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. 1997 Jun;179(11):3721–3728. doi: 10.1128/jb.179.11.3721-3728.1997

Insertion mutagenesis of the lac repressor and its implications for structure-function analysis.

B D Nelson 1, C Manoil 1, B Traxler 1
PMCID: PMC179170  PMID: 9171422

Abstract

We recently developed a simple technique for the generation of relatively large (31-codon) insertion mutations in cloned genes. To test whether the analysis of such mutations could provide insight into structure-function relationships in proteins, we examined a set of insertion mutants of the Escherichia coli lac repressor (LacI). Representatives of several LacI mutant classes were recovered, including mutants which exhibit fully active, inducer-insensitive, or weak dominant-negative phenotypes. The various properties of the recovered mutants agree with previous biophysical, biochemical, and genetic data for the protein. In particular, the results support the prior designation of mutationally tolerant spacer regions of LacI as well as proposed differences in dimerization interactions among regions of the protein core domain. These findings suggest that the analysis of 31-codon insertion mutations may provide a simple approach for characterizing structure-function relationships in proteins for which high-resolution structures are not available.

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Selected References

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  1. Adler K., Beyreuther K., Fanning E., Geisler N., Gronenborn B., Klemm A., Müller-Hill B., Pfahl M., Schmitz A. How lac repressor binds to DNA. Nature. 1972 Jun 9;237(5354):322–327. doi: 10.1038/237322a0. [DOI] [PubMed] [Google Scholar]
  2. Alberti S., Oehler S., von Wilcken-Bergmann B., Krämer H., Müller-Hill B. Dimer-to-tetramer assembly of Lac repressor involves a leucine heptad repeat. New Biol. 1991 Jan;3(1):57–62. [PubMed] [Google Scholar]
  3. Alberti S., Oehler S., von Wilcken-Bergmann B., Müller-Hill B. Genetic analysis of the leucine heptad repeats of Lac repressor: evidence for a 4-helical bundle. EMBO J. 1993 Aug;12(8):3227–3236. doi: 10.1002/j.1460-2075.1993.tb05992.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Amann E., Ochs B., Abel K. J. Tightly regulated tac promoter vectors useful for the expression of unfused and fused proteins in Escherichia coli. Gene. 1988 Sep 30;69(2):301–315. doi: 10.1016/0378-1119(88)90440-4. [DOI] [PubMed] [Google Scholar]
  5. Barkley M. D., Riggs A. D., Jobe A., Burgeois S. Interaction of effecting ligands with lac repressor and repressor-operator complex. Biochemistry. 1975 Apr 22;14(8):1700–1712. doi: 10.1021/bi00679a024. [DOI] [PubMed] [Google Scholar]
  6. Betz J. L. Cloning and characterization of several dominant-negative and tight-binding mutants of lac repressor. Gene. 1986;42(3):283–292. doi: 10.1016/0378-1119(86)90232-5. [DOI] [PubMed] [Google Scholar]
  7. Blaber M., Baase W. A., Gassner N., Matthews B. W. Alanine scanning mutagenesis of the alpha-helix 115-123 of phage T4 lysozyme: effects on structure, stability and the binding of solvent. J Mol Biol. 1995 Feb 17;246(2):317–330. doi: 10.1006/jmbi.1994.0087. [DOI] [PubMed] [Google Scholar]
  8. Boyd D., Manoil C., Beckwith J. Determinants of membrane protein topology. Proc Natl Acad Sci U S A. 1987 Dec;84(23):8525–8529. doi: 10.1073/pnas.84.23.8525. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Chakerian A. E., Matthews K. S. Characterization of mutations in oligomerization domain of Lac repressor protein. J Biol Chem. 1991 Nov 25;266(33):22206–22214. [PubMed] [Google Scholar]
