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. 1991 Mar;173(6):1944–1950. doi: 10.1128/jb.173.6.1944-1950.1991

Hierarchies of base pair preferences in the P22 ant promoter.

H Moyle 1, C Waldburger 1, M M Susskind 1
PMCID: PMC207725  PMID: 2001998

Abstract

Oligonucleotide-directed mutagenesis was used to complete a collection of mutations in the -35 and -10 hexamers of the ant promoter of Salmonella phage P22. The effects of all 36 single-base-pair substitutions on promoter strength in vivo were measured in strains carrying the mutant promoters fused to an ant-lacZ gene on a single-copy prophage. The results of these assays show that certain consensus base pairs are more important than others; in general, the least-critical positions are among the most poorly conserved. Some mutations within the hexamers have smaller effects on promoter strength than certain mutations outside the hexamers in this and other promoters. Several different patterns of base pair preferences are observed. These hierarchies of base pair preferences correlate well (but not perfectly) with the hierarchies defined by the frequency distribution of base pairs at each position among wild-type promoters. The hierarchies observed in the ant promoter also agree well with most of the available information on base pair preferences in other promoters.

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Selected References

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  1. Auble D. T., Allen T. L., deHaseth P. L. Promoter recognition by Escherichia coli RNA polymerase. Effects of substitutions in the spacer DNA separating the -10 and -35 regions. J Biol Chem. 1986 Aug 25;261(24):11202–11206. [PubMed] [Google Scholar]
  2. Ayers D. G., Auble D. T., deHaseth P. L. Promoter recognition by Escherichia coli RNA polymerase. Role of the spacer DNA in functional complex formation. J Mol Biol. 1989 Jun 20;207(4):749–756. doi: 10.1016/0022-2836(89)90241-6. [DOI] [PubMed] [Google Scholar]
  3. Berman M. L., Beckwith J. Use of gene fusions to isolate promoter mutants in the transfer RNA gene tyrT of Escherichia coli. J Mol Biol. 1979 May 25;130(3):303–315. doi: 10.1016/0022-2836(79)90543-6. [DOI] [PubMed] [Google Scholar]
  4. Berman M. L., Landy A. Promoter mutations in the transfer RNA gene tyrT of Escherichia coli. Proc Natl Acad Sci U S A. 1979 Sep;76(9):4303–4307. doi: 10.1073/pnas.76.9.4303. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Bingham A. H., Ponnambalam S., Chan B., Busby S. Mutations that reduce expression from the P2 promoter of the Escherichia coli galactose operon. Gene. 1986;41(1):67–74. doi: 10.1016/0378-1119(86)90268-4. [DOI] [PubMed] [Google Scholar]
  6. Carpousis A. J., Stefano J. E., Gralla J. D. 5' nucleotide heterogeneity and altered initiation of transcription at mutant lac promoters. J Mol Biol. 1982 Jun 5;157(4):619–633. doi: 10.1016/0022-2836(82)90502-2. [DOI] [PubMed] [Google Scholar]
  7. 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]
  8. Daniels D. W., Bertrand K. P. Promoter mutations affecting divergent transcription in the Tn10 tetracycline resistance determinant. J Mol Biol. 1985 Aug 20;184(4):599–610. doi: 10.1016/0022-2836(85)90306-7. [DOI] [PubMed] [Google Scholar]
  9. Daniels D., Zuber P., Losick R. Two amino acids in an RNA polymerase sigma factor involved in the recognition of adjacent base pairs in the -10 region of a cognate promoter. Proc Natl Acad Sci U S A. 1990 Oct;87(20):8075–8079. doi: 10.1073/pnas.87.20.8075. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Gaal T., Barkei J., Dickson R. R., deBoer H. A., deHaseth P. L., Alavi H., Gourse R. L. Saturation mutagenesis of an Escherichia coli rRNA promoter and initial characterization of promoter variants. J Bacteriol. 1989 Sep;171(9):4852–4861. doi: 10.1128/jb.171.9.4852-4861.1989. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Gardella T., Moyle H., Susskind M. M. A mutant Escherichia coli sigma 70 subunit of RNA polymerase with altered promoter specificity. J Mol Biol. 1989 Apr 20;206(4):579–590. doi: 10.1016/0022-2836(89)90567-6. [DOI] [PubMed] [Google Scholar]
  12. Graña D., Gardella T., Susskind M. M. The effects of mutations in the ant promoter of phage P22 depend on context. Genetics. 1988 Oct;120(2):319–327. doi: 10.1093/genetics/120.2.319. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. 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]
  14. 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]
  15. 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]
  16. Helmann J. D., Chamberlin M. J. Structure and function of bacterial sigma factors. Annu Rev Biochem. 1988;57:839–872. doi: 10.1146/annurev.bi.57.070188.004203. [DOI] [PubMed] [Google Scholar]
  17. Horwitz A. H., Morandi C., Wilcox G. Deoxyribonucleic acid sequence of araBAD promoter mutants of Escherichia coli. J Bacteriol. 1980 May;142(2):659–667. doi: 10.1128/jb.142.2.659-667.1980. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Hwang J. J., Brown S., Gussin G. N. Characterization of a doubly mutant derivative of the lambda PRM promoter. Effects of mutations on activation of PRM. J Mol Biol. 1988 Apr 20;200(4):695–708. doi: 10.1016/0022-2836(88)90481-0. [DOI] [PubMed] [Google Scholar]
