Reduction/oxidation-phosphorylation control of DNA binding in the bZIP dimerization network

BMC Genomics

Volumn 7, Issue , 2006, Pages

  Amoutzias, Gregory D ^a,b   Bornberg Bauer, Erich ^a,c   Oliver, Stephen G ^a   Robertson, David L ^a  

^a UNIVERSITY OF MANCHESTER   (United Kingdom)

^b UNIVERSITY OF LAUSANNE   (Switzerland)

^c UNIVERSITY OF MÜNSTER   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; LEUCINE ZIPPER PROTEIN; TRANSCRIPTION FACTOR;

ARTICLE; BIOSENSOR; DIMERIZATION; DNA BINDING; DNA SEQUENCE; ENVIRONMENTAL FACTOR; FREQUENCY ANALYSIS; GENETIC CONSERVATION; GENOMICS; HUMAN; NONHUMAN; OXIDATION REDUCTION REACTION; OXIDATIVE STRESS; PHYLOGENY; PREDICTION; PROMOTER REGION; PROTEIN DOMAIN; PROTEIN FUNCTION; PROTEIN PHOSPHORYLATION; PROTEIN PROTEIN INTERACTION; REGULATORY MECHANISM; SEQUENCE ANALYSIS;

AMINO ACID SEQUENCE; ANIMALS; DIMERIZATION; DNA; DNA-BINDING PROTEINS; HUMANS; MOLECULAR SEQUENCE DATA; OXIDATION-REDUCTION; OXIDATIVE STRESS; PHOSPHORYLATION; PROTEIN BINDING; PROTEIN STRUCTURE, TERTIARY; SEQUENCE HOMOLOGY, AMINO ACID; TRANSCRIPTION FACTORS;

EUKARYOTA; FUNGI; MAGNOLIOPHYTA; MAMMALIA;

EID: 33745092020     PISSN: 14712164     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-7-107     Document Type: Article

References (36)

1. Iguchi-Ariga SM, Schaffner W. CpG methylation of the cAMP-responsive enhancer/promoter sequence TGACGTCA abolishes specific factor binding as well as transcriptional activation. Genes Dev 1989, 3:612-9.
2. Mahoney CW, Shuman J, McKnight SL, Chen HC, Huang KP: Phosphorylation of CCAAT-enhancer binding protein by protein kinase C attenuates site-selective DNA binding. J Biol Chem 1992, 267:19396-403.
3. Abate C, Patel L, Rauscher FJ 3rd, Curran T: Redox regulation of fos and jun DNA-binding activity in vitro. Science 1990, 249:1157-61.
4. Moll JR, Acharya A, Gal J, Mir AA Vinson C: Magnesium is required for specific DNA binding of the CREB B-ZIP domain. Nucleic Acids Res 2002, 30:1240-6.
5. Fujii Y, Shimizu T, Toda T, Yanagida M, Hakoshima T: Structural basis for the diversity of DNA recognition by bZIP transcription factors. Nat Struct Biol 2000, 7:889-93.
6. Miller M, Shuman JD, Sebastian T, Dauter Z, Johnson PF: Structural basis for DNA recognition by the basic region leucine zipper transcription factor CCAAT/enhancer-binding protein alpha. J Biol Chem 2003, 278:15178-84.
7. Deppmann CD, Thornton TM, Utama FE, Taparowsky EJ: Phosphorylation of BATF regulates DNA binding: a novel mechanism for AP-I (activator protein-I) regulation. Biochem J 2003, 374:423-31.
8. Xanthoudakis S, Miao G, Wang F, Pan YC, Curran T: Redox activation of Fos-Jun DNA binding activity is mediated by a DNA repair enzyme. EMBO J 1992, 11:3323-35.
9. Marshall HE, Merchant K, Stamler JS: Nitrosation and oxidation in the regulation of gene expression. FASEB J 2000, 14:1889-900.
10. Klatt P, Molina EP, De Lacoba MG, Padilla CA, Martinez-Galesteo E, Barcena JA, Lamas S: Redox regulation of c-Jun DNA binding by reversible S-glutathiolation. FASEB J 1999, 13:1481-90.
11. Jindra. M, Gaziova I, Uhlirova M, Okabe M, Hiromi Y, Hirose S: Coactivator MBFI preserves the redox-dependent AP-I activity during oxidative stress in Drosophila. EMBO J 2004, 23:3538-47.
12. Okuno H, Akahori A, Sato H, Xanthoudakis S, Curran T, Iba H: Escape from redox regulation enhances the transforming activity of Fos. Oncogene 1993, 8:695-701.
13. Morgan IM, Havarstein LS, Wong WY, Luu P, Vogt PK: Efficient induction of fibrosarcomas by v-jun requires mutations in the DNA binding region and the transactivation domain. Oncogene 1994, 9:2793-7.
14. Trautwein C, van der Geer P, Karin M, Hunter T, Chojkier M: Protein kinase A and C site-specific phosphorylations of LAP (NF-IL6) modulate its binding affinity to DNA recognition elements. J Clin Invest 1994, 93:2554-61.
15. Fernandes L, Rodrigues-Pousada C, Struhl K: Yap, a novel family of eight bZIP proteins in Saccharomyces cerevisiae with distinct biological functions. Mol Cell Biol 1997, 17:6982-93.
16. Barabasi AL, Oltvai ZN: Network biology: understanding the cell's functional organization. Nat Rev Genet 2004, 5:101-113.
17. Amoutzias GD, Robertson DL, Oliver SG, Bornberg-Bauer E: Convergent evolution of gene networks by single-gene duplications in higher eukaryotes. EMBO Rep 2004, 5:274-9.
18. Cinquin O, Demongeot J: High-dimensional switches and the modelling of cellular differentiation. J Theor Biol 2005, 233:391-411.
19. Newman JR, Keating AE: Comprehensive identification of human bZIP interactions with coiled-coil arrays. Science 2003, 300:2097-101.
20. Schelcher C, Valencia S, Delecluse HJ, Hicks M, Sinclair AJ: Mutation of a single amino acid residue in the basic region of the Epstein-Barr virus (EBV) lytic cycle switch protein Zta (BZLFI) prevents reactivation of EBV from latency. J Virol 2005, 79:13822-8.
21. Cowell IG, Hurst HC: Transcriptional repression by the human bZIP factor E4BP4: definition of a minimal repression domain. Nucleic Acids Res 1994, 22:59-65.
22. Bower KE, Zeller RW, Wachsman W, Martinez T, McGuire KL: Correlation of transcriptional repression by p21(SNFT) with changes in DNA.NF-AT complex Interactions. J Biol Chem 2002, 277:34967-77.
23. Hai T, Hartman MG: The molecular biology and nomenclature of the activating transcription factor/cAMP responsive element binding family of transcription factors: activating transcription factor proteins and homeostasis. Gene 2001, 273:1-11.
24. Martinez-Jimenez CP, Gomez-Lechon MJ, Castell JV, Jover R: Transcriptional regulation of the human hepatic CYP3A4: Identification of a new distal enhancer region responsive to CCAAT/enhancer binding protein beta isoforms (LAP and LIP). Mol. Pharmacol 2005, 6:2088- 101.
25. Parkin SE, Baer M, Copeland TD, Schwartz RC, Johnson PF: Regulation of CCAAT/enhancer-binding protein (C/EBP) activator proteins by heterodimerization with C/EBPgamma (IgEBP). J Biol Chem 2002, 277:23563-72.
26. Morel Y, Barouki R: Repression of gene expression by oxidative stress. Biochem J 1999, 342(Pt 3):481-96.
27. Toone WM, Morgan BA, Jones N: Redox control of AP-I-like factors in yeast and beyond. Oncogene 2001, 20-2336-2346.
28. Eddy SR: Hidden Markov models. Curr Opin Struct Biol 1996, 6:361-365.
29. Matys V, Fricke E, Geffers R, Gossling E, Haubrock M, Hehl R, Hornischer K, Karas D, Kel AE, Kel-Margoulis OV, Kloos DU, Land S, Lewicki-Potapov B, Michael H, Munch R, Reuter I, Rotert S, Saxel H, Scheer M, Thiele S, Wingender E: TRANSFAC: transcriptional regulation, from patterns to profiles. Nucleic Acids Res 2003, 31:374-378.
30. Vinson C, Myakishev M, Acharya A, Mir AA, Moll JR, Bonovich M: Classification of human B-ZIP proteins based on dimerization properties. Mol Cell Biol 2002, 22:6321-35.
31. Bornberg-Bauer E, Rivals E, Vingron M: Computational approaches to identify leucine zippers. Nucleic Acids Res 1998, 26:2740-2746.
32. Brendel V, Karlin S: Too many leucine zippers? Nature 1989, 341:574-5.
33. Notredame C, Higgins DG, Heringa J: T-Coffee: A novel method for fast and accurate multiple sequence alignment. J Mol Biol 2000, 302:205-17.
34. Thompson JD, Higgins DG, Gibson TJ: CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 1994, 22:4673-80.
35. [http://evolution.genetics.washington.edu].
36. [http://evolve.zoo.ox.ac.uk/software/TreeEdit/main.html].