  10. Chakerian A. E., Tesmer V. M., Manly S. P., Brackett J. K., Lynch M. J., Hoh J. T., Matthews K. S. Evidence for leucine zipper motif in lactose repressor protein. J Biol Chem. 1991 Jan 25;266(3):1371–1374. [PubMed] [Google Scholar]
  11. Chamness G. C., Willson C. D. An unusual lac repressor mutant. J Mol Biol. 1970 Nov 14;53(3):561–565. doi: 10.1016/0022-2836(70)90084-7. [DOI] [PubMed] [Google Scholar]
  12. Charbit A., Boulain J. C., Ryter A., Hofnung M. Probing the topology of a bacterial membrane protein by genetic insertion of a foreign epitope; expression at the cell surface. EMBO J. 1986 Nov;5(11):3029–3037. doi: 10.1002/j.1460-2075.1986.tb04602.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Charbit A., Ronco J., Michel V., Werts C., Hofnung M. Permissive sites and topology of an outer membrane protein with a reporter epitope. J Bacteriol. 1991 Jan;173(1):262–275. doi: 10.1128/jb.173.1.262-275.1991. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Chen J., Matthews K. S. Deletion of lactose repressor carboxyl-terminal domain affects tetramer formation. J Biol Chem. 1992 Jul 15;267(20):13843–13850. [PubMed] [Google Scholar]
  15. Daly T. J., Matthews K. S. Characterization and modification of a monomeric mutant of the lactose repressor protein. Biochemistry. 1986 Sep 23;25(19):5474–5478. doi: 10.1021/bi00367a019. [DOI] [PubMed] [Google Scholar]
  16. Files J. G., Weber K. Limited proteolytic digestion of lac repressor by trypsin. Chemical nature of the resulting trypsin-resistant core. J Biol Chem. 1976 Jun 10;251(11):3386–3391. [PubMed] [Google Scholar]
  17. Friedman A. M., Fischmann T. O., Steitz T. A. Crystal structure of lac repressor core tetramer and its implications for DNA looping. Science. 1995 Jun 23;268(5218):1721–1727. doi: 10.1126/science.7792597. [DOI] [PubMed] [Google Scholar]
  18. Geisler N., Weber K. Escherichia coli lactose repressor: isolation of two different homogeneous headpieces and the existence of a hinge region between residues 50 and 60 in the repressor molecule. FEBS Lett. 1978 Mar 15;87(2):215–218. doi: 10.1016/0014-5793(78)80335-4. [DOI] [PubMed] [Google Scholar]
  19. Gilbert W., Müller-Hill B. The lac operator is DNA. Proc Natl Acad Sci U S A. 1967 Dec;58(6):2415–2421. doi: 10.1073/pnas.58.6.2415. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Gordon A. J., Burns P. A., Fix D. F., Yatagai F., Allen F. L., Horsfall M. J., Halliday J. A., Gray J., Bernelot-Moens C., Glickman B. W. Missense mutation in the lacI gene of Escherichia coli. Inferences on the structure of the repressor protein. J Mol Biol. 1988 Mar 20;200(2):239–251. doi: 10.1016/0022-2836(88)90237-9. [DOI] [PubMed] [Google Scholar]
  21. JACOB F., MONOD J. Genetic regulatory mechanisms in the synthesis of proteins. J Mol Biol. 1961 Jun;3:318–356. doi: 10.1016/s0022-2836(61)80072-7. [DOI] [PubMed] [Google Scholar]
  22. Kaptein R., Lamerichs R. M., Boelens R., Rullmann J. A. Two-dimensional NMR study of a protein-DNA complex. lac repressor headpiece-operator interaction. Biochem Pharmacol. 1990 Jul 1;40(1):89–96. doi: 10.1016/0006-2952(90)90183-l. [DOI] [PubMed] [Google Scholar]
  23. Kleina L. G., Miller J. H. Genetic studies of the lac repressor. XIII. Extensive amino acid replacements generated by the use of natural and synthetic nonsense suppressors. J Mol Biol. 1990 Mar 20;212(2):295–318. doi: 10.1016/0022-2836(90)90126-7. [DOI] [PubMed] [Google Scholar]
