Genetic analysis of Xenopus transcription factor IIIA

Journal of Molecular Biology

Volumn 284, Issue 5, 1998, Pages 1307-1322

  Bumbulis, Michael J ^a,b   Wroblewski, Greggory ^a,b   McKean, David ^a   Setzer, David R ^a  

^a CASE WESTERN RESERVE UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b BALDWIN WALLACE COLLEGE   (United States)

Author keywords

5 S RNA; DNA binding; TFIIIA; Transcription; Zinc finger

Indexed keywords

BETA GALACTOSIDASE; DNA BINDING PROTEIN; RIBOSOME RNA; RNA 5S; RNA POLYMERASE II; TRANSCRIPTION FACTOR; ZINC FINGER PROTEIN;

AMINO TERMINAL SEQUENCE; ARTICLE; BINDING AFFINITY; CONTROLLED STUDY; DNA RECOMBINATION; GENE ACTIVATION; GENETIC ANALYSIS; IMMUNOBLOTTING; MUTAGENESIS; NONHUMAN; PHENOTYPE; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; PROTEIN DNA BINDING; REPORTER GENE; TRANSCRIPTION INITIATION; XENOPUS; YEAST CELL;

AMPHIBIA; REPTILIA; XENOPUS;

EID: 0032545166     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1998.2285     Document Type: Article

References (59)

