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. 1992 Jul;1(7):831–842. doi: 10.1002/pro.5560010701

Structural and functional analyses of the repressor, RbsR, of the ribose operon of Escherichia coli.

C A Mauzy 1, M A Hermodson 1
PMCID: PMC2142159  PMID: 1304369

Abstract

The DNA sequence encoding the rbs repressor protein, RbsR, has been determined. Amino acid sequence analyses of the product of an rbsR-lacZ fusion and of affinity-purified RbsR demonstrate that translation begins at an unusual codon, TTG, and that the initial amino acid is removed during maturation of the protein. DNA-binding assays indicate that RbsR binds to a region of perfect dyad symmetry spanning the rbs operon transcriptional start site and that the affinity for the rbs operator is reduced by addition of ribose, consistent with ribose being the inducer of the operon. RbsR is a member of a family of homologous repressor proteins having very similar DNA-binding sites and binding to similar operator sequences.

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Selected References

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  1. Abou-Sabé M., Pilla J., Hazuda D., Ninfa A. Evolution of the D-ribose operon on Escherichia coli B/r. J Bacteriol. 1982 May;150(2):762–769. doi: 10.1128/jb.150.2.762-769.1982. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Bell A. W., Buckel S. D., Groarke J. M., Hope J. N., Kingsley D. H., Hermodson M. A. The nucleotide sequences of the rbsD, rbsA, and rbsC genes of Escherichia coli K12. J Biol Chem. 1986 Jun 15;261(17):7652–7658. [PubMed] [Google Scholar]
  3. Birnboim H. C. A rapid alkaline extraction method for the isolation of plasmid DNA. Methods Enzymol. 1983;100:243–255. doi: 10.1016/0076-6879(83)00059-2. [DOI] [PubMed] [Google Scholar]
  4. Chodosh L. A., Carthew R. W., Sharp P. A. A single polypeptide possesses the binding and transcription activities of the adenovirus major late transcription factor. Mol Cell Biol. 1986 Dec;6(12):4723–4733. doi: 10.1128/mcb.6.12.4723. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. David J., Wiesmeyer H. Regulation of ribose metabolism in Escherichia coli. I. The ribose catabolic pathway. Biochim Biophys Acta. 1970 Apr 14;208(1):45–55. doi: 10.1016/0304-4165(70)90047-4. [DOI] [PubMed] [Google Scholar]
  6. Gold L., Pribnow D., Schneider T., Shinedling S., Singer B. S., Stormo G. Translational initiation in prokaryotes. Annu Rev Microbiol. 1981;35:365–403. doi: 10.1146/annurev.mi.35.100181.002053. [DOI] [PubMed] [Google Scholar]
  7. Groarke J. M., Mahoney W. C., Hope J. N., Furlong C. E., Robb F. T., Zalkin H., Hermodson M. A. The amino acid sequence of D-ribose-binding protein from Escherichia coli K12. J Biol Chem. 1983 Nov 10;258(21):12952–12956. [PubMed] [Google Scholar]
  8. Hanahan D. Studies on transformation of Escherichia coli with plasmids. J Mol Biol. 1983 Jun 5;166(4):557–580. doi: 10.1016/s0022-2836(83)80284-8. [DOI] [PubMed] [Google Scholar]
  9. Hendrickson W., Schleif R. A dimer of AraC protein contacts three adjacent major groove regions of the araI DNA site. Proc Natl Acad Sci U S A. 1985 May;82(10):3129–3133. doi: 10.1073/pnas.82.10.3129. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Hope J. N., Bell A. W., Hermodson M. A., Groarke J. M. Ribokinase from Escherichia coli K12. Nucleotide sequence and overexpression of the rbsK gene and purification of ribokinase. J Biol Chem. 1986 Jun 15;261(17):7663–7668. [PubMed] [Google Scholar]
