Functional switches in transcription regulation; molecular mimicry and plasticity in protein-protein interactions

Biochemistry

Volumn 43, Issue 25, 2004, Pages 7983-7991

  Beckett, Dorothy ^a  

^a Bldg 142   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

MOLECULAR BIOLOGY; MOLECULAR STRUCTURE; PLASTICITY; PROBABILITY; PROTEINS;

BIOLOGICAL PROCESSES; COMPARTMENTALIZATION; FUNCTIONAL SWITCHES; TRANSCRIPTION;

BIOCHEMISTRY;

BETA CATENIN; BIOTIN; HELICASE; NUCLEAR FACTOR; NUCLEAR FACTOR I; TRANSCRIPTION FACTOR;

COMPLEX FORMATION; DIMERIZATION; LIGAND BINDING; MOLECULAR MIMICRY; NONHUMAN; PLASTICITY; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN FUNCTION; PROTEIN PROTEIN INTERACTION; PROTEIN SECONDARY STRUCTURE; REVIEW; RNA REPLICATION; STRUCTURE ANALYSIS; TRANSCRIPTION INITIATION; TRANSCRIPTION REGULATION;

ANIMALS; BETA CATENIN; CYTOSKELETAL PROTEINS; DNA-BINDING PROTEINS; HEPATOCYTE NUCLEAR FACTOR 1; HEPATOCYTE NUCLEAR FACTOR 1-ALPHA; HUMANS; HYDRO-LYASES; MODELS, MOLECULAR; MOLECULAR MIMICRY; NUCLEAR PROTEINS; PROTEIN BINDING; PROTEIN CONFORMATION; REPRESSOR PROTEINS; TRANS-ACTIVATION (GENETICS); TRANS-ACTIVATORS; TRANSCRIPTION FACTORS; TRANSCRIPTION, GENETIC;

EID: 3042565522     PISSN: 00062960     EISSN: None     Source Type: Journal    
DOI: 10.1021/bi049890b     Document Type: Review

References (57)

