Nucleosome binding properties and co-remodeling activities of native and in vivo acetylated HMGB-1 and HMGB-2 proteins

Biochemistry

Volumn 48, Issue 27, 2009, Pages 6502-6507

  Ugrinova, Iva ^a   Pashev, Iliya G ^a   Pasheva, Evdokia A ^a  

^a INSTITUTE OF MOLECULAR BIOLOGY   (Bulgaria)

Author keywords

[No Author keywords available]

Indexed keywords

ATP-ASE ACTIVITY; BINDING PROPERTIES; CHROMATIN REMODELING; CORE PARTICLES; IN-VIVO; LINKER DNA; NUCLEOSOME; NUCLEOSOME SLIDING; NUCLEOSOMES; REMODELING ACTIVITY; SWI/SNF;

ACETYLATION; BINDING ENERGY; NUCLEIC ACIDS;

PROTEINS;

ADENOSINE TRIPHOSPHATASE; DNA; HIGH MOBILITY GROUP B1 PROTEIN; HIGH MOBILITY GROUP B2 PROTEIN; TRANSCRIPTION FACTOR SNF;

ACETYLATION; ARTICLE; CHROMATIN ASSEMBLY AND DISASSEMBLY; ENZYME ACTIVITY; NUCLEOSOME; PRIORITY JOURNAL; PROTEIN PROTEIN INTERACTION;

ACETYLATION; BASE SEQUENCE; DNA PRIMERS; ELECTROPHORETIC MOBILITY SHIFT ASSAY; HMGB1 PROTEIN; HMGB2 PROTEIN; NUCLEOSOMES; PROTEIN BINDING;

EID: 67650047868     PISSN: 00062960     EISSN: None     Source Type: Journal    
DOI: 10.1021/bi9004304     Document Type: Article

References (41)

1. Van Holde, K. (1988) Chromatin , Springer Verlag KG, Berlin.
2. Tsanev, R., Russev, G., Pashev, I., and Zlatanova, J. (1993) Replication and Transcription of Chromatin , CRC Press Inc., Boca Raton, FL.
3. Arents, G., Burlingame, R. W., Wang, B. C., Love, W. E., and Moudrianakis, E. N. (1991) The nucleosomal core histone octamer at 3.1 Å resolution: A tripartite protein assembly and a left-handed superhelix. Proc. Natl. Acad. Sci. U.S.A. 88, 10148-10152.
4. Luger, K., Mäder, A. W., Richmond, R. U., Sargent, D. F., and Richmond, T. J. (1997) Crystal structure of the nucleosomal core particle at 2.8 Å resolution. Nature 389, 251-260.
5. Ausio, J., Dong, F., and van Holde, K. E. (1989) Use of selectively trypsinized nucleosome core particles to analyze the role of the histone "tails" in the stabilization of the nucleosome. J. Mol. Biol. 206, 451-463.
6. de la Barre, A. E., Angelov, D., Molla, A., and Dimitrov, S. (2001) The N-terminus of histone H2B, but not that of histone H3 or its phosphorylation, is essential for chromosome condensation. EMBO J. 20, 6383-6393.
7. Strahl, B. D., and Allis, C. D. (2000) The language of covalent histone modifications. Nature 403, 41-45.
8. Brown, C. E., Lechner, T., Howe, L., and Workman, J. L. (2000) The many HATs of transcription coactivators. Trends Biochem. Sci. 25, 15-19.
9. Angelov, D., Verdel, A., An, W., Bondarenko, V., Hans, F., Doyen, C. M., Studitsky, V. M., Hamiche, A., Roeder, R. G., Bouvet, P., and Dimitrov, S. (2004) SWI/SNF remodeling and p300-dependent transcription of histone variant H2ABbd nucleosