Molecular genetic analysis of transposase-end DNA sequence recognition: Cooperativity of three adjacent base-pairs in specific interaction with a mutant Tn5 transposase

Journal of Molecular Biology

Volumn 276, Issue 5, 1998, Pages 913-925

  Zhou, Maggie ^a   Bhasin, Archna ^a   Reznikoff, William S ^a  

^a UNIVERSITY OF WISCONSIN MADISON   (United States)

Author keywords

Base pair cooperativity; Protein DNA interaction; Tn5 transposon; Transposase; Transposition

Indexed keywords

DNA; MUTANT PROTEIN; TRANSPOSASE;

ARTICLE; BASE PAIRING; CONTROLLED STUDY; DNA SEQUENCE; DNA TRANSPOSITION; GENETIC ANALYSIS; MOLECULAR GENETICS; NONHUMAN; PRIORITY JOURNAL; PROTEIN DNA BINDING;

EID: 0032513010     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1997.1579     Document Type: Article

References (38)

1. Ades S.E., Sauer R.T. Specificity of minor-groove and major-groove interactions in a homeodomain-DNA complex. Biochemistry. 34:1995;14601-14608
2. Arciszewska L.K., Craig N.L. Interaction of the Tn7-encoded transposition protein TnsB with the ends of the transposon. Nucl. Acids Res. 19:1991;5021-5029
3. Berg D.E. Transposon Tn5. Berg D.E., Howe M.M. Mobile DNA. 1989;185-210 American Society for Microbiology, Washington, DC
4. Calladine C.R. Mechanics of sequence-dependent stacking of bases in B-DNA. J. Mol. Biol. 161:1982;343-352
5. de la Cruz N.B., Weinreich M.D., Wiegand T.W., Krebs M.P., Reznikoff W.S. Characterization of the Tn5 transposase and inhibitor proteins a model for the inhibition of transposition. J. Bacteriol. 175:1993;6932-6938
6. Derbyshire K.M., Grindley N.D.F. Binding of the IS903 transposase to its inverted repeat in vitro. EMBO J. 11:1992;3449-3455
7. Dickerson R.E. Base sequence and helix structure variation in B and A DNA. J. Mol. Biol. 166:1983;419-441
8. Dodson K.W., Berg D.E. Saturation mutagenesis of the inside end of insertion sequence IS50. Gene. 85:1989;75-81
9. Frank D.E., Saecker R.M., Bond J.P., Capp M.W., Tsodikov O.V., Melcher S.E., Levandoski M.M., Record M.T. Jr. Thermodynamics of the interactions of lac repressor with variants of the symmetric lac operator effects of converting a consensus site to a non-specific site. J. Mol. Biol. 267:1997;1186-1206
10. Goryshin I.Y., Kil Y.V., Reznikoff W.S. DNA length, bending, and twisting constraints on IS50 transposition. Proc. Natl Acad. Sci. USA. 91:1994;10834-10838
11. Goryshin I.Y., Reznikoff W.S. T5 in vitro transposition. J. Biol. Chem. 1998;. In the press
12. Huisman O., Errada P.R., Signon L., Kleckner N. Mutational analysis of IS10's outside end. EMBO J. 8:1989;2101-2109
13. Ichikawa H., Ikeda K., Amemura J., Ohtsubo E. Two domains in the terminal inverted-repeat sequence of transposon Tn3. Gene. 86:1990;11-17
14. Jilk R.A., York D., Reznikoff W.S. The organization of the outside end of transposon Tn5. J. Bacteriol. 178:1996;1671-1679
15. Koudelka G.B., Harbury P., Harrison S.C., Ptashne M. DNA twisting and the affinity of bacteriophage 434 operator for bacteriophage 434 repressor. Proc. Natl Acad. Sci. USA. 85:1988;4633-4637
16. Krebs M.P., Reznikoff W.S. Use of a T5 derivative that creates lacZ translational fusions to obtain a transposition mutant. Gene. 63:1988;277-285
