DNA binding domains and nuclear localization signal of LEDGF: Contribution of two helix-turn-helix (HTH)-like domains and a stretch of 58 amino acids of the N-terminal to the trans-activation potential of LEDGF

Journal of Molecular Biology

Volumn 355, Issue 3, 2006, Pages 379-394

  Singh, Dhirendra P ^a   Kubo, E ^b   Takamura, Y ^a   Shinohara, T ^a   Kumar, A ^c   Chylack Jr , Leo T ^d   Fatma, N ^a  

^a UNIVERSITY OF NEBRASKA MEDICAL CENTER   (United States)

^b UNIVERSITY OF FUKUI   (Japan)

^c PONCE SCHOOL OF MEDICINE   (Puerto Rico)

^d HARVARD MEDICAL SCHOOL   (United States)

Author keywords

DNA binding domain; Lens epithelium derived growth factor; PWWP domain; Stress and heat shock elements; Transcription regulation

Indexed keywords

AMINO ACID; HEAT SHOCK PROTEIN; HELIX LOOP HELIX PROTEIN; LENS EPITHELIUM DERIVED GROWTH FACTOR;

AMINO TERMINAL SEQUENCE; ANIMAL CELL; ARTICLE; BINDING ASSAY; CARBOXY TERMINAL SEQUENCE; CELL PROTECTION; DNA BINDING; DNA SEQUENCE; GENE CONTROL; GENE EXPRESSION; GENETIC TRANSCRIPTION; HOMEOSTASIS; MICROENVIRONMENT; NONHUMAN; PHYSIOLOGY; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN DOMAIN; PROTEIN FUNCTION; PROTEIN LOCALIZATION; PROTEIN STRUCTURE; SIGNAL TRANSDUCTION; STRESS; STRUCTURE ANALYSIS; TRANSACTIVATION; TRANSCRIPTION REGULATION;

ANIMALIA;

EID: 29044449057     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2005.10.054     Document Type: Article

References (64)

1. M. Ptashne How eukaryotic transcriptional activators work Nature 335 1988 683 689
2. P.J. Mitchell, and R. Tjian Transcriptional regulation in mammalian cells by sequence-specific DNA binding proteins Science 245 1989 371 378
3. M. Vandromme, C. Gauthier-Rouviere, N. Lamb, and A. Fernandez Regulation of transcription factor localization: fine-tuning of gene expression Trends Biochem. Sci. 21 1996 59 64
4. D.P. Singh, N. Ohguro, L.T. Chylack Jr, and T. Shinohara Lens epithelium-derived growth factor: increased resistance to thermal and oxidative stresses Ophthalmol. Vis. Sci. 40 1999 1444 1451
5. E. Kubo, N. Fatma, P. Sharma, T. Shinohara, L.T. Chylack Jr, Y. Akagi, and D.P. Singh Transactivation of involucrin, a marker of differentiation in keratinocytes, by lens epithelium-derived growth factor (LEDGF) J. Mol. Biol. 320 2002 1053 1063
6. E. Kubo, D.P. Singh, N. Fatma, T. Shinohara, P. Zelenka, V.N. Reddy, and L.T. Chylack Cellular distribution of lens epithelium-derived growth factor (LEDGF) in the rat eye: loss of LEDGF from nuclei of differentiating cells Histochem. Cell Biol. 119 2003 289 299
7. P. Sharma, D.P. Singh, N. Fatma, L.T. Chylack Jr, and T. Shinohara Activation of LEDGF gene by thermal-and oxidative-stresses Biochem. Biophys. Res. Commun. 276 2000 1320 1324
8. H. Nakamura, Y. Izumoto, H. Kambe, T. Kuroda, T. Mori, and K. Kawamura Molecular cloning of complementary DNA for a novel human hepatoma-derived growth factor. Its homology with high mobility group-1 protein J. Biol. Chem. 269 1994 25143 25149
9. Y. Izumoto, T. Kuroda, H. Harada, T. Kishimoto, and H. Nakamura Hepatoma-derived growth factor belongs to a gene family in mice showing significant homology in the amino terminus Biochem. Biophys. Res. Commun. 238 1997 26 32
10. D.P. Singh, N. Fatma, A. Kimura, L.T. Chylack Jr, and T. Shinohara LEDGF binds to heat shock and stress-related element to activate the expression of stress-related genes Biochem. Biophys. Res. Commun. 283 2001 943 955
11. H. Ge, Y. Si, and R.G. Roeder Isolation of cDNAs encoding novel transcriptional factor co-activators p52 and p75 reveals an alternate regulatory mechanism of transcriptional activation EMBO J. 17 1998 6723 6729
12. S. Machida, P. Chaudhary, T. Shinohara, D.P. Singh, V.N. Reddy, and L.T. Chylack Jr Lens epithelium-derived growth factor (LEDGF) promotes photoreceptor survival in light-damaged and Royal College of Surgeons (RCS) rats Invest. Ophthal. Vis. Sci. 42 2001 1087 1095
13. H. Matsui, L.R. Lin, D.P. Singh, T. Shinohara, and V.N. Reddy Lens-epithelium-derived growth factor: increased survival and decreased DNA breakage of human RPE cells induced by oxidative stress Invest. Ophthal. Vis. Sci. 42 2001 2935 2941
14. M. Nakamura, D.P. Singh, E. Kubo, L.T. Chylack Jr, and T. Shinohara LEDGF: survival of embryonic chick retinal photoreceptor cells Invest. Ophthal. Vis. Sci. 41 2000 1168 1175
15. D.P. Singh, N. Ohguro, T. Kikuchi, T. Sueno, V.N. Reddy, and K. Yuge Lens epithelium-derived growth factor: effects on growth and survival of lens epithelial cells, keratinocytes and fibroblasts Biochem. Biophys. Res. Commun. 267 2000 373 381
16. N. Fatma, D.P. Singh, T. Shinohara, and L.T. Chylack Jr Transcriptional regulation of the antioxidant protein 2 gene, a thiol-specific antioxidant, by lens epithelium-derived growth factor to protect cells from oxidative stress J. Biol. Chem. 276 2001 48899 48907
17. N. Fatma, E. Kubo, L.T. Chylack Jr, T. Shinohara, Y. Akagi, and D.P. Singh LEDGF regulation of alcohol and aldehyde dehydrogenases in lens epithelial cells: stimulation of retinoic acid production and protection from ethanol toxicity Am. J. Physiol. Cell Physiol. 287 2004 C508 C516
18. P. Cherepanov, G. Maertens, P. Proost, B. Devreese, J. Van Beeumen, and Y. Engelborghs HIV-1 integrase forms stable tetramers and associates with LEDGF/p75 protein in human cells J. Biol. Chem. 278 2003 372 381
19. M. Ayaki, N. Ohoguro, N. Azuma, Y. Majima, K. Yata, and N. Ibaraki Detection of cytotoxic anti-LEDGF autoantibodies in atopic dermatitis Autoimmunity 35 2002 319 327
20. M. Ayaki, T. Sueno, D.P. Singh, L.T. Chylack Jr, and T. Shinohara Antibodies to lens epithelium-derived growth factor (LEDGF) kill epithelial cells of whole lenses in organ culture Expt. Eye Res. 69 1999 139 142
21. X. Wu, T. Daniels, C. Molinaro, M.B. Lilly, and C.A. Casiano Caspase cleavage of the nuclear autoantigen LEDGF/p75 abrogates its pro-survival function: implications for autoimmunity in atopic disorders Cell Death Differ. 9 2002 915 925
22. M. Okamoto, Y. Ogawa, A. Watanabe, K. Sugiura, Y. Shimomura, and N. Aoki Autoantibodies to DFS70/LEDGF are increased in alopecia areata patients J. Autoimmun. 23 2004 257 266
23. D.J. Hussey, S. Moore, M. Nicola, and A. Dobrovic Fusion of the NUP98 gene with the LEDGF/p52 gene defines a recurrent acute myeloid leukemia translocation BMC Genet. 2 2001 20
24. H.G. Ahuja, J. Hong, P.D. Aplan, L. Tcheurekdjian, S.J. Forman, and M.L. Slovak t(9;11)(p22;p15) in acute myeloid leukemia results in a fusion between NUP98 and the gene encoding transcriptional coactivators p52 and p75-lens epithelium-derived growth factor (LEDGF) Cancer Res. 60 2000 6227 6229
25. L.T. Chylack Jr, L. Fu, R. Mancini, M.D. Martin-Rehrmann, A.J. Saunders, and G. Konopka Lens epithelium-derived growth factor (LEDGF/p75) expression in fetal and adult human brain Expt. Eye Res. 79 2004 941 948
26. M. Llano, M. Vanegas, O. Fregoso, D. Saenz, S. Chung, M. Peretz, and E.M. Poeschla LEDGF/p75 determines cellular trafficking of diverse lentiviral but not murine oncoretroviral integrase proteins and is a component of functional lentiviral preintegration complexes J. Virol. 78 2004 9524 9537
27. P. Sharma, N. Fatma, E. Kubo, T. Shinohara, L.T. Chylack Jr, and D.P. Singh Lens epithelium-derived growth factor relieves transforming growth factor-beta1-induced transcription repression of heat shock proteins in human lens epithelial cells J. Biol. Chem. 278 2003 20037 20046
28. -/- mice lens epithelial cells by reactive oxygen species: Increased expression and activation of TGFβ Cell Death Differ. 12 2005 734 750
29. H. Feng, H. Xiang, Y.W. Mao, J. Wang, J.P. Liu, and X.Q. Huang Human Bcl-2 activates ERK signaling pathway to regulate activating protein-1, lens epithelium-derived growth factor and downstream genes Oncogene 23 2004 7310 7321
30. T. Daniels, J. Zhang, I. Gutierrez, M.L. Elliot, B. Yamada, and M.J. Heeb Antinuclear autoantibodies in prostate cancer: immunity to LEDGF/p75, a survival protein highly expressed in prostate tumors and cleaved during apoptosis Prostate 62 2005 14 26
31. Y. Nishizawa, J. Usukura, D.P. Singh, L.T. Chylack Jr, and T. Shinohara Spatial and temporal dynamics of two alternatively spliced regulatory factors, lens epithelium-derived growth factor (ledgf/p75) and p52, in the nucleus Cell Tissue Res. 305 2001 107 114
32. D.P. Singh, N. Fatma, L.T. Chylack Jr, and T. Shinohara Distinct nuclear localization signal and DNA-binding domains of LEDGF Invest. Opthalmol. Vis. Sci (suppl) 42 2001 2909
33. T. Shinohara, D.P. Singh, and N. Fatma LEDGF, a survival factor, activates stress-related genes Prog. Retin. Eye Res. 21 2002 341 358
34. G. Maertens, P. Cherepanov, Z. Debyser, Y. Engelborghs, and A. Engelman Identification and characterization of a functional nuclear localization signal in the HIV-1integrase interactor LEDGF/p75 J. Biol. Chem. 279 2004 33421 33429
35. M. Vanegas, M. Llano, S. Delgado, D. Thompson, M. Peretz, and E. Poeschla Identification of the LEDGF/p75 HIV-1 integrase-interaction domain and NLS revealsNLS-independent chromatin tethering J. Cell Sci. 118 2005 1733 1743
36. K. Busschots, J. Vercammen, S. Emiliani, R. Benarous, Y. Engelborghs, F. Christ, and Z. Debyser The interaction of LEDGF/p75 with integrase is lentivirus-specific and promotes DNA binding J. Biol. Chem. 280 2005 17841 17847
37. C. Qiu, K. Sawada, X. Zhang, and X. Cheng The PWWP domain of mammalian DNA methyltransferase Dnmt3b defines a new family of DNA-binding folds Nature Struct. Biol. 9 2002 217 224
38. L.M. Slater, M.D. Allen, and M. Bycroft Structural variation in PWWP domains J. Mol. Biol. 330 2003 571 576
39. Y.Z. GE, M.T. Pu, H. Gowher, H.P. Wu, J.P. Ding, A. Jeltsch, and G.L. Xu Chromatin targeting of de novo DNA methyltransferases by the PWWP domain J. Biol. Chem. 279 2004 25447 25454
40. J. Liu, H. Tan, and B. Rost Loopy proteins appear conserved in evolution J. Mol. Biol. 322 2002 53 64
41. P. Cherepanov, E. Devroe, P.A. Silver, and A. Engelman Identification of an evolutionarily conserved domain in human lens epithelium-derived growth factor/transcriptional co-activator p75 (LEDGF/p75) that binds HIV-1 integrase J. Biol. Chem. 279 2004 48883 48892
42. J. Schultz, F. Milpetz, P. Bork, and C.P. Ponting SMART, a simple modular architecture research tool: identification of signaling domains Proc. Natl Acad. Sci. USA 95 1998 5857 5864
43. I. Letunic, R.R. Copley, S. Schmidt, F.D. Ciccarelli, T. Doerks, and J. Schultz SMART 4.0: towards genomic data integration Nucl. Acids Res. 32 2004 D142 D144
44. N. Fatma, D.P. Singh, T. Shinohara, and L.T. Chylack Jr Heparin's roles in stabilizing, potentiating, and transporting LEDGF into the nucleus Invest. Ophthalmol. Vis. Sci. 41 2000 2648 2657
45. A. Song, A. Patel, K. Thamatrakoln, C. Liu, D. Feng, C. Clayberger, and A.M. Krensky Functional domains and DNA-binding sequences of RFLAT-1/KLF13, a Kruppel-like transcription factor of activated T lymphocytes J. Biol. Chem. 277 2002 30055 30065
46. S.A. Phelan, and M.R. Loeken Identification of a new binding motif for the paired domain of Pax-3 and unusual characteristics of spacing of bipartite recognition elements on binding and transcription activation J. Biol. Chem. 273 1998 19153 19159
47. H.Y. Yang, and T. Evans Distinct roles for the two cGATA-1 finger domains Mol. Cell. Biol. 12 1992 4562 4570
48. T. Chen, N. Tsujimoto, and E. Li The PWWP domain of Dnmt3a and Dnmt3b is required for directing DNA methylation to the major satellite repeats at pericentric heterochromatin Mol. Cell. Biol. 24 2004 9048 9058
49. M. Ehrlich The ICF syndrome, a DNA methyltransferase 3B deficiency and immunodeficiency disease Clin. Immunol. 109 2003 17 28
50. L. Aravind, and D. Landsman AT-hook motifs identified in a wide variety of DNA-binding proteins Nucl. Acids Res. 26 1998 4413 4421
51. E.C. LaCasse, and Y.A. Lefebvre Nuclear localization signals overlap DNA- or RNA-binding domains in nucleic acid-binding proteins Nucl. Acids Res. 23 1995 1647 1656
52. M. Cokol, R. Nair, and B. Rost Finding nuclear localization signals EMBO Rep. 1 2000 411 415
53. Z. Otwinowski, R.W. Scheivitz, R.G. Zhang, C.L. Lawson, and P.B. Sigler Crystal structure of trp repressor/operator complex at atomic resolution Nature 335 1988 321 329
54. S.R. Jordan, and C.O. Pabo Structure of the lambda complex at 2.5 Å resolution: details of the repressor-operator interactions Science 242 1988 893 899
55. I.A. Hope, and K. Struhl GCN4, a eukaryotic transactivator protein, binds as dimmer to target DNA EMBO J. 6 1987 2781 2784
56. V. Kumar, and P. Chambon The estrogen receptor binds tightly to its responsive element as ligand induced homodimer Cell 55 1988 145 156
57. D. Rhodes, and A. Klug An underlying repeat in some transcriptional control sequences corresponding to half a double helical turn of DNA Cell 46 1986 123 132
58. R.D. Jong, J.V. Heiden, and F. Meijlink DNA-binding specificity of the S8 homeodomain Nucl. Acids Res. 21 1993 4711 4720
59. Y.Z. Ge, M.T. Pu, H. Gowher, H.P. Wu, J.P. Ding, A. Jeltsch, and G.L. Xu Chromatin targeting of de novo DNA methyltransferases by the PWWP domain J. Biol. Chem. 279 2004 25447 25454
60. I. Stec, S.B. Nagl, G.J. van Ommen, and J.T. den Dunnen The PWWP domain: a potential protein-protein interaction domain in nuclear proteins influencing differentiation? FEBS Letters 473 2000 1 5
61. J. Sambrook, and M.J. Gething Protein structure. Chaperones, paperones Nature 342 1989 224 225
62. M.M. Bradford A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding Anal. Biochem. 72 1976 248 254
63. R. Pollock, and R. Treisman A sensitive method for the determination of protein-DNA binding specificities Nucl. Acids Res. 18 1990 6197 6204
64. A.R. Oliphant, C.J. Brandl, and K. Struhl Defining the sequence specificity of DNA-binding proteins by selecting binding sites from random-sequence oligonucleotides: analysis of yeast GCN4 protein Mol. Cell. Biol. 9 1989 2944 2949