnt repressor. DNA binding and effects on transcription in vitro. J Mol Biol. 1987 May 20;195(2):311–322. doi: 10.1016/0022-2836(87)90652-8. [DOI] [PubMed] [Google Scholar]
  22. Vieira J., Messing J. The pUC plasmids, an M13mp7-derived system for insertion mutagenesis and sequencing with synthetic universal primers. Gene. 1982 Oct;19(3):259–268. doi: 10.1016/0378-1119(82)90015-4. [DOI] [PubMed] [Google Scholar]
  23. Weinstock G. M., Susskind M. M., Botstein D. Regional specificity of illegitimate recombination by the translocatable ampicillin-resistance element Tn1 in the genome of phage P22. Genetics. 1979 Jul;92(3):685–710. doi: 10.1093/genetics/92.3.685. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. Wu T. H., Liao S. M., McClure W. R., Susskind M. M. Control of gene expression in bacteriophage P22 by a small antisense RNA. II. Characterization of mutants defective in repression. Genes Dev. 1987 Apr;1(2):204–212. doi: 10.1101/gad.1.2.204. [DOI] [PubMed] [Google Scholar]
  25. Youderian P., Bouvier S., Susskind M. M. Sequence determinants of promoter activity. Cell. 1982 Oct;30(3):843–853. doi: 10.1016/0092-8674(82)90289-6. [DOI] [PubMed] [Google Scholar]
  26. Youderian P., Susskind M. M. Bacteriophage P22 proteins specified by the region between genes 9 and erf. Virology. 1980 Nov;107(1):270–282. doi: 10.1016/0042-6822(80)90292-5. [DOI] [PubMed] [Google Scholar]

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