Anatomy of a flexer-DNA complex inside a higher-order transposition intermediate

Cell

Volumn 85, Issue 5, 1996, Pages 761-771

  Lavoie, Brigitte D ^a   Shaw, Gary S ^a   Millner, Anders M ^a   Chaconas, George ^a  

^a UNIVERSITY OF WESTERN ONTARIO   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

CURVED DNA; DNA BINDING PROTEIN;

AMINO ACID SEQUENCE; ANATOMY; ANIMAL CELL; ARTICLE; DNA CLEAVAGE; DNA TRANSPOSITION; ENZYME LOCALIZATION; ESCHERICHIA COLI; MOLECULAR MODEL; NONHUMAN; PRIORITY JOURNAL; PROTEIN DNA INTERACTION; PROTEIN STRUCTURE;

ANIMALIA; ESCHERICHIA COLI;

EID: 0029973105     PISSN: 00928674     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0092-8674(00)81241-6     Document Type: Article

References (55)

1. Aki, T., Choy, H.E., and Adhya, S. (1996). Histone-like protein HU as a specific transcriptional regulator: co-factor role in repression of gal transcription by GAL repressor. Genes to Cells 2, in press.
2. Baker, T.A., Mizuuchi, M., Savilahti, H., and Mizuuchi, K. (1993). Division of labor among monomers within the Mu transposase tetramer. Cell 74, 723-733.
3. Bianchi, M.E. (1994). Prokaryotic HU and eukaryotic HMG1: a kinked relationship. Mol. Microbiol. 14, 1-5.
4. Bonnefoy, E., and Rouviere-Yaniv, J. (1991). HU and IHF, two homologous histone-like proteins of Escherichia coli, form different protein-DNA complexes with short DNA fragments. EMBO J. 10, 687-696.
5. Bonnefoy, E., Takahashi, M., and Yaniv, J.R. (1994). DNA-binding parameters of the HU protein of Escherichia coli to cruciform DNA. J. Mol. Biol. 242, 116-129.
6. Calladine, C.R., and Drew, H.R. (1992). Understanding DNA (London, England: Academic Press Ltd).
7. Castaing, B., Zelwer, C., Laval, J., and Boiteux, S. (1995). HU protein of Escherichia coli binds specifically to DNA that contains single-strand breaks or gaps. J. Biol. Chem. 270, 10291-10296.
8. Craig, N.L. (1995). Unity in transposition reactions. Science 270, 253-254.
9. Dickerson, R.E. (1992). DNA structure from A to Z. Meth. Enzymol. 211, Part A, 67-111.
10. Ebright, Y.W., Chen, Y., Pendergrast, P.S., and Ebright, R.H. (1992). Incorporation of an EDTA-metal complex at a rationally selected site within a protein: application to EDTA-iron DNA affinity cleaving with catabolite gene activator protein (CAP) and Cro. Biochemistry 31, 10664-10670.
11. Echols, H. (1990). Nucleoprotein structures initiating DNA replication, transcription, and site-specific recombination. J. Biol. Chem. 265, 14697-14700.
12. Ermácora, M.R., Delfino, J.M., Cuenoud, B., Schepartz, A., and Fox, R.O. (1992). Conformation-dependent cleavage of staphylococcal nuclease with a disulfide-linked iron chelate. Proc. Natl. Acad. Sci. USA 89, 6383-6387.
13. Funnell, B.E., Baker, T.A., and Kornberg, A. (1987). In vitro assembly of a prepriming complex at the origin of the Escherichia coli chromosome. J. Biol. Chem. 262, 10327-10334.
14. Goshima, N., Kohno, K., Imamoto, F., and Kano, Y. (1990). HU-1 mutants of Escherichia coli deficient in DNA binding. Gene 96, 141-145.
15. Grosschedl, R. (1995). Higher-order nucleoprotein complexes in transcription: analogies with site-specific recombination. Curr.Opin. Cell. Biol. 7, 362-370.
16. Grosschedl, R., Giese, K., and Pagel, J. (1994). HMG domain proteins: architectural elements in the assembly of nucleoprotein structures. Trends Genet. 10, 94-100.
17. Hayes, J.J., and Wolffe, A.P. (1993). Preferential and asymmetric interaction of linker histones with 5S DNA in the nucleosome. Proc. Natl. Acad. Sci. USA 90, 6415-6419.