1. Citron, B. A., Davis, M. D., Milstien, S., Gutierrez, J., Mendel, D. B., Crabtree, G. R., and Kaufman, S. (1992) Identity of 4a-carbinolamine dehydratase, a component of the phenylalanine hydroxylation system, and DCoH, a transregulator of homeodomain proteins, Proc. Natl. Acad. Sci. U.S.A. 89, 11891-11894.
2. Mendel, D. B., Khavari, P. A., Conley, P. B., Graves, M. K., Hansen, L. P., Admon, A., and Crabtree, G. R. (1991) Characterization of a cofactor that regulates dimerization of a mammalian homeodomain protein, Science 254, 1762-1767.
3. Mendel, D. B., and Crabtree, G. R. (1991) HNF-1, a member of a novel class of dimerizing homeodomain proteins, J. Biol. Chem. 266, 677-680.
4. Rhee, K. H., Stier, G., Becker, P. B., Suck, D., and Sandaltzopoulos, R. (1997) The bifunctional protein DCoH modulates interactions of the homeodomain transcription factor HNF1 with nucleic acids, J. Mol. Biol. 265, 20-29.
5. Lei, X. D., and Kaufman, S. (1998) Identification of hepatic nuclear factor 1 binding sites in the 5′ flanking region of the human phenylalanine hydroxylase gene: Implication of a dual function of phenylalanine hydroxylase stimulator in the phenylalanine hydroxylation system, Proc. Natl. Acad. Sci. U.S.A. 95, 1500-1504.
6. Endrizzi, J. A., Cronk, J. D., Wang, W., Crabtree, G. R., and Alber, T. (1995) Crystal structure of DCoH, a bifunctional, protein-binding transcriptional coactivator, Science 268, 556-559.
7. Ficner, R., Sauer, U. H., Stier, G., and Suck, D. (1995) Three-dimensional structure of the bifunctional protein pcd/DCoH, a cytoplasmic enzyme interacting with transcription factor HNF1, EMBO J. 14, 2034-2042.
8. Rose, R. B., Endrizzi, J. A., Cronk, J. D., Holton, J., and Alber, T. (2000) High-resolution structure of the HNF-1α dimerization domain, Biochemistry 39, 15062-15070.
9. Narayana, N., Hua, Q., and Weiss, M. A. (2001) The dimerization domain of HNF-1alpha: Structure and plasticity of an intertwined four-helix bundle with application to diabetes mellitus, J. Mol. Biol. 310, 635-658.
10. Rose, R. B., Bayle, J. H., Endrizzi, J. A., Cronk, J. D., Crabtree, G. R., and Alber, T. (2000) Structural basis of dimerization, coactivator recognition and mody3 mutations in HNF-1alpha, Nat. Struct. Biol. 7, 744-748.
11. Bayle, J. H., Randazzo, F., Johnen, G., Kaufman, S., Nagy, A., Rossant, J., and Crabtree, G. R. (2002) Hyperphenylalaninemia and impaired glucose tolerance in mice lacking the bifunctional DCoH gene, J. Biol. Chem. 277, 28884-28891.
12. Pogge yon Strandmann, E., and Ryffel, G. U. (1995) Developmental expression of the maternal protein xDCoH, the dimerization cofactor of the homeoprotein 1fb1 (HNF1), Development 121, 1217-1226.
13. Yap, A. S., Brieher, W. M., and Gumbiner, B. M. (1997) Molecular and functional analysis of cadherin-based adherens junctions, Annu. Rev. Cell Dev. Biol. 13, 119-146.
14. Polakis, P. (2000) Wnt signaling and cancer, Genes Dev. 14, 1837-1851.
15. Aberle, H., Bauer, A., Stappert, J., Kispert, A., and Kemler, R. (1997) Beta-catenin is a target for the ubiquitin-proteasome pathway, EMBO J. 16, 3797-3804.
16. Orford, K., Crockett, C., Jensen, J. P., Weissman, A. M., and Byers, S. W. (1997) Serine phosphorylation-regulated ubiquitination and degradation of beta-catenin, J. Biol. Chem. 272, 24735-24738.
17. Behrens, J., Jerchow, B. A., Wurtele, M., Grimm, J., Asbrand, C., Wirtz, R., Kuhl, M., Wedlich, D., and Birchmeier, W. (1998) Functional interaction of an axin homolog, conductin, with beta-catenin, APC, and GSK3beta, Science 280, 596-599.
18. Hulsken, J., Birchmeier, W., and Behrens, J. (1994) E-cadherin and APC compete for the interaction with beta-catenin and the cytoskeleton, J. Cell Biol. 127, 2061-2069.
19. Ikeda, S., Kishida, S., Yamamoto, H., Murai, H., Koyama, S., and Kikuchi, A. (1998) Axin, a negative regulator of the wnt signaling pathway, forms a complex with GSK-3beta and beta-catenin and promotes GSK-3beta-dependent phosphorylation of beta-catenin, EMBO J. 17, 1371-1384.