  11. Iida A., Harayama S., Iino T., Hazelbauer G. L. Molecular cloning and characterization of genes required for ribose transport and utilization in Escherichia coli K-12. J Bacteriol. 1984 May;158(2):674–682. doi: 10.1128/jb.158.2.674-682.1984. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Kaptein R., Zuiderweg E. R., Scheek R. M., Boelens R., van Gunsteren W. F. A protein structure from nuclear magnetic resonance data. lac repressor headpiece. J Mol Biol. 1985 Mar 5;182(1):179–182. doi: 10.1016/0022-2836(85)90036-1. [DOI] [PubMed] [Google Scholar]
  13. Kraft R., Tardiff J., Krauter K. S., Leinwand L. A. Using mini-prep plasmid DNA for sequencing double stranded templates with Sequenase. Biotechniques. 1988 Jun;6(6):544-6, 549. [PubMed] [Google Scholar]
  14. Laemmli U. K. Cleavage of structural proteins during the assembly of the head of bacteriophage T4. Nature. 1970 Aug 15;227(5259):680–685. doi: 10.1038/227680a0. [DOI] [PubMed] [Google Scholar]
  15. Lopilato J. E., Garwin J. L., Emr S. D., Silhavy T. J., Beckwith J. R. D-ribose metabolism in Escherichia coli K-12: genetics, regulation, and transport. J Bacteriol. 1984 May;158(2):665–673. doi: 10.1128/jb.158.2.665-673.1984. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Matsudaira P. Sequence from picomole quantities of proteins electroblotted onto polyvinylidene difluoride membranes. J Biol Chem. 1987 Jul 25;262(21):10035–10038. [PubMed] [Google Scholar]
  17. Mauzy C. A., Hermodson M. A. Structural homology between rbs repressor and ribose binding protein implies functional similarity. Protein Sci. 1992 Jul;1(7):843–849. doi: 10.1002/pro.5560010702. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. 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]
  19. Munson L. M., Stormo G. D., Niece R. L., Reznikoff W. S. lacZ translation initiation mutations. J Mol Biol. 1984 Aug 25;177(4):663–683. doi: 10.1016/0022-2836(84)90043-3. [DOI] [PubMed] [Google Scholar]
  20. Pabo C. O., Sauer R. T. Protein-DNA recognition. Annu Rev Biochem. 1984;53:293–321. doi: 10.1146/annurev.bi.53.070184.001453. [DOI] [PubMed] [Google Scholar]
  21. Reidl J., Römisch K., Ehrmann M., Boos W. MalI, a novel protein involved in regulation of the maltose system of Escherichia coli, is highly homologous to the repressor proteins GalR, CytR, and LacI. J Bacteriol. 1989 Sep;171(9):4888–4899. doi: 10.1128/jb.171.9.4888-4899.1989. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Rolfes R. J., Zalkin H. Purification of the Escherichia coli purine regulon repressor and identification of corepressors. J Bacteriol. 1990 Oct;172(10):5637–5642. doi: 10.1128/jb.172.10.5637-5642.1990. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. Schulz V. P., Reznikoff W. S. In vitro secondary structure analysis of mRNA from lacZ translation initiation mutants. J Mol Biol. 1990 Jan 20;211(2):427–445. doi: 10.1016/0022-2836(90)90363-Q. [DOI] [PubMed] [Google Scholar]
  24. Tabor S., Richardson C. C. Selective inactivation of the exonuclease activity of bacteriophage T7 DNA polymerase by in vitro mutagenesis. J Biol Chem. 1989 Apr 15;264(11):6447–6458. [PubMed] [Google Scholar]
  25. Tobin J. F., Schleif R. F. Purification and properties of RhaR, the positive regulator of the L-rhamnose operons of Escherichia coli. J Mol Biol. 1990 Jan 5;211(1):75–89. doi: 10.1016/0022-2836(90)90012-B. [DOI] [PubMed] [Google Scholar]

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