  24. Lee E., Manoil C. Mutations eliminating the protein export function of a membrane-spanning sequence. J Biol Chem. 1994 Nov 18;269(46):28822–28828. [PubMed] [Google Scholar]
  25. Lewis M., Chang G., Horton N. C., Kercher M. A., Pace H. C., Schumacher M. A., Brennan R. G., Lu P. Crystal structure of the lactose operon repressor and its complexes with DNA and inducer. Science. 1996 Mar 1;271(5253):1247–1254. doi: 10.1126/science.271.5253.1247. [DOI] [PubMed] [Google Scholar]
  26. Lippincott J., Traxler B. MalFGK complex assembly and transport and regulatory characteristics of MalK insertion mutants. J Bacteriol. 1997 Feb;179(4):1337–1343. doi: 10.1128/jb.179.4.1337-1343.1997. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. Lopilato J., Bortner S., Beckwith J. Mutations in a new chromosomal gene of Escherichia coli K-12, pcnB, reduce plasmid copy number of pBR322 and its derivatives. Mol Gen Genet. 1986 Nov;205(2):285–290. doi: 10.1007/BF00430440. [DOI] [PubMed] [Google Scholar]
  28. Manoil C., Bailey J. A simple screen for permissive sites in proteins: analysis of Escherichia coli lac permease. J Mol Biol. 1997 Mar 28;267(2):250–263. doi: 10.1006/jmbi.1996.0881. [DOI] [PubMed] [Google Scholar]
  29. Mao B., Pear M. R., McCammon J. A., Quiocho F. A. Hinge-bending in L-arabinose-binding protein. The "Venus's-flytrap" model. J Biol Chem. 1982 Feb 10;257(3):1131–1133. [PubMed] [Google Scholar]
  30. Markiewicz P., Kleina L. G., Cruz C., Ehret S., Miller J. H. Genetic studies of the lac repressor. XIV. Analysis of 4000 altered Escherichia coli lac repressors reveals essential and non-essential residues, as well as "spacers" which do not require a specific sequence. J Mol Biol. 1994 Jul 29;240(5):421–433. doi: 10.1006/jmbi.1994.1458. [DOI] [PubMed] [Google Scholar]
  31. Miller J. H., Coulondre C., Hofer M., Schmeissner U., Sommer H., Schmitz A., Lu P. Genetic studies of the lac repressor. IX. Generation of altered proteins by the suppression of nonsence mutations. J Mol Biol. 1979 Jun 25;131(2):191–222. doi: 10.1016/0022-2836(79)90073-1. [DOI] [PubMed] [Google Scholar]
  32. Miller J. H. Genetic studies of the lac repressor. XII. Amino acid replacements in the DNA binding domain of the Escherichia coli lac repressor. J Mol Biol. 1984 Nov 25;180(1):205–212. doi: 10.1016/0022-2836(84)90438-8. [DOI] [PubMed] [Google Scholar]
  33. Mowbray S. L., Cole L. B. 1.7 A X-ray structure of the periplasmic ribose receptor from Escherichia coli. J Mol Biol. 1992 May 5;225(1):155–175. doi: 10.1016/0022-2836(92)91033-l. [DOI] [PubMed] [Google Scholar]
  34. Newton S. M., Klebba P. E., Michel V., Hofnung M., Charbit A. Topology of the membrane protein LamB by epitope tagging and a comparison with the X-ray model. J Bacteriol. 1996 Jun;178(12):3447–3456. doi: 10.1128/jb.178.12.3447-3456.1996. [DOI] [PMC free article] [PubMed] [Google Scholar]
  35. Nichols J. C., Vyas N. K., Quiocho F. A., Matthews K. S. Model of lactose repressor core based on alignment with sugar-binding proteins is concordant with genetic and chemical data. J Biol Chem. 1993 Aug 15;268(23):17602–17612. doi: 10.2210/pdb1ltp/pdb. [DOI] [PubMed] [Google Scholar]
