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. 1989 Feb;171(2):1178–1184. doi: 10.1128/jb.171.2.1178-1184.1989

Effect of mutations in the cyclic AMP receptor protein-binding site on araBAD and araC expression.

L Stoltzfus 1, G Wilcox 1
PMCID: PMC209717  PMID: 2521619

Abstract

Maximum expression of the adjacent but divergently transcribed araBAD operon and araC gene requires the presence of cyclic AMP (cAMP) and the cAMP receptor protein (CRP). DNase I protection studies have previously revealed a high-affinity CRP-binding site in the ara regulatory region. Deletion mutations introduced into this site resulted in reduced expression of araBAD and araC. However, other experiments have demonstrated that spacing changes in the ara regulatory region may have multiple effects due to disruption of a DNA loop. Thus, the deletions could have destroyed the CRP-binding site, the ability to form a loop, or both. In the present study, substitution mutations were introduced into the CRP site in order to avoid creating spacing changes. We found that a 3-base-pair substitution resulted in a 30% reduction in araBAD expression, whereas a 6-base-pair substitution resulted in an 80% reduction. Both of these substitution mutations reduced araC expression threefold. We conclude that CRP bound to this site regulates expression in both directions. We found that a spacing change in the CRP site does not alter araBAD expression any more than does a substitution mutation.