1. Archambault, J., Milne, C. A., Schappert, K. T., Baum, B., Friesen, J. D. & Segall, J. (1992). The deduced sequence of the transcription factor TFIIIA from Saccharomyces cerevisiae reveals extensive sequence divergence from Xenopus TFIIIA. J. Biol. Chem. 267, 3282-3288.
2. Berg, J. M. (1988). Proposed structure for the zinc-binding domains from transcription factor IIIA and related proteins. Proc. Natl. Acad. Sci. USA, 85, 99-102.
3. Bitter, G. A. & Egan, K. M. (1984). Expression of heterologous genes in Saccharomyces cerevisiae from vectors utilizing the glyceraldehyde-3-phosphate dehydrogenase gene promoter. Gene, 32, 263-274.
4. Brow, D. A. & Geiduschek, E. P. (1987). Modulation of yeast 5 S rRNA synthesis in vitro by ribosomal protein YL3. A possible regulatory loop. J. Biol. Chem. 262, 13953-1398.
5. Brown, R. S., Ferguson, C., Kingswell, A., Winkler, F. K. & Leonard, K. R. (1988). Electron microscopic study of crystals of the Xenopus laevis transcription factor IIIA-5 S ribosomal RNA complex. Proc. Natl Acad. Sci. USA, 85, 3802-3804.
6. Bumbulis, M. J. (1997). A Novel Genetic Screen for Mutations Affecting Sequence-specific DNA Binding by Xenopus Transcription Factor IIIA, Case Western Reserve University, Cleveland, OH.
7. Carey, M., Lin, Y.-S., Green, M. R. & Ptashne, M. (1990). A mechanism for synergistic activation of a mammalian gene by GAL4 derivatives. Nature, 345, 361-364.
8. Choo, Y. & Klug, A. (1993). A role in DNA binding for the linker sequences of the first three zinc fingers of TFIIIA. Nucl. Acids Res. 21, 3341-3346.
9. Christensen, J. H., Hansen, P. K., Lillelund, O. & Thogersen, H. C. (1991). Sequence-specific binding of the N-terminal three-finger fragment of Xenopus transcription factor IIIA to the internal control region of a 5 S RNA gene. FEBS Letters, 281, 181-184.
10. Clemens, K. R., Liao, X., Wolf, V., Wright, P. E. & Gottesfeld, J. M. (1992). Definition of the binding sites of individual zinc fingers in the transcription factor IIIA-5 S RNA gene complex. Proc. Natl Acad. Sci. USA, 89, 10822-10826.
11. Clemens, K. R., Wolf, V., McBryant, S. J., Zhang, P., Liao, X., Wright, P. E. & Gottesfeld, J. M. (1993). Molecular basis for specific recognition of both RNA and DNA by a zinc finger protein. Science, 260, 530-533.
12. Clemens, K. R., Zhang, P., Liao, X., McBryant, S. J., Wright, P. E. & Gottesfeld, J. M. (1994). Relative contributions of the zinc fingers of transcription factor IIIA to the energetics of DNA binding. J. Mol. Biol. 244, 23-35.
13. Darby, M. K. & Joho, K. E. (1992). Differential binding of zinc fingers from Xenopus TFIIIA and p43 to 5 S RNA and the 5 S RNA gene. Mol. Cell. Biol. 12, 3155-3164.
14. Del, Rio S. & Setzer, D. R. (1991). High yield purification of active transcription factor IIIA expressed in E. coli. Nucl. Acids Res. 19, 6197-6203.
15. Del, Rio S. & Setzer, D. R. (1993). The role of zinc fingers in transcriptional activation by transcription factor IIIA. Proc. Natl Acad. Sci. USA, 90, 168-172.
16. Del, Rio S., Menezes, S. R. & Setzer, D. R. (1993). The function of individual zinc fingers in sequence-specific DNA recognition by transcription factor IIIA. J. Mol. Biol. 233, 567-579.
17. Elrod-Erickson, M., Rould, M. A., Nekludova, L. & Pabo, C. O. (1996). Zif268 protein-DNA complex refined at 1.6 A: a model system for understanding zinc finger-DNA interactions. Structure, 4, 1171-1180.
18. Fairall, L., Schwabe, J. W. R., Chapman, L., Finch, J. T. & Rhodes, D. (1993). The crystal structure of a two zinc-finger peptide reveals an extension of the rules for zinc finger/DNA recognition. Nature, 366, 483-487.
19. Foster, M. P., Wuttke, D. S., Radhakrishnan, I., Case, D. A., Gottesfeld, J. M. & Wright, P. E. (1997). Domain packing and dynamics in the DNA complex of the N-terminal zinc fingers of TFIIIA. Nature Struct. Biol. 4, 605-608.
20. Ginsberg, A. M., King, B. O. & Roeder, R. G. (1984). Xenopus 5 S gene transcription factor, TFIIIA: characterization of a cDNA clone and measurement of RNA levels throughout development. Cell, 39, 479-489.
21. Gough, J. A. & Murray, N. E. (1983). Sequence diversity among related genes for recognition of specific targets in DNA molecules. J. Mol. Biol. 166, 1-10.
22. Hanas, J. S., Gaskins, C. J., Smith, J. F. & Ogilvie, M. K. (1992). Structure, function, evolution of transcription factor IIIA. Prog. Nucl. Acid Res. Mol. Biol. 43, 205-239.
23. Hayes, J. J. & Clemens, K. R. (1992). Locations of contacts between individual zinc fingers of Xenopus laevis transcription factor IIIA and the internal control region of a 5 S RNA gene. Biochemistry, 31, 11600-11605.
24. Hayes, J. J. & Tullius, T. D. (1992). Structure of the TFIIIA-5 S DNA complex. J. Mol. Biol. 227, 407-417.
25. Houbaviy, H. B., Usheva, A., Shenk, T. & Burley, S. K. (1996). Cocrystal structure of YY1 bound to the adeno-associated virus P5 initiator. Proc. Natl Acad. Sci. USA, 93, 13577-13582.
26. Ito, H., Fukuda, Y., Murata, K. & Kimura, A. (1983). Transformation of intact yeast cells treated with alkali cations. J. Bacteriol. 153, 163-168.
27. Jacobs, G. H. (1992). Determination of the base recognition positions of zinc fingers from sequence analysis. EMBO J. 11, 4507-4517.
28. Johnson, D. L., Fan, R. S. & Treinies, M. L. (1991). Analysis of the molecular mechanisms for the species-specific transcription of Drosophila and human tRNA gene transcription components. J. Biol. Chem. 266, 16037-16043.
