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. 1990 May;172(5):2642–2649. doi: 10.1128/jb.172.5.2642-2649.1990

Regulation of the glyoxylate bypass operon: cloning and characterization of iclR.

A Sunnarborg 1, D Klumpp 1, T Chung 1, D C LaPorte 1
PMCID: PMC208908  PMID: 2185227

Abstract

In Escherichia coli, expression of the glyoxylate bypass operon appears to be controlled, in part, by the product of iclR+. Mutations in iclR have been found to yield constitutive expression of this operon, suggesting that iclR+ encodes a repressor protein. We have cloned iclR+ by taking advantage of its tight genetic linkage with the glyoxylate bypass operon. The clone complemented a mutant allele of iclR in trans, restoring an inducible phenotype for this operon. Deletion analysis identified a region of ca. 900 base pairs that was necessary and sufficient for complementation. The nucleotide sequence of the insert was then determined. Translation of this sequence revealed an open reading frame capable of encoding a protein with Mr 29,741 preceded by a potential Shine-Dalgarno ribosome-binding site. The deduced amino acid sequence includes a region at the amino terminus that may form a helix-turn-helix motif, a structure found in many DNA-binding domains.

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Selected References

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  1. Anderson W. F., Ohlendorf D. H., Takeda Y., Matthews B. W. Structure of the cro repressor from bacteriophage lambda and its interaction with DNA. Nature. 1981 Apr 30;290(5809):754–758. doi: 10.1038/290754a0. [DOI] [PubMed] [Google Scholar]
  2. Bochner B. R., Huang H. C., Schieven G. L., Ames B. N. Positive selection for loss of tetracycline resistance. J Bacteriol. 1980 Aug;143(2):926–933. doi: 10.1128/jb.143.2.926-933.1980. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Brice C. B., Kornberg H. L. Genetic control of isocitrate lyase activity in Escherichia coli. J Bacteriol. 1968 Dec;96(6):2185–2186. doi: 10.1128/jb.96.6.2185-2186.1968. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Chung T., Klumpp D. J., LaPorte D. C. Glyoxylate bypass operon of Escherichia coli: cloning and determination of the functional map. J Bacteriol. 1988 Jan;170(1):386–392. doi: 10.1128/jb.170.1.386-392.1988. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Cortay J. C., Bleicher F., Duclos B., Cenatiempo Y., Gautier C., Prato J. L., Cozzone A. J. Utilization of acetate in Escherichia coli: structural organization and differential expression of the ace operon. Biochimie. 1989 Sep-Oct;71(9-10):1043–1049. doi: 10.1016/0300-9084(89)90109-0. [DOI] [PubMed] [Google Scholar]
  6. Csonka L. N., Clark A. J. Construction of an Hfr strain useful for transferring recA mutations between Escherichia coli strains. J Bacteriol. 1980 Jul;143(1):529–530. doi: 10.1128/jb.143.1.529-530.1980. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Garnak M., Reeves H. C. Phosphorylation of Isocitrate dehydrogenase of Escherichia coli. Science. 1979 Mar 16;203(4385):1111–1112. doi: 10.1126/science.34215. [DOI] [PubMed] [Google Scholar]
  8. 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]
  9. 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]
  10. Herskowitz I. Functional inactivation of genes by dominant negative mutations. Nature. 1987 Sep 17;329(6136):219–222. doi: 10.1038/329219a0. [DOI] [PubMed] [Google Scholar]
  11. Holms W. H., Bennett P. M. Regulation of isocitrate dehydrogenase activity in Escherichia coli on adaptation to acetate. J Gen Microbiol. 1971 Jan;65(1):57–68. doi: 10.1099/00221287-65-1-57. [DOI] [PubMed] [Google Scholar]
  12. Igo M. M., Ninfa A. J., Silhavy T. J. A bacterial environmental sensor that functions as a protein kinase and stimulates transcriptional activation. Genes Dev. 1989 May;3(5):598–605. doi: 10.1101/gad.3.5.598. [DOI] [PubMed] [Google Scholar]