  36. Oehler S., Eismann E. R., Krämer H., Müller-Hill B. The three operators of the lac operon cooperate in repression. EMBO J. 1990 Apr;9(4):973–979. doi: 10.1002/j.1460-2075.1990.tb08199.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  37. Ogata R. T., Gilbert W. An amino-terminal fragment of lac repressor binds specifically to lac operator. Proc Natl Acad Sci U S A. 1978 Dec;75(12):5851–5854. doi: 10.1073/pnas.75.12.5851. [DOI] [PMC free article] [PubMed] [Google Scholar]
  38. Platt T., Files J. G., Weber K. Lac repressor. Specific proteolytic destruction of the NH 2 -terminal region and loss of the deoxyribonucleic acid-binding activity. J Biol Chem. 1973 Jan 10;248(1):110–121. [PubMed] [Google Scholar]
  39. Platt T., Weber K., Ganem D., Miller J. H. Translational restarts: AUG reinitiation of a lac repressor fragment. Proc Natl Acad Sci U S A. 1972 Apr;69(4):897–901. doi: 10.1073/pnas.69.4.897. [DOI] [PMC free article] [PubMed] [Google Scholar]
  40. Reidhaar-Olson J. F., Sauer R. T. Combinatorial cassette mutagenesis as a probe of the informational content of protein sequences. Science. 1988 Jul 1;241(4861):53–57. doi: 10.1126/science.3388019. [DOI] [PubMed] [Google Scholar]
  41. Rennell D., Bouvier S. E., Hardy L. W., Poteete A. R. Systematic mutation of bacteriophage T4 lysozyme. J Mol Biol. 1991 Nov 5;222(1):67–88. doi: 10.1016/0022-2836(91)90738-r. [DOI] [PubMed] [Google Scholar]
  42. Sams C. F., Vyas N. K., Quiocho F. A., Matthews K. S. Predicted structure of the sugar-binding site of the lac repressor. Nature. 1984 Aug 2;310(5976):429–430. doi: 10.1038/310429a0. [DOI] [PubMed] [Google Scholar]
  43. Schmitz A., Schmeissner U., Miller J. H. Mutations affecting the quaternary structure of the lac repressor. J Biol Chem. 1976 Jun 10;251(11):3359–3366. [PubMed] [Google Scholar]
  44. Schumacher M. A., Choi K. Y., Lu F., Zalkin H., Brennan R. G. Mechanism of corepressor-mediated specific DNA binding by the purine repressor. Cell. 1995 Oct 6;83(1):147–155. doi: 10.1016/0092-8674(95)90243-0. [DOI] [PubMed] [Google Scholar]
  45. Schumacher M. A., Choi K. Y., Zalkin H., Brennan R. G. Crystal structure of LacI member, PurR, bound to DNA: minor groove binding by alpha helices. Science. 1994 Nov 4;266(5186):763–770. doi: 10.1126/science.7973627. [DOI] [PubMed] [Google Scholar]
  46. Spotts R. O., Chakerian A. E., Matthews K. S. Arginine 197 of lac repressor contributes significant energy to inducer binding. Confirmation of homology to periplasmic sugar binding proteins. J Biol Chem. 1991 Dec 5;266(34):22998–23002. [PubMed] [Google Scholar]
  47. Suckow J., Markiewicz P., Kleina L. G., Miller J., Kisters-Woike B., Müller-Hill B. Genetic studies of the Lac repressor. XV: 4000 single amino acid substitutions and analysis of the resulting phenotypes on the basis of the protein structure. J Mol Biol. 1996 Aug 30;261(4):509–523. doi: 10.1006/jmbi.1996.0479. [DOI] [PubMed] [Google Scholar]
  48. Traxler B., Beckwith J. Assembly of a hetero-oligomeric membrane protein complex. Proc Natl Acad Sci U S A. 1992 Nov 15;89(22):10852–10856. doi: 10.1073/pnas.89.22.10852. [DOI] [PMC free article] [PubMed] [Google Scholar]
  49. WILLSON C., PERRIN D., COHN M., JACOB F., MONOD J. NON-INDUCIBLE MUTANTS OF THE REGULATOR GENE IN THE "LACTOSE" SYSTEM OF ESCHERICHIA COLI. J Mol Biol. 1964 Apr;8:582–592. doi: 10.1016/s0022-2836(64)80013-9. [DOI] [PubMed] [Google Scholar]
  50. Wales M. E., Wild J. R. Analysis of structure-function relationships by formation of chimeric enzymes produced by gene fusion. Methods Enzymol. 1991;202:687–706. doi: 10.1016/0076-6879(91)02032-5. [DOI] [PubMed] [Google Scholar]

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