18. Haykinson, M.J., and Johnson, R.C. (1993). DNA looping and the helical repeat in vitro and in vivo: effect of HU protein and enhancer location on Hin invertasome assembly. EMBO J. 12, 2503-2512.
19. Hodges-Garcia, Y., Hagerman, P.J., and Pettijohn, D.E. (1989). DNA ring closure mediated by protein HU. J. Biol. Chem. 264, 14621-14623.
20. Hwang, D.S., and Kornberg, A. (1992). Opening of the replication origin of Escherichia coli by Dna A protein with protein HU or IHF. J. Biol. Chem. 267, 23083-23086.
21. Kahn, J.D., and Crothers, D.M. (1992). Protein-induced bending and DNA cyclization. Proc. Natl. Acad. Sci. USA 89, 6343-6347.
22. Kao, L.R., Megraw, T.L., and Chae, C.B. (1993). Essential role of the HMG domain in the function of yeast mitochondrial histone HM: functional complementation of HM by the nuclear nonhistone protein NHP6A. Proc. Natl. Acad. Sci. USA 90, 5598-5602.
23. Kraulis, P.J. (1991). MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures. J. Appl. Cryst. 24, 946-950.
24. Lavoie, B.D., and Chaconas, G. (1993). Site-specific HU binding in the Mu transpososome: conversion of a sequence-independent DNA-binding protein into a chemical nuclease. Genes Dev. 7, 2510-2519.
25. Lavoie, B.D., and Chaconas, G. (1994). A second high affinity HU binding site in the phage Mu transpososome. J. Biol. Chem. 269, 15571-15576.
26. Lavoie, B.D., and Chaconas, G. (1995). Transposition of phage Mu DNA. Curr. Topics Microbiol. Immunol. 204, 83-99.
27. Lavoie, B.D., Chan, B.S., Allison, R.G., and Chaconas, G. (1991). Structural aspects of a higher order nucleoprotein complex: induction of an altered DNA structure at the Mu-host junction of the Mu type 1 transpososome. EMBO J. 10, 3051-3059.
28. Lee, E.C., Hales, L.M., Gumport, R.I., and Gardner, J.F. (1992). The isolation and characterization of mutants of the integration host factor (IHF) of Escherichia coli with altered, expanded DNA-binding specificities. EMBO J. 11, 305-313.
29. Mazzarelli, J.M., Ermácora, M.R., Fox, R.O., and Grindley, N.D. (1993). Mapping interactions between the catalytic domain of resolvase and its DNA substrate using cysteine-coupled EDTA-iron. Biochemistry 32, 2979-2986.
30. Megraw, T.L., and Chae, C.B. (1993). Functional complementarity between the HMG1-like yeast mitochondrial histone HM and the bacterial histone-like protein HU. J. Biol. Chem. 268, 12758-12763.
31. Mizuuchi, M., Baker, T.A., and Mizuuchi, K. (1992). Assembly of the active form of the transposase-Mu DNA complex: a critical control point in Mu transposition. Cell 70, 303-311.
32. Nash, H.A. (1996). The E. coli HU and IHF proteins: accessory factors forcomplex protein-DNAassemblies. In Regulation of Gene Expression in Escherichia coli, E.C.C.L.A.S. Lynch, ed. (Austin, Texas: R.G. Landes Company), pp. 149-179.
33. Ner, S.S., Travers, A.A., and Churchill, M.E.A. (1994). Harnessing the writhe: a role for DNA chaperones in nucleoprotein complex formation. Trends Biochem. Sci. 19, 185-187.
34. Nunes-Duby, S.E., Smith-Mungo, L.I., and Landy, A. (1995). Single base-pair precision and structural rigidity in a small IHF-induced DNA loop. J. Mol. Biol. 253, 228-242.
35. Oberto, J., Drlica, K., and Rouviere-Yaniv, J. (1994). Histones, HMG, HU, IHF: meme combat. Biochimie 76, 901-908.
36. Onate, S.A., Prendergast, P., Wagner, J.P., Nissen, M., Reeves, R., Pettijohn, D.E., and Edwards, D.P. (1994). The DNA-bending protein HMG-1 enhances progesterone receptor binding to its target DNA sequences. Mol. Cell. Biol. 14, 3376-3391.
37. Parvin, J.D., McCormick, R.J., Sharp, P.A., and Fisher, D.E. (1995). Pre-bending of apromoter sequence enhances affinity for the TATA-binding factor. Nature 373, 724-727.
38. Paull, T.T., Haykinson, M.J., and Johnson, R.C. (1993). The nonspecific DNA-binding and -bending proteins HMG1 and HMG2 promote the assembly of complex nucleoprotein structures. Genes Dev. 7, 1521-1534.
39. Pontiggia, A., Negri, A., Beltrame, M., and Bianchi, M.E. (1993). Protein HU binds specifically to kinked DNA. Mol. Microbiol. 7, 343-350.
40. Savilahti, H., Rice, P.A., and Mizuuchi, K. (1995). The phage Mu transpososome core: DNA requirements for assembly and function. EMBO J. 14, 4893-4903.
41. Shindo, H., Furubayashi, A. ,Shimizu, M., Miyake, M., and Imamoto, F. (1992). Preferential binding of E. coli histone-like protein HU alpha to negatively supercoiled DNA. Nucl. Acids Res. 20, 1553-1558.
42. Shindo, H., Kurumizaka, H., Furubayashi, A., Sakuma, C., Matsumoto, U., Yanagida, A., Goshima, N., Kano, Y., and Imamoto, F. (1993). Proton NMR study on a histone-like protein, HU alpha, from Escherichia coli and its complex with oligo DNAs. Biol. Pharm. Bull. 16, 437-443.
43. Shykind, B.M., Kim, J., and Sharp, P.A. (1995). Activation of the TFIID-TFIIA complex with HMG-2. Genes Dev. 9, 1354-1365.
44. Skarstad, K., Baker, T.A., and Kornberg, A. (1990). Strand separation required for initiation of replication at the chromosomal origin of E.coli is facilitated by a distant RNA-DNA hybrid. EMBO J. 9, 2341-2348.
45. Surette, M.G., and Chaconas, G. (1989). A protein factor which reduces the negative supercoiling requirement in the Mu DNA strand transfer reaction is Escherichia coli integration host factor. J. Biol. Chem. 264, 3028-3034.
46. Tanaka, I., Appelt, K., Dijk, J., White, S.W., and Wilson, K.S. (1984). 3-A resolution structure of a protein with histone-like properties in prokaryotes. Nature 310, 376-381.
47. Tanaka, H., Goshima, N., Kohno, K., Kano, Y., and Imamoto, F. (1993). Properties of DNA-binding of HU heterotypic and homotypic dimers from Escherichia coli. J. Biochem. (Tokyo) 113, 568-572.
48. Thompson, J.F., and Landy, A. (1988). Empirical estimation of protein-induced DNA bending angles: applications to lambda site-specific recombination complexes. Nucl. Acids Res. 16, 9687-9705.
49. Vis, H., Mariani, M., Vorgias, C.E., Wilson, K.S., Kaptein, R., and Boelens, R. (1995). Solution structure of the HU protein from Bacillus stearothermophilus. J. Mol. Biol. 254, 692-703.
50. Wang, Z., Namgoong, S.-Y., Zhang, X., and Harshey, R.M. (1996). Kinetic and structural probing of the pre-cleavage synaptic complex (type 0) formed during phage Mu transposition: action of metal ions and reagents specific to single stranded DNA. J. Biol. Chem. 271, 9619-9626.
51. Watson, M.A., and Chaconas, G. (1996). Three-site synapsis during Mu DNA transposition: a critical intermediate preceding engagement of the active site. Cell 85, 435-445.
52. Werner, M.H., Clore, G.M., Gronenborn, A.M., and Nash, H.A. (1994). Symmetry and asymmetry in the function of Escherichia coli integration host factor: implications for target identification by DNA-binding proteins. Curr. Biol. 4, 477-487.
53. Werner, M.H., Gronenborg, A.M., and Clore, G.M. (1996). Intercalation, DNA kinking, and the control of transcription. Science 271, 778-784.
54. White, S.W., Appelt, K., Wilson, K.S., and Tanaka, I. (1989). A protein structural motif that bends DNA. Proteins 5, 281-288.
55. Yang, C.C., and Nash, H.A. (1989). The interaction of E. coli IHF protein with its specific binding sites. Cell 57, 869-880.