  13. Iuchi S., Cameron D. C., Lin E. C. A second global regulator gene (arcB) mediating repression of enzymes in aerobic pathways of Escherichia coli. J Bacteriol. 1989 Feb;171(2):868–873. doi: 10.1128/jb.171.2.868-873.1989. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. KORNBERG H. L., MADSEN N. B. Synthesis of C4-dicarboxylic acids from acetate by a glyoxylate bypass of the tricarboxylic acid cycle. Biochim Biophys Acta. 1957 Jun;24(3):651–653. doi: 10.1016/0006-3002(57)90268-8. [DOI] [PubMed] [Google Scholar]
  15. Kelley R. L., Yanofsky C. Mutational studies with the trp repressor of Escherichia coli support the helix-turn-helix model of repressor recognition of operator DNA. Proc Natl Acad Sci U S A. 1985 Jan;82(2):483–487. doi: 10.1073/pnas.82.2.483. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Kornberg H. L. The role and control of the glyoxylate cycle in Escherichia coli. Biochem J. 1966 Apr;99(1):1–11. doi: 10.1042/bj0990001. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Kornberg H. L. The role and maintenance of the tricarboxylic acid cycle in Escherichia coli. Biochem Soc Symp. 1970;30:155–171. [PubMed] [Google Scholar]
  18. LOWRY O. H., ROSEBROUGH N. J., FARR A. L., RANDALL R. J. Protein measurement with the Folin phenol reagent. J Biol Chem. 1951 Nov;193(1):265–275. [PubMed] [Google Scholar]
  19. LaPorte D. C., Chung T. A single gene codes for the kinase and phosphatase which regulate isocitrate dehydrogenase. J Biol Chem. 1985 Dec 5;260(28):15291–15297. [PubMed] [Google Scholar]
  20. LaPorte D. C., Koshland D. E., Jr A protein with kinase and phosphatase activities involved in regulation of tricarboxylic acid cycle. Nature. 1982 Dec 2;300(5891):458–460. doi: 10.1038/300458a0. [DOI] [PubMed] [Google Scholar]
  21. LaPorte D. C., Koshland D. E., Jr Phosphorylation of isocitrate dehydrogenase as a demonstration of enhanced sensitivity in covalent regulation. Nature. 1983 Sep 22;305(5932):286–290. doi: 10.1038/305286a0. [DOI] [PubMed] [Google Scholar]
  22. LaPorte D. C., Thorsness P. E., Koshland D. E., Jr Compensatory phosphorylation of isocitrate dehydrogenase. A mechanism for adaptation to the intracellular environment. J Biol Chem. 1985 Sep 5;260(19):10563–10568. [PubMed] [Google Scholar]
  23. LaPorte D. C., Walsh K., Koshland D. E., Jr The branch point effect. Ultrasensitivity and subsensitivity to metabolic control. J Biol Chem. 1984 Nov 25;259(22):14068–14075. [PubMed] [Google Scholar]
  24. Maloy S. R., Nunn W. D. Genetic regulation of the glyoxylate shunt in Escherichia coli K-12. J Bacteriol. 1982 Jan;149(1):173–180. doi: 10.1128/jb.149.1.173-180.1982. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Matthews B. W., Ohlendorf D. H., Anderson W. F., Takeda Y. Structure of the DNA-binding region of lac repressor inferred from its homology with cro repressor. Proc Natl Acad Sci U S A. 1982 Mar;79(5):1428–1432. doi: 10.1073/pnas.79.5.1428. [DOI] [PMC free article] [PubMed] [Google Scholar]
  26. 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]
  27. McKay D. B., Steitz T. A. Structure of catabolite gene activator protein at 2.9 A resolution suggests binding to left-handed B-DNA. Nature. 1981 Apr 30;290(5809):744–749. doi: 10.1038/290744a0. [DOI] [PubMed] [Google Scholar]
  28. Neidhardt F. C., Bloch P. L., Smith D. F. Culture medium for enterobacteria. J Bacteriol. 1974 Sep;119(3):736–747. doi: 10.1128/jb.119.3.736-747.1974. [DOI] [PMC free article] [PubMed] [Google Scholar]
  29. Nimmo G. A., Nimmo H. G. The regulatory properties of isocitrate dehydrogenase kinase and isocitrate dehydrogenase phosphatase from Escherichia coli ML308 and the roles of these activities in the control of isocitrate dehydrogenase. Eur J Biochem. 1984 Jun 1;141(2):409–414. doi: 10.1111/j.1432-1033.1984.tb08206.x. [DOI] [PubMed] [Google Scholar]
  30. Nunn W. D. A molecular view of fatty acid catabolism in Escherichia coli. Microbiol Rev. 1986 Jun;50(2):179–192. doi: 10.1128/mr.50.2.179-192.1986. [DOI] [PMC free article] [PubMed] [Google Scholar]
  31. Ohlendorf D. H., Anderson W. F., Lewis M., Pabo C. O., Matthews B. W. Comparison of the structures of cro and lambda repressor proteins from bacteriophage lambda. J Mol Biol. 1983 Sep 25;169(3):757–769. doi: 10.1016/s0022-2836(83)80169-7. [DOI] [PubMed] [Google Scholar]
  32. Pabo C. O., Lewis M. The operator-binding domain of lambda repressor: structure and DNA recognition. Nature. 1982 Jul 29;298(5873):443–447. doi: 10.1038/298443a0. [DOI] [PubMed] [Google Scholar]
  33. Ronson C. W., Nixon B. T., Ausubel F. M. Conserved domains in bacterial regulatory proteins that respond to environmental stimuli. Cell. 1987 Jun 5;49(5):579–581. doi: 10.1016/0092-8674(87)90530-7. [DOI] [PubMed] [Google Scholar]
  34. Sanger F., Coulson A. R. A rapid method for determining sequences in DNA by primed synthesis with DNA polymerase. J Mol Biol. 1975 May 25;94(3):441–448. doi: 10.1016/0022-2836(75)90213-2. [DOI] [PubMed] [Google Scholar]
  35. Sauer R. T., Yocum R. R., Doolittle R. F., Lewis M., Pabo C. O. Homology among DNA-binding proteins suggests use of a conserved super-secondary structure. Nature. 1982 Jul 29;298(5873):447–451. doi: 10.1038/298447a0. [DOI] [PubMed] [Google Scholar]
  36. Schevitz R. W., Otwinowski Z., Joachimiak A., Lawson C. L., Sigler P. B. The three-dimensional structure of trp repressor. 1985 Oct 31-Nov 6Nature. 317(6040):782–786. doi: 10.1038/317782a0. [DOI] [PubMed] [Google Scholar]
  37. Sharp P. M., Li W. H. Codon usage in regulatory genes in Escherichia coli does not reflect selection for 'rare' codons. Nucleic Acids Res. 1986 Oct 10;14(19):7737–7749. doi: 10.1093/nar/14.19.7737. [DOI] [PMC free article] [PubMed] [Google Scholar]
  38. Simons R. W., Houman F., Kleckner N. Improved single and multicopy lac-based cloning vectors for protein and operon fusions. Gene. 1987;53(1):85–96. doi: 10.1016/0378-1119(87)90095-3. [DOI] [PubMed] [Google Scholar]
  39. Steitz T. A., Ohlendorf D. H., McKay D. B., Anderson W. F., Matthews B. W. Structural similarity in the DNA-binding domains of catabolite gene activator and cro repressor proteins. Proc Natl Acad Sci U S A. 1982 May;79(10):3097–3100. doi: 10.1073/pnas.79.10.3097. [DOI] [PMC free article] [PubMed] [Google Scholar]
  40. Vinopal R. T., Fraenkel D. G. Phenotypic suppression of phosphofructokinase mutations in Escherichia coli by constitutive expression of the glyoxylate shunt. J Bacteriol. 1974 Jun;118(3):1090–1100. doi: 10.1128/jb.118.3.1090-1100.1974. [DOI] [PMC free article] [PubMed] [Google Scholar]
  41. Walsh K., Koshland D. E., Jr Branch point control by the phosphorylation state of isocitrate dehydrogenase. A quantitative examination of fluxes during a regulatory transition. J Biol Chem. 1985 Jul 15;260(14):8430–8437. [PubMed] [Google Scholar]
  42. Wilson R. B., Maloy S. R. Isolation and characterization of Salmonella typhimurium glyoxylate shunt mutants. J Bacteriol. 1987 Jul;169(7):3029–3034. doi: 10.1128/jb.169.7.3029-3034.1987. [DOI] [PMC free article] [PubMed] [Google Scholar]
  43. Yudkin M. D. The prediction of helix-turn-helix DNA-binding regions in proteins. Protein Eng. 1987 Oct-Nov;1(5):371–372. doi: 10.1093/protein/1.5.371. [DOI] [PubMed] [Google Scholar]
  44. Zuiderweg E. R., Kaptein R., Wüthrich K. Secondary structure of the lac repressor DNA-binding domain by two-dimensional 1H nuclear magnetic resonance in solution. Proc Natl Acad Sci U S A. 1983 Oct;80(19):5837–5841. doi: 10.1073/pnas.80.19.5837. [DOI] [PMC free article] [PubMed] [Google Scholar]

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