17. Kuo C.-F., Zou A., Jayaram M., Getzoff E., Harshey R. DNA-protein complexes during attachment-site synapsis in Mu DNA transposition. EMBO J. 10:1991;1585-1591
18. Lesser D.R., Kurpiewski M.R., Jen-Jacobson L. The energetic basis of specificity in the EcoRI endonuclease-DNA interaction. Science. 250:1990;776-786
19. 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. 271:1996;1247-1254
20. Makris J.C. Modulation of IS50 and Tn5 transposition. PhD thesis. 1989;University of Wisconsin-Madison
21. Makris J.C., Nordmann P.L., Reznikoff W.S. Mutational analysis of insertion sequence 50 (IS50) and transposon 5 (Tn5) ends. Proc. Natl Acad. Sci. USA. 85:1988;2224-2228
22. Mossing M.C., Record M.T. Jr. Thermodynamic origins of specificity in the lac repressor-operator interactions. J. Mol. Biol. 186:1985;295-305
23. Phadnis S.H., Berg D.E. Identification of base pairs in the IS50 O end needed for IS50 and Tn5 transposition. Proc. Natl Acad. Sci. USA. 84:1987;9118-9122
24. Pütz J., Puglisi J.D., Florentz C., Giege R. Additive, cooperative and anti-cooperative effects between identity nucleotides of a tRNA. EMBO J. 12:1993;2949-2957
25. Reich N.O., Sweetnam K.R. Sequence-dependent effects on DNA stabilty resulting from guanosine replacements by inosine. Nucl. Acids Res. 22:1994;2089-2093
26. Reznikoff W.S. The Tn5 transposon. Annu. Rev. Microbiol. 47:1993;945-963
27. Seeman N.C., Rosenberg J.M., Rich A. Sequence-specific recognition of double helical nucleic acids by proteins. Proc. Natl Acad. Sci. USA. 73:1976;804-808
28. Studier F.W., Rosenberg A.H., Dunn J.J., Dubendorff J.W. Use of T7 RNA polymerase to direct expression of cloned genes. Methods Enzymol. 185:1990;60-89
29. Tomcsanyi T., Berg D.E. Effects of adenine (Dam) methylation on transposition activity of O end mutants of IS50. J. Mol. Biol. 209:1989;191-193
30. Weinreich M.D., Mahnke-Braam L., Reznikoff W.S. A functional analysis of the Tn5 transposase, identification of domains required for DNA binding and mutlimerization. J. Mol. Biol. 241:1993;166-177
31. Weinreich M.D., Gasch A., Reznikoff W.S. Evidence that the cis preference of the Tn5 transposase is caused by nonproductive multimerization. Genes Dev. 8:1994;2363-2374
32. Wiegand T.W., Reznikoff W.S. Characterization of two hypertransposing Tn5 mutants. J. Bacteriol. 174:1992;1229-1239
33. Wright S. The shifting balance theory and macroevolution. Annu. Rev. Genet. 16:1982;1-19
34. Yin J.C., Reznikoff W.S. dnaA, an essential host gene, and Tn5 transposition. J. Bacteriol. 169:1987;1812-1817
35. Yin J.C., Krebs M.P., Reznikoff W.S. Effect of Dam methylation on Tn5 transposition. J. Mol. Biol. 199:1988;35-45
36. York D., Reznikoff W.S. Purification and biochemical analyses of a monomeric form of Tn5 transposase. Nucl. Acid. Res. 24:1996;3790-3796
37. Zhou M. Interactions between Tn5 transposase and Tn5 end sequences: study of the DNA binding step. PhD thesis. 1997;University of Wisconsin-Madison
38. Zhou M., Reznikoff W.S. Tn5 transposase mutants that alter DNA binding specificity. J. Mol. Biol. 271:1997;362-373