Intrinsic disorder of human Yin Yang 1 protein

Proteins: Structure, Function and Bioinformatics

Volumn 83, Issue 7, 2015, Pages 1284-1296

  Górecki, Andrzej ^a   Bonarek, Piotr ^a   Górka, Adam Kazimierz ^a   Figiel, Małgorzata ^a   Wilamowski, Mateusz ^a   Dziedzicka Wasylewska, Marta ^a  

^a JAGIELLONIAN UNIVERSITY   (Poland)

Author keywords

Carcinogenesis; CD; Denaturation; Fluorescence; Hydrodynamics; IDP; SEC; TFE; Transcription factor; YY1

Indexed keywords

INTRINSICALLY DISORDERED PROTEIN; TRANSCRIPTION FACTOR YY1; TRYPSIN; YY1 PROTEIN, HUMAN;

AMINO TERMINAL SEQUENCE; ARTICLE; CARBOXY TERMINAL SEQUENCE; COMPUTER MODEL; CONFORMATIONAL TRANSITION; DNA BINDING; ESCHERICHIA COLI; HUMAN; MOLECULAR WEIGHT; NONHUMAN; PRIORITY JOURNAL; PROTEIN EXPRESSION; PROTEIN FUNCTION; PROTEIN PURIFICATION; PROTEIN SECONDARY STRUCTURE; PROTEIN STRUCTURE; PROTEIN TERTIARY STRUCTURE; BIOLOGY; CHEMISTRY; CIRCULAR DICHROISM; GENE EXPRESSION; GENETICS; METABOLISM; MOLECULAR CLONING; PROCEDURES; PROTEIN DEGRADATION; PROTEIN FOLDING; PROTEIN UNFOLDING; SIZE EXCLUSION CHROMATOGRAPHY;

CHROMATOGRAPHY, GEL; CIRCULAR DICHROISM; CLONING, MOLECULAR; COMPUTATIONAL BIOLOGY; ESCHERICHIA COLI; GENE EXPRESSION; HUMANS; INTRINSICALLY DISORDERED PROTEINS; PROTEIN FOLDING; PROTEIN UNFOLDING; PROTEOLYSIS; TRYPSIN; YY1 TRANSCRIPTION FACTOR;

EID: 84931007179     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.24822     Document Type: Article

References (73)