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Selected References

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

  1. Bass R., Heffernan L., Sweadner K., Englesberg E. The site for catabolite deactivation in the L-arabinose BAD operon in Escherichia coli B/r. Arch Microbiol. 1976 Oct 11;110(1):135–143. doi: 10.1007/BF00416978. [DOI] [PubMed] [Google Scholar]
  2. 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]
  3. Borowiec J. A., Zhang L., Sasse-Dwight S., Gralla J. D. DNA supercoiling promotes formation of a bent repression loop in lac DNA. J Mol Biol. 1987 Jul 5;196(1):101–111. doi: 10.1016/0022-2836(87)90513-4. [DOI] [PubMed] [Google Scholar]
  4. Brown C. E., Hogg R. W. A second transport system for L-arabinose in Escherichia coli B-r controlled by the araC gene. J Bacteriol. 1972 Aug;111(2):606–613. doi: 10.1128/jb.111.2.606-613.1972. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Busby S., Aiba H., de Crombrugghe B. Mutations in the Escherichia coli operon that define two promoters and the binding site of the cyclic AMP receptor protein. J Mol Biol. 1982 Jan 15;154(2):211–227. doi: 10.1016/0022-2836(82)90061-4. [DOI] [PubMed] [Google Scholar]
  6. Casadaban M. J. Regulation of the regulatory gene for the arabinose pathway, araC. J Mol Biol. 1976 Jul 5;104(3):557–566. doi: 10.1016/0022-2836(76)90120-0. [DOI] [PubMed] [Google Scholar]
  7. Dickson R. C., Abelson J., Johnson P. Nucleotide sequence changes produced by mutations in the lac promoter of Escherichia coli. J Mol Biol. 1977 Mar 25;111(1):65–75. doi: 10.1016/s0022-2836(77)80132-0. [DOI] [PubMed] [Google Scholar]
  8. Dunn T. M., Hahn S., Ogden S., Schleif R. F. An operator at -280 base pairs that is required for repression of araBAD operon promoter: addition of DNA helical turns between the operator and promoter cyclically hinders repression. Proc Natl Acad Sci U S A. 1984 Aug;81(16):5017–5020. doi: 10.1073/pnas.81.16.5017. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Dunn T. M., Schleif R. Deletion analysis of the Escherichia coli ara PC and PBAD promoters. J Mol Biol. 1984 Nov 25;180(1):201–204. doi: 10.1016/0022-2836(84)90437-6. [DOI] [PubMed] [Google Scholar]
  10. Ebright R. H., Cossart P., Gicquel-Sanzey B., Beckwith J. Mutations that alter the DNA sequence specificity of the catabolite gene activator protein of E. coli. Nature. 1984 Sep 20;311(5983):232–235. doi: 10.1038/311232a0. [DOI] [PubMed] [Google Scholar]
  11. Englesberg E., Sheppard D., Squires C., Meronk F., Jr An analysis of "revertants" of a deletion mutant in the C gene of the L-arabinose gene complex in Escherichia coli B-r: isolation of initiator constitutive mutants (Ic). J Mol Biol. 1969 Jul 28;43(2):281–298. doi: 10.1016/0022-2836(69)90268-x. [DOI] [PubMed] [Google Scholar]
  12. Englesberg E., Squires C., Meronk F., Jr The L-arabinose operon in Escherichia coli B-r: a genetic demonstration of two functional states of the product of a regulator gene. Proc Natl Acad Sci U S A. 1969 Apr;62(4):1100–1107. doi: 10.1073/pnas.62.4.1100. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Englesberg E., Wilcox G. Regulation: positive control. Annu Rev Genet. 1974;8:219–242. doi: 10.1146/annurev.ge.08.120174.001251. [DOI] [PubMed] [Google Scholar]
  14. Epstein W., Rothman-Denes L. B., Hesse J. Adenosine 3':5'-cyclic monophosphate as mediator of catabolite repression in Escherichia coli. Proc Natl Acad Sci U S A. 1975 Jun;72(6):2300–2304. doi: 10.1073/pnas.72.6.2300. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Gielow L., Largen M., Englesberg E. Initiator constitutive mutants of the L-arabinose operon (OIBAD) of Escherichia coli B/r. Genetics. 1971 Nov;69(3):289–302. doi: 10.1093/genetics/69.3.289. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Greenfield L., Boone T., Wilcox G. DNA sequence of the araBAD promoter in Escherichia coli B/r. Proc Natl Acad Sci U S A. 1978 Oct;75(10):4724–4728. doi: 10.1073/pnas.75.10.4724. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Hahn S., Schleif R. In vivo regulation of the Escherichia coli araC promoter. J Bacteriol. 1983 Aug;155(2):593–600. doi: 10.1128/jb.155.2.593-600.1983. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Hamilton E. P., Lee N. Three binding sites for AraC protein are required for autoregulation of araC in Escherichia coli. Proc Natl Acad Sci U S A. 1988 Mar;85(6):1749–1753. doi: 10.1073/pnas.85.6.1749. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Horazdovsky B. F., Hogg R. W. High-affinity L-arabinose transport operon. Gene product expression and mRNAs. J Mol Biol. 1987 Sep 5;197(1):27–35. doi: 10.1016/0022-2836(87)90606-1. [DOI] [PubMed] [Google Scholar]