  19. Inouye S., Inouye M. Up-promoter mutations in the lpp gene of Escherichia coli. Nucleic Acids Res. 1985 May 10;13(9):3101–3110. doi: 10.1093/nar/13.9.3101. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Jacques J. P., Susskind M. M. Pseudo-templated transcription by Escherichia coli RNA polymerase at a mutant promoter. Genes Dev. 1990 Oct;4(10):1801–1810. doi: 10.1101/gad.4.10.1801. [DOI] [PubMed] [Google Scholar]
  21. 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]
  22. Keilty S., Rosenberg M. Constitutive function of a positively regulated promoter reveals new sequences essential for activity. J Biol Chem. 1987 May 5;262(13):6389–6395. [PubMed] [Google Scholar]
  23. Kenney T. J., York K., Youngman P., Moran C. P., Jr Genetic evidence that RNA polymerase associated with sigma A factor uses a sporulation-specific promoter in Bacillus subtilis. Proc Natl Acad Sci U S A. 1989 Dec;86(23):9109–9113. doi: 10.1073/pnas.86.23.9109. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. Knaus R., Bujard H. PL of coliphage lambda: an alternative solution for an efficient promoter. EMBO J. 1988 Sep;7(9):2919–2923. doi: 10.1002/j.1460-2075.1988.tb03150.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Kunkel T. A., Alexander P. S. The base substitution fidelity of eucaryotic DNA polymerases. Mispairing frequencies, site preferences, insertion preferences, and base substitution by dislocation. J Biol Chem. 1986 Jan 5;261(1):160–166. [PubMed] [Google Scholar]
  26. Kunkel T. A. Rapid and efficient site-specific mutagenesis without phenotypic selection. Proc Natl Acad Sci U S A. 1985 Jan;82(2):488–492. doi: 10.1073/pnas.82.2.488. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. 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]
  28. 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]
  29. Munson L. M., Mandecki W., Caruthers M. H., Reznikoff W. S. Oligonucleotide mutagenesis of the lacPUV5 promoter. Nucleic Acids Res. 1984 May 11;12(9):4011–4017. doi: 10.1093/nar/12.9.4011. [DOI] [PMC free article] [PubMed] [Google Scholar]
  30. Piette J., Cunin R., Boyen A., Charlier D., Crabeel M., Van Vliet F., Glansdorff N., Squires C., Squires C. L. The regulatory region of the divergent argECBH operon in Escherichia coli K-12. Nucleic Acids Res. 1982 Dec 20;10(24):8031–8048. doi: 10.1093/nar/10.24.8031. [DOI] [PMC free article] [PubMed] [Google Scholar]
  31. Rosenberg M., Court D. Regulatory sequences involved in the promotion and termination of RNA transcription. Annu Rev Genet. 1979;13:319–353. doi: 10.1146/annurev.ge.13.120179.001535. [DOI] [PubMed] [Google Scholar]
  32. SMITH H. O., LEVINE M. TWO SEQUENTIAL REPRESSIONS OF DNA SYNTHESIS IN THE ESTABLISHMENT OF LYSOGENY BY PHAGE P22 AND ITS MUTANTS. Proc Natl Acad Sci U S A. 1964 Aug;52:356–363. doi: 10.1073/pnas.52.2.356. [DOI] [PMC free article] [PubMed] [Google Scholar]
  33. 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]
  34. Siegele D. A., Hu J. C., Walter W. A., Gross C. A. Altered promoter recognition by mutant forms of the sigma 70 subunit of Escherichia coli RNA polymerase. J Mol Biol. 1989 Apr 20;206(4):591–603. doi: 10.1016/0022-2836(89)90568-8. [DOI] [PubMed] [Google Scholar]
  35. 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]
  36. 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]
  37. 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]
  38. 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]
  39. Waldburger C., Gardella T., Wong R., Susskind M. M. Changes in conserved region 2 of Escherichia coli sigma 70 affecting promoter recognition. J Mol Biol. 1990 Sep 20;215(2):267–276. doi: 10.1016/s0022-2836(05)80345-6. [DOI] [PubMed] [Google Scholar]
  40. Weisemann J. M., Weinstock G. M. Direct selection of mutations reducing transcription or translation of the recA gene of Escherichia coli with a recA-lacZ protein fusion. J Bacteriol. 1985 Aug;163(2):748–755. doi: 10.1128/jb.163.2.748-755.1985. [DOI] [PMC free article] [PubMed] [Google Scholar]
  41. Wulff D. L., Mahoney M., Shatzman A., Rosenberg M. Mutational analysis of a regulatory region in bacteriophage lambda that has overlapping signals for the initiation of transcription and translation. Proc Natl Acad Sci U S A. 1984 Jan;81(2):555–559. doi: 10.1073/pnas.81.2.555. [DOI] [PMC free article] [PubMed] [Google Scholar]
  42. 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]
  43. Youderian P., Vershon A., Bouvier S., Sauer R. T., Susskind M. M. Changing the DNA-binding specificity of a repressor. Cell. 1983 Dec;35(3 Pt 2):777–783. doi: 10.1016/0092-8674(83)90110-1. [DOI] [PubMed] [Google Scholar]
  44. Zagursky R. J., Berman M. L. Cloning vectors that yield high levels of single-stranded DNA for rapid DNA sequencing. Gene. 1984 Feb;27(2):183–191. doi: 10.1016/0378-1119(84)90139-2. [DOI] [PubMed] [Google Scholar]
  45. Zuber P., Healy J., Carter H. L., 3rd, Cutting S., Moran C. P., Jr, Losick R. Mutation changing the specificity of an RNA polymerase sigma factor. J Mol Biol. 1989 Apr 20;206(4):605–614. doi: 10.1016/0022-2836(89)90569-x. [DOI] [PubMed] [Google Scholar]

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