1. Shi Y, Seto E, Chang LS, Shenk T. Transcriptional repression by yy1, a human GLI-Kruppel-related protein, and relief of repression by adenovirus E1A protein. Cell 1991;67:377-388.
2. Hariharan N, Kelley DE, Perry RP. Delta, a transcription factor that binds to downstream elements in several polymerase II promoters, is a functionally versatile zinc finger protein. Proc Natl Acad Sci USA 1991;88:9799-9803.
3. Oei SL, Shi Y. Poly(ADP-ribosyl)ation of transcription factor yin yang 1 under conditions of DNA damage. Biochem Biophys Res Commun 2001;285:27-31.
4. Joo M, Wright JG, Hu NN, Sadikot RT, Park GY, Blackwell TS, Christman JW. Yin yang 1 enhances cyclooxygenase-2 gene expression in macrophages. Am J Physiol Lung Cellular Mol Physiol 2007;292:L1219-1226.
5. Hsu KW, Hsieh RH, Lee YH, Chao CH, Wu KJ, Tseng MJ, Yeh TS. The activated notch1 receptor cooperates with alpha-enolase and MBP-1 in modulating c-myc activity. Mol Cellular Biol 2008;28:4829-4842.
6. Cai Y, Jin J, Yao T, Gottschalk AJ, Swanson SK, Wu S, Shi Y, Washburn MP, Florens L, Conaway RC, Conaway JW. Yy1 functions with ino80 to activate transcription. Nat Struct Mol Biol 2007;14:872-874.
7. Park K, Atchison ML. Isolation of a candidate repressor/activator, NF-e1 (YY-1, delta), that binds to the immunoglobulin kappa 3' enhancer and the immunoglobulin heavy-chain mu e1 site. Proc Natl Acad Sci USA 1991;88:9804-9808.
8. Zhou Q, Gedrich RW, Engel DA. Transcriptional repression of the c-fos gene by yy1 is mediated by a direct interaction with ATF/CREB. J Virol 1995;69:4323-4330.
9. Ye J, Zhang X, Dong Z. Characterization of the human granulocyte-macrophage colony-stimulating factor gene promoter: an ap1 complex and an Sp1-related complex transactivate the promoter activity that is suppressed by a yy1 complex. Mol Cellular Biol 1996;16:157-167.
10. Sweetser MT, Hoey T, Sun YL, Weaver WM, Price GA, Wilson CB. The roles of nuclear factor of activated T cells and ying-yang 1 in activation-induced expression of the interferon-gamma promoter in T cells. J Biol Chem 1998;273:34775-34783.
11. Moriuchi M, Moriuchi H, Margolis DM, Fauci AS. USF/c-myc enhances, while Yin-yang 1 suppresses, the promoter activity of cxcr4, a coreceptor for HIV-1 entry. J Immunol 1999;162:5986-5992.
12. Weill L, Shestakova E, Bonnefoy E. Transcription factor yy1 binds to the murine beta interferon promoter and regulates its transcriptional capacity with a dual activator/repressor role. J Virol 2003;77:2903-2914.
13. Usheva A, Shenk T. Yy1 transcriptional initiator: protein interactions and association with a DNA site containing unpaired strands. Proc Natl Acad Sci USA 1996;93:13571-13576.
14. Emran F, Florens L, Ma B, Swanson SK, Washburn MP, Hernandez N. A role for yin Yang-1 (yy1) in the assembly of snRNA transcription complexes. Gene 2006;377:96-108.
15. Shi Y, Lee JS, Galvin KM. Everything you have ever wanted to know about yin yang 1. Biochim Biophys Acta 1997;1332:F49-66.
16. Chang PJ, Chen LW, Shih YC, Tsai PH, Liu AC, Hung CH, Liou JY, Wang SS. Role of the cellular transcription factor yy1 in the latent-lytic switch of kaposi's sarcoma-associated herpesvirus. Virology 2011;413:194-204.
17. Coull JJ, Romerio F, Sun JM, Volker JL, Galvin KM, Davie JR, Shi Y, Hansen U, Margolis DM. The human factors yy1 and LSF repress the human immunodeficiency virus type 1 long terminal repeat via recruitment of histone deacetylase 1. J Virol 2000;74:6790-6799.
18. Lewis BA, Tullis G, Seto E, Horikoshi N, Weinmann R, Shenk T. Adenovirus E1A proteins interact with the cellular yy1 transcription factor. J Virol 1995;69:1628-1636.
19. Thomas MJ, Seto E. Unlocking the mechanisms of transcription factor yy1: are chromatin modifying enzymes the key?. Gene 1999;236:197-208.
20. Zhu W, Olson SY, Garban H. Transcription regulator Yin-yang 1: from silence to cancer. Crit Rev Oncog 2011;16:227-238.
21. Vella P, Barozzi I, Cuomo A, Bonaldi T, Pasini D. Yin yang 1 extends the Myc-related transcription factors network in embryonic stem cells. Nucleic Acids Res 2012;40:3403-3418.
22. Yang WM, Yao YL, Sun JM, Davie JR, Seto E. Isolation and characterization of cDNAs corresponding to an additional member of the human histone deacetylase gene family. J Biol Chem 1997;272:28001-28007.
23. Atchison L, Ghias A, Wilkinson F, Bonini N, Atchison ML. Transcription factor yy1 functions as a PcG protein in vivo. EMBO J 2003;22:1347-1358.