20. von Kries, J. P., Winbeck, G., Asbrand, C., Schwarz-Romond, T., Sochnikova, N., Dell'Oro, A., Behrens, J., and Birchmeier, W. (2000) Hot spots in beta-catenin for interactions with LEF-1, conductin and APC, Nat. Struct. Biol. 7, 800-807.
21. Peifer, M., Berg, S., and Reynolds, A. B. (1994) A repeating amino acid motif shared by proteins with diverse cellular roles, Cell 76, 789-791.
22. Huber, A. H., Nelson, W. J., and Weis, W. I. (1997) Three-dimensional structure of the armadillo repeat region of beta-catenin, Cell 90, 871-882.
23. Ozawa, M., Baribault, H., and Kemler, R. (1989) The cytoplasmic domain of the cell adhesion molecule uvomorulin associates with three independent proteins structurally related in different species, EMBO J. 8, 1711-1717.
24. Ozawa, M., Ringwald, M., and Kemler, R. (1990) Uvomorulin-catenin complex formation is regulated by a specific domain in the cytoplasmic region of the cell adhesion molecule, Proc. Natl. Acad. Sci. U.S.A. 87, 4246-4250.
25. Huber, A. H., and Weis, W. I. (2001) The structure of the beta-catenin/E-cadherin complex and the molecular basis of diverse ligand recognition by beta-catenin, Cell 105, 391-402.
26. Roose, J., and Clevers, H. (1999) Tcf transcription factors: Molecular switches in carcinogenesis, Biochim. Biophys. Acta 1424, M23-M37.
27. Graham, T. A., Weaver, C., Mao, F., Kimelman, D., and Xu, W. (2000) Crystal structure of a beta-catenin/Tcf complex, Cell 103, 885-896.
28. Rubinfeld, B., Albert, I., Porfiri, E., Munemitsu, S., and Polakis, P. (1997) Loss of beta-catenin regulation by the APC tumor suppressor protein correlates with loss of structure due to common somatic mutations of the gene, Cancer Res. 57, 4624-4630.
29. Eklof Spink, K., Fridman, S. G., and Weis, W. I. (2001) Molecular mechanisms of beta-catenin recognition by adenomatous polyposis coli revealed by the structure of an APC-beta-catenin complex, EMBO J. 20, 6203-6212.
30. Knapp, S., Zamai, M., Volpi, D., Nardese, V., Avanzi, N., Breton, J., Plyte, S., Flocco, M., Marconi, M., Isacchi, A., and Caiolfa, V. R. (2001) Thermodynamics of the high-affinity interaction of Tcf4 with beta-catenin, J. Mol. Biol. 306, 1179-1189.
31. Fasolini, M., Wu, X., Flocco, M., Trosset, J. Y., Oppermann, U., and Knapp, S. (2003) Hot spots in Tcf4 for the interaction with beta-catenin, J. Biol. Chem. 278, 21092-21098.
32. del Solar, G., Giraldo, R., Ruiz-Echevarria, M. J., Espinosa, M., and Diaz-Orejas, R. (1998) Replication and control of circular bacterial plasmids, Microbiol. Mol. Biol. Rev. 62, 434-464.
33. Diaz-Lopez, T., Lages-Gonzalo, M., Serrano-Lopez, A., Alfonso, C., Rivas, G., Diaz-Orejas, R., and Giraldo, R. (2003) Structural changes in Repa, a plasmid replication initiator, upon binding to origin DNA, J. Biol. Chem. 278, 18606-18616.
34. Ishiai, M., Wada, C., Kawasaki, Y., and Yura, T. (1994) Replication initiator protein Repe of mini-f plasmid: Functional differentiation between monomers (initiator) and dimers (autogenous repressor), Proc. Natl. Acad. Sci. U.S.A. 91, 3839-3843.
35. Garcia de Viedma, D., Giraldo, R., Ruiz-Echevarria, M. J., Lutz, R., and Diaz-Orejas, R. (1995) Transcription of Repa, the gene of the initiation protein of the pseudomonas plasmid pPS10, is autoregulated by interactions of the Repa protein at a symmetrical operator, J. Mol. Biol. 247, 211-223.
36. Wickner, S., Hoskins, J., and McKenney, K. (1991) Function of DNAj and DNAk as chaperones in origin-specific DNA binding by Repa, Nature 350, 165-167.
37. Wickner, S., Hoskins, J., and McKenney, K. (1991) Monomerization of Repa dimers by heat shock proteins activates binding to DNA replication origin, Proc. Natl. Acad. Sci. U.S.A. 88, 7903-7907.
38. Wickner, S., Gottesman, S., Skowyra, D., Hoskins, J., McKenney, K., and Maurizi, M. R. (1994) A molecular chaperone, clpa, functions like DNAk and DNAj, Proc. Natl. Acad. Sci. U.S.A. 91, 12218-12222.
39. Komori, H., Matsunaga, F., Higuchi, Y., Ishiai, M., Wada, C., and Miki, K. (1999) Crystal structure of a prokaryotic replication initiator protein bound to DNA at 2.6 Å resolution, EMBO J. 18, 4597-4607.
40. Giraldo, R., Fernandez-Tomero, C., Evans, P. R., Diaz-Orejas, R., and Romero, A. (2003) A conformational switch between transcriptional repression and replication initiation in the Repa dimerization domain, Nat. Struct. Biol. 10, 565-571.
41. Barker, D. F., and Campbell, A. M. (1981) The BirA gene of Escherichia coli encodes a biotin holoenzyme synthetase, J. Mol. Biol. 146, 451-467.
42. Barker, D. F., and Campbell, A. M. (1981) Genetic and biochemical characterization of the BirA gene and its product: Evidence for a direct role of biotin holoenzyme synthetase in repression of the biotin operon in Escherichia coli, J. Mol. Biol. 146, 469-492.
43. Lane, M. D., Rominger, K. L., Young, D. L., and Lynen, F. (1964) The enzymatic synthesis of holotranscarboxylase from apo-transcarboxylase and (+)-biotin, J. Biol. Chem. 239, 2865-2871.
44. Prakash, O., and Eisenberg, M. A. (1979) Biotinyl 5′-adenylate: Corepressor role in the regulation of the biotin genes of Escherichia coli k-12, Proc. Natl. Acad. Sci. U.S.A. 76, 5592-5595.
45. Wilson, K. P., Shewchuk, L. M., Brennan, R. G., Otsuka, A. J., and Matthews, B. W. (1992) Escherichia coli biofin holoenzyme synthetase/bio repressor crystal structure delineates the biotin- and DNA-binding domains, Proc. Natl. Acad. Sci. U.S.A. 89, 9257-9261.
46. Koradi, R., Billeter, M., and Wuthrich, K. (1996) Molmol: A program for display and analysis of macromolecular structures, J. Mol. Graphics 14, 51-55, 29-32.
47. Streaker, E. D., Gupta, A., and Beckett, D. (2002) The biotin repressor: Thermodynamic coupling of corepressor binding, protein assembly, and sequence-specific DNA binding, Biochemistry 41, 14263-14271.
48. Weaver, L. H., Kwon, K., Beckett, D., and Matthews, B. W. (2001) Corepressor-induced organization and assembly of the biotin repressor: A model for allosteric activation of a transcriptional regulator, Proc. Natl. Acad. Sci. U.S.A. 98, 6045-6050.
49. Eisenstein, E., and Beckett, D. (1999) Dimerization of the Escherichia coli biotin repressor: Corepressor function in protein assembly, Biochemistry 38, 13077-13084.
50. Kwon, K., Streaker, E. D., Ruparelia, S., and Beckett, D. (2000) Multiple disordered loops function in corepressor-induced dimerization of the biotin repressor, J. Mol. Biol. 304, 821-833.
51. Cronan, J. E., Jr. (1988) Expression of the biotin biosynthetic operon of Escherichia coli is regulated by the rate of protein biotination, J. Biol. Chem. 263, 10332-10336.
52. Athappilly, F. K., and Hendrickson, W. A. (1995) Structure of the biotinyl domain of acetyl-coenzyme a carboxylase determined by mad phasing, Structure 3, 1407-1419.
53. Yao, X., Wei, D., Soden, C., Jr., Summers, M. F., and Beckett, D. (1997) Structure of the carboxy-terminal fragment of the apo-biotin carboxyl carrier subunit of Escherichia coli acetyl-CoA carboxylase, Biochemistry 36, 15089-15100.
54. Weaver, L. H., Kwon, K., Beckett, D., and Matthews, B. W. (2001) Competing protein: Protein interactions are proposed to control the biological switch of the E. coli biotin repressor, Protein Sci. 10, 2618-2622.
55. Polyak, S. W., Chapman-Smith, A., Mulhem, T. D., Cronan, J. E., Jr., and Wallace, J. C. (2001) Mutational analysis of protein substrate presentation in the posttranslational attachment of biotin to biotin domains, J. Biol. Chem. 276, 3037-3045.
56. Reche, P. A., Howard, M. J., Broadhurst, R. W., and Perham, R. N. (2000) Heteronuclear NMR studies of the specificity of the posttranslational modification of biotinyl domains by biotinyl protein ligase, FEBS Lett. 479, 93-98.
57. Nooren, I. M., and Thornton, J. M. (2003) Diversity of protein-protein interactions, EMBO J. 22, 3486-3492.