  20. Horwitz A. H., Miyada C. G., Wilcox G. Functional limits of the araIc promoter suggest an additional regulatory site for araBAD expression. J Bacteriol. 1984 Apr;158(1):141–147. doi: 10.1128/jb.158.1.141-147.1984. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Hull R. A., Gill R. E., Hsu P., Minshew B. H., Falkow S. Construction and expression of recombinant plasmids encoding type 1 or D-mannose-resistant pili from a urinary tract infection Escherichia coli isolate. Infect Immun. 1981 Sep;33(3):933–938. doi: 10.1128/iai.33.3.933-938.1981. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Kolodrubetz D., Schleif R. L-arabinose transport systems in Escherichia coli K-12. J Bacteriol. 1981 Nov;148(2):472–479. doi: 10.1128/jb.148.2.472-479.1981. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. Lee N. L., Gielow W. O., Wallace R. G. Mechanism of araC autoregulation and the domains of two overlapping promoters, Pc and PBAD, in the L-arabinose regulatory region of Escherichia coli. Proc Natl Acad Sci U S A. 1981 Feb;78(2):752–756. doi: 10.1073/pnas.78.2.752. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. Lee N., Francklyn C., Hamilton E. P. Arabinose-induced binding of AraC protein to araI2 activates the araBAD operon promoter. Proc Natl Acad Sci U S A. 1987 Dec;84(24):8814–8818. doi: 10.1073/pnas.84.24.8814. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Lee N., Gielow W., Martin R., Hamilton E., Fowler A. The organization of the araBAD operon of Escherichia coli. Gene. 1986;47(2-3):231–244. doi: 10.1016/0378-1119(86)90067-3. [DOI] [PubMed] [Google Scholar]
  26. Lee N., Wilcox G., Gielow W., Arnold J., Cleary P., Englesberg E. In vitro activation of the transcription of araBAD operon by araC activator. Proc Natl Acad Sci U S A. 1974 Mar;71(3):634–638. doi: 10.1073/pnas.71.3.634. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. Lichenstein H. S., Hamilton E. P., Lee N. Repression and catabolite gene activation in the araBAD operon. J Bacteriol. 1987 Feb;169(2):811–822. doi: 10.1128/jb.169.2.811-822.1987. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. Martin K., Huo L., Schleif R. F. The DNA loop model for ara repression: AraC protein occupies the proposed loop sites in vivo and repression-negative mutations lie in these same sites. Proc Natl Acad Sci U S A. 1986 Jun;83(11):3654–3658. doi: 10.1073/pnas.83.11.3654. [DOI] [PMC free article] [PubMed] [Google Scholar]
  29. Messing J., Gronenborn B., Müller-Hill B., Hans Hopschneider P. Filamentous coliphage M13 as a cloning vehicle: insertion of a HindII fragment of the lac regulatory region in M13 replicative form in vitro. Proc Natl Acad Sci U S A. 1977 Sep;74(9):3642–3646. doi: 10.1073/pnas.74.9.3642. [DOI] [PMC free article] [PubMed] [Google Scholar]
  30. Miyada C. G., Horwitz A. H., Cass L. G., Timko J., Wilcox G. DNA sequence of the araC regulatory gene from Escherichia coli B/r. Nucleic Acids Res. 1980 Nov 25;8(22):5267–5274. doi: 10.1093/nar/8.22.5267. [DOI] [PMC free article] [PubMed] [Google Scholar]
  31. Miyada C. G., Soberón X., Itakura K., Wilcox G. The use of synthetic oligodeoxyribonucleotides to produce specific deletions in the araBAD promoter of Escherichia coli B/r. Gene. 1982 Feb;17(2):167–177. doi: 10.1016/0378-1119(82)90070-1. [DOI] [PubMed] [Google Scholar]
  32. Miyada C. G., Stoltzfus L., Wilcox G. Regulation of the araC gene of Escherichia coli: catabolite repression, autoregulation, and effect on araBAD expression. Proc Natl Acad Sci U S A. 1984 Jul;81(13):4120–4124. doi: 10.1073/pnas.81.13.4120. [DOI] [PMC free article] [PubMed] [Google Scholar]
  33. Ogden S., Haggerty D., Stoner C. M., Kolodrubetz D., Schleif R. The Escherichia coli L-arabinose operon: binding sites of the regulatory proteins and a mechanism of positive and negative regulation. Proc Natl Acad Sci U S A. 1980 Jun;77(6):3346–3350. doi: 10.1073/pnas.77.6.3346. [DOI] [PMC free article] [PubMed] [Google Scholar]
  34. Pastan I., Perlman R. Cyclic adenosine monophosphate in bacteria. Science. 1970 Jul 24;169(3943):339–344. doi: 10.1126/science.169.3943.339. [DOI] [PubMed] [Google Scholar]
  35. Scripture J. B., Voelker C., Miller S., O'Donnell R. T., Polgar L., Rade J., Horazdovsky B. F., Hogg R. W. High-affinity L-arabinose transport operon. Nucleotide sequence and analysis of gene products. J Mol Biol. 1987 Sep 5;197(1):37–46. doi: 10.1016/0022-2836(87)90607-3. [DOI] [PubMed] [Google Scholar]
  36. Tsao S. G., Brunk C. F., Pearlman R. E. Hybridization of nucleic acids directly in agarose gels. Anal Biochem. 1983 Jun;131(2):365–372. doi: 10.1016/0003-2697(83)90185-9. [DOI] [PubMed] [Google Scholar]
  37. Wallace R. G., Lee N., Fowler A. V. The araC gene of Escherichia coli: transcriptional and translational start-points and complete nucleotide sequence. Gene. 1980 Dec;12(3-4):179–190. doi: 10.1016/0378-1119(80)90100-6. [DOI] [PubMed] [Google Scholar]
  38. West R. W., Jr, Rodriguez R. L. Construction and characterization of E. coli promoter-probe plasmid vectors. III. pBR322 derivatives with deletions in the tetracycline resistance promoter region. Gene. 1982 Dec;20(2):291–304. doi: 10.1016/0378-1119(82)90047-6. [DOI] [PubMed] [Google Scholar]
  39. Wilcox G., Boulter J., Lee N. Direction of transcription of the regulatory gene araC in Escherichia coli B-r. Proc Natl Acad Sci U S A. 1974 Sep;71(9):3635–3639. doi: 10.1073/pnas.71.9.3635. [DOI] [PMC free article] [PubMed] [Google Scholar]
  40. Yu X. M., Reznikoff W. S. Deletion analysis of the Escherichia coli lactose promoter P2. Nucleic Acids Res. 1985 Apr 11;13(7):2457–2468. doi: 10.1093/nar/13.7.2457. [DOI] [PMC free article] [PubMed] [Google Scholar]
  41. Zubay G., Schwartz D., Beckwith J. Mechanism of activation of catabolite-sensitive genes: a positive control system. Proc Natl Acad Sci U S A. 1970 May;66(1):104–110. doi: 10.1073/pnas.66.1.104. [DOI] [PMC free article] [PubMed] [Google Scholar]
  42. de Crombrugghe B., Busby S., Buc H. Cyclic AMP receptor protein: role in transcription activation. Science. 1984 May 25;224(4651):831–838. doi: 10.1126/science.6372090. [DOI] [PubMed] [Google Scholar]

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