29. Kehres, D. G., Subramanyan, G. S., Hung, V. S., Rogers, G. W., Jr. & Setzer, D. R. (1997). Energetically unfavorable interactions among the zinc fingers of transcription factor IIIA when bound to the 5 S rRNA gene. J. Biol. Chem. 272, 20152-20161.
30. Kunkel, T. A., Roberts, J. D. & Zakour, R. A. (1987). Rapid and efficient site-specific mutagenesis without phenotypic selection. Methods Enzymol. 154, 367-382.
31. Liao, X., Clemens, K. R., Tennant, L., Wright, P. E. & Gottesfeld, J. M. (1992). Specific interaction of the first three zinc fingers of TFIIIA with the internal control region of the Xenopus 5 S RNA gene. J. Mol. Biol. 223, 857-871.
32. Michael, S. F., Kilfoil, V. J., Schmidt, M. H., Amann, B. T. & Berg, J. M. (1992). Metal binding and folding properties of a minimalist Cys2His2 zinc finger peptide. Proc. Natl Acad. Sci. USA, 89, 4796-4800.
33. Miller, J., McLachlan, A. D. & Klug, A. (1985). Repetitive zinc-binding domains in the protein transcription factor IIIA from Xenopus oocytes. EMBO J. 4, 1609-1614.
34. Muhlrad, D., Hunter, R. & Parker, R. (1992). A rapid method for localized mutagenesis of yeast genes. Yeast, 8, 79-82.
35. Nolte, R. T., Conlin, R. M., Harrison, S. C. & Brown, R. S. (1998). Differing roles for zinc fingers in DNA recognition: structure of a six-finger transcription factor IIIA complex. Proc. Natl Acad. Sci. USA, 95, 2938-2943.
36. Pavletich, N. P. & Pabo, C. O. (1991). Zinc finger-DNA recognition: crystal structure of a Zif268-DNA complex at 2.1 A. Science, 252, 809-817.
37. Pavletich, N. P. & Pabo, C. O. (1993). Crystal structure of a five-finger GLI-DNA complex: new perspectives on zinc fingers. Science, 261, 1701-1707.
38. Pelham, H. R. & Brown, D. D. (1980). A specific transcription factor that can bind either the 5 S RNA gene or 5 S RNA. Proc. Natl Acad. Sci. USA, 77, 4170-4174.
39. Pieler, T. & Theunissen, O. (1993). TFIIIA: nine fingers-three hands. Trends Biochem. Sci. 18, 226-230.
40. Pieler, T. & Rudt, F. (1997). Nucleocytoplasmic transport of 5 S ribosomal RNA. Semin. Cell Dev. Biol. 8, 79-82.
41. Pieler, T., Appel, B., Oei, S. L., Mentzel, H. & Erdmann, V. A. (1985). Point mutational analysis of the Xenopus laevis 5 S gene promoter. EMBO J. 4, 1847-1853.
42. Pieler, T., Hamm, J. & Roeder, R. G. (1987). The 5 S gene internal control region is composed of three distinct sequence elements, organized as two functional domains with variable spacing. Cell, 48, 91-100.
43. Rollins, M. B., Del, Rio S., Galey, A. L., Setzer, D. R. & Andrews, M. T. (1993). Role of TFIIIA zinc fingers in vivo: analysis of single- finger function in developing Xenopus embryos. Mol. Cell. Biol. 13, 4776-4783.
44. Rose, M. D., Winston, F. & Hieter, P. (1990). Methods in Yeast Genetics: A Laboratory Course Manual, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
45. Ryan, R. F. & Darby, M. K. (1998). The role of zinc finger linkers in p43 and TFIIIA binding to 5 S rRNA and DNA. Nucl. Acids Res. 26, 703-709.
46. Schena, M. & Yamamoto, K. R. (1988). Mammalian glucocorticoid receptor derivatives enhance transcription in yeast. Science, 241, 965-967.
47. Setzer, D. R., Hmiel, R. M. & Liao, S. Y. (1990). A simple vector modification to facilitate oligonucleotide-directed mutagenesis. Nucl. Acids Res. 18, 4175-4178.
48. Setzer, D. R., Menezes, S. R., Del, Rio S., Hung, V. S. & Subramanyan, G. (1996). Functional Interactions between the zinc fingers of Xenopus transcription factor IIIA during 5 S rRNA binding. RNA, 2, 1254-1269.
49. Smith, J. F., Hawkins, J., Leonard, R. E. & Hanas, J. S. (1991). Structural elements in the N-terminal half of transcription factor IIIA required for factor binding to the 5 S RNA gene internal control region. Nucl. Acids Res. 19, 6871-6876.
50. Struksnes, K., Forus, A., Gabrielsen, O. S. & Oyen, T. B. (1991). Yeast TFIIIA + TFIIIC/τ-factor, but not yeast TFIIIA alone, interacts with the Xenopus 5 S rRNA gene. Nucl. Acids Res. 19, 565-571.
51. Studier, F. W., Rosenberg, A. H., Dunn, J. J. & Dubendorff, J. W. (1990). Use of T7 RNA polymerase to direct expression of cloned genes. Methods Enzymol. 185, 60-88.
52. Theunissen, O., Rudt, F., Guddat, U., Mentzel, H. & Pieler, T. (1992). RNA and DNA binding zinc fingers in Xenopus TFIIIA. Cell, 71, 679-690.
53. Triezenberg, S. J., Kingsbury, R. C. & McKnight, S. L. (1988). Functional dissection of VP16, the trans-activator of herpes simplex virus immediate early gene expression. Genes Dev. 2, 718-729.
54. Veldhoen, N., You, Q., Setzer, D. R. & Romaniuk, P. J. (1994). Contribution of individual base pairs to the interaction of TFIIIA with the Xenopus 5 S RNA gene. Biochemistry, 33, 7568-7575.
55. Vrana, K. E., Churchill, M. E., Tullius, T. D. & Brown, D. D. (1988). Mapping functional regions of transcription factor TFIIIA. Mol. Cell. Biol. 8, 1684-1696.
56. Wang, C. K. & Weil, P. A. (1989). Purification and characterization of Saccharomyces cerevisiae transcription factor IIIA. J. Biol. Chem. 264, 1092-1099.
57. Ward, A. C. (1990). Single-step purification of shuttle vectors from yeast for high frequency back-transformation into E. coli. Nucl. Acids Res. 18, 5319.
58. Wuttke, D. S., Foster, M. P., Case, D. A., Gottesfeld, J. M. & Wright, P. E. (1997). Solution structure of the first three zinc fingers of TFIIIA bound to the cognate DNA sequence: determinants of affinity and sequence specificity. J. Mol. Biol. 273, 183-206.
59. Zang, W. Q., Veldhoen, N. & Romaniuk, P. J. (1995). Effects of zinc finger mutations on the nucleic acid binding activities of Xenopus transcription factor IIIA. Biochemistry, 34, 15545-15552.