24. Wilkinson FH, Park K, Atchison ML. Polycomb recruitment to DNA in vivo by the yy1 REPO domain. Proc Natl Acad Sci USA 2006;103:19296-19301.
25. Wu S, Shi Y, Mulligan P, Gay F, Landry J, Liu H, Lu J, Qi HH, Wang W, Nickoloff JA Wu C., Shi Y. A YY1-ino80 complex regulates genomic stability through homologous recombination-based repair. Nat Struct Mol Biol 2007;14:1165-1172.
26. Sui G, Affar eB, Shi Y, Brignone C, Wall NR, Yin P, Donohoe M, Luke MP, Calvo D Grossman SR, Shi Y. Yin yang 1 is a negative regulator of p53. Cell 2004;117:859-872.
27. Liu H, Schmidt-Supprian M, Shi Y, Hobeika E, Barteneva N, Jumaa H, Pelanda R, Reth M, Skok J, Rajewsky K, Shi Y. Yin yang 1 is a critical regulator of B-cell development. Genes Dev 2007;21:1179-1189.
28. Houbaviy HB, Usheva A, Shenk T, Burley SK. Cocrystal structure of yy1 bound to the adeno-associated virus p5 initiator. Proc Natl Acad Sci USA 1996;93:13577-13582.
29. Alfieri C, Gambetta MC, Matos R, Glatt S, Sehr P, Fraterman S, Wilm M, Muller J, Muller CW. Structural basis for targeting the chromatin repressor sfmbt to polycomb response elements. Genes Dev 2013;27:2367-2379.
30. Bushmeyer S, Park K, Atchison ML. Characterization of functional domains within the multifunctional transcription factor, yy1. J Biol Chem 1995;270:30213-30220.
31. Atchison ML. Function of yy1 in Long-distance DNA interactions. Front Immunol 2014;5:45
32. Yang WM, Inouye C, Zeng Y, Bearss D, Seto E. Transcriptional repression by yy1 is mediated by interaction with a mammalian homolog of the yeast global regulator rpd3. Proc Natl Acad Sci USA 1996;93:12845-12850.
33. Uversky VN. Natively unfolded proteins: a point where biology waits for physics. Protein Sci 2002;11:739-756.
34. Golebiowski FM, Gorecki A, Bonarek P, Dziedzicka-Wasylewska M. Efficient overexpression and purification of active full-length human transcription factor yin yang 1 in escherichia coli. Protein Express Purif 2011;77:198-206.
35. Golebiowski FM, Gorecki A, Bonarek P, Rapala-Kozik M, Kozik A, Dziedzicka-Wasylewska M. An investigation of the affinities, specificity and kinetics involved in the interaction between the yin yang 1 transcription factor and DNA. FEBS J 2012;279:3147-3158.
36. Verdery RB, Benham DF, Baldwin HL, Goldberg AP, Nichols AV. Measurement of normative HDL subfraction cholesterol levels by gaussian summation analysis of gradient gels. J Lipid Res 1989;30:1085-1095.
37. de Haen C. Molecular weight standards for calibration of gel filtration and sodium dodecyl sulfate-polyacrylamide gel electrophoresis: ferritin and apoferritin. Anal Biochem 1987;166:235-245.
38. Dziedzic-Letka A, Rymarczyk G, Kaplon TM, Gorecki A, Szamborska-Gbur A, Wojtas M, Dobryszycki P, Ozyhar A. Intrinsic disorder of drosophila melanogaster hormone receptor 38 N-terminal domain. Proteins 2011;79:376-392.
39. Tcherkasskaya O, Uversky VN. Denatured collapsed states in protein folding: example of apomyoglobin. Proteins 2001;44:244-254.
40. Tayyab S, Qamar S, Islam M. Size exclusion chromatography and size exclusion hplc of proteins. Biochem Educ 1991;19:149-152.
41. Uversky VN. What does it mean to be natively unfolded?. Eur J Biochem/FEBS 2002;269:2-12.
42. Kelly SM, Jess TJ, Price NC. How to study proteins by circular dichroism. Biochimica Et Biophys Acta 2005; 751:119-139.
43. Sreerama N, Woody RW. Estimation of protein secondary structure from circular dichroism spectra: comparison of CONTIN, SELCON, and CDSSTR methods with an expanded reference set. Anal Biochem 2000;287:252-260.
44. Kats M, St Germain ME. Spectroscopic determination of protein concentrations from proteinase K digests. Anal Biochem 2002;307:212-218.
45. Uversky VN, Dunker AK. Understanding protein non-folding. Biochim Biophys Acta 2010;1804:1231-1264.
46. Tompa P. Intrinsically unstructured proteins. Trends Biochem Sci 2002;27:527-533.
47. Vihinen M, Torkkila E, Riikonen P. Accuracy of protein flexibility predictions. Proteins 1994;19:141-149.
48. Xue B, Dunbrack RL, Williams RW, Dunker AK, Uversky VN. PONDR-FIT: a meta-predictor of intrinsically disordered amino acids. Biochim Biophys Acta 2010;1804:996-1010.
49. Uversky VN, Gillespie JR, Fink AL. Why are "natively unfolded" proteins unstructured under physiologic conditions?. Proteins 2000;41:415-427.
50. Dosztanyi Z, Csizmok V, Tompa P, Simon I. IUPred: web server for the prediction of intrinsically unstructured regions of proteins based on estimated energy content. Bioinformatics 2005;21:3433-3434.
51. Boden M, Bailey TL. Identifying sequence regions undergoing conformational change via predicted continuum secondary structure. Bioinformatics 2006;22:1809-1814.
52. Austen M, Luscher B, Luscher-Firzlaff JM. Characterization of the transcriptional regulator yy1. The bipartite transactivation domain is independent of interaction with the TATA box-binding protein, transcription factor IIB, tafii55, or cAMP-responsive element-binding protein (CPB)-binding protein. J Biol Chem 1997;272:1709-1717.
53. Perticaroli S, Nickels JD, Ehlers G, Mamontov E, Sokolov AP. Dynamics and rigidity in an intrinsically disordered protein, beta-casein. J Phys Chem B 2014;118:7317-7326.
54. Campen A, Williams RM, Brown CJ, Meng J, Uversky VN, Dunker AK. TOP-IDP-scale: a new amino acid scale measuring propensity for intrinsic disorder. Protein Pept Lett 2008;15:956-963.
55. Uversky VN. Intrinsically disordered proteins and their environment: effects of strong denaturants, temperature, pH, counter ions, membranes, binding partners, osmolytes, and macromolecular crowding. Protein J 2009;28:305-325.
56. Kim JD, Faulk C, Kim J. Retroposition and evolution of the DNA-binding motifs of yy1, yy2 and rex1. Nucleic Acids Res 2007;35:3442-3452.
57. Bradford MM. A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding. Anal Biochem 1976;72:248-254.
58. Lowry OH, Rosebrough NJ, Farr AL, Randall RJ. Protein measurement with the folin phenol reagent. J Biol Chem 1951;193:265-275.
59. Smith PK, Krohn RI, Hermanson GT, Mallia AK, Gartner FH, Provenzano MD, Fujimoto EK, Goeke NM, Olson BJ, Klenk DC. Measurement of protein using bicinchoninic acid. Anal Biochem 1985;150:76-85.
60. Szollosi E, Hazy E, Szasz C, Tompa P. Large systematic errors compromise quantitation of intrinsically unstructured proteins. Anal Biochem 2007;360:321-323.
61. Sreerama N, Venyaminov SY, Woody RW. Estimation of protein secondary structure from circular dichroism spectra: inclusion of denatured proteins with native proteins in the analysis. Anal Biochem 2000;287:243-251.
62. Zhao DX, Ding ZC, Liu YQ, Huang ZX. Overexpression and purification of single zinc finger peptides of human zinc finger protein znf191. Protein Express Purif 2007;53:232-237.
63. Seneque O, Latour JM. Coordination properties of zinc finger peptides revisited: ligand competition studies reveal higher affinities for zinc and cobalt. J Am Chem Soc 2010;132:17760-17774.
64. Habchi J, Tompa P, Longhi S, Uversky VN. Introducing protein intrinsic disorder. Chem Rev 2014;114:6561-6588.
65. Kelly SM, Price NC. The use of circular dichroism in the investigation of protein structure and function. Curr Protein Pept Sci 2000;1:349-384.
66. Neira JL, Roman-Trufero M, Contreras LM, Prieto J, Singh G, Barrera FN, Renart ML, Vidal M. The transcriptional repressor RYBP is a natively unfolded protein which folds upon binding to DNA. Biochemistry 2009;48:1348-1360.
67. Shen C, Menon R, Das D, Bansal N, Nahar N, Guduru N, Jaegle S, Peckham J, Reshetnyak YK. The protein fluorescence and structural toolkit: database and programs for the analysis of protein fluorescence and structural data. Proteins 2008;71:1744-1754.
68. Brokx RD, Scheek RM, Weljie AM, Vogel HJ. Backbone dynamic properties of the central linker region of calcium-calmodulin in 35% trifluoroethanol. J Struct Biol 2004;146:272-280.
69. Buck M. Trifluoroethanol and colleagues: cosolvents come of age. Recent studies with peptides and proteins. Q Rev Biophys 1998;31:297-355.
70. Hirota N, Mizuno K, Goto Y. Group additive contributions to the alcohol-induced alpha-helix formation of melittin: implication for the mechanism of the alcohol effects on proteins. J Mol Biol 1998;275:365-378.
71. Luo P, Baldwin RL. Mechanism of helix induction by trifluoroethanol: a framework for extrapolating the helix-forming properties of peptides from trifluoroethanol/water mixtures back to water. Biochemistry 1997;36:8413-8421.
72. Deng Z, Cao P, Wan MM, Sui G. Yin yang 1: a multifaceted protein beyond a transcription factor. Transcription 2010;1:81-84.
73. Van Hoy M, Leuther KK, Kodadek T, Johnston SA. The acidic activation domains of the gcn4 and gal4 proteins are not alpha helical but form beta sheets. Cell 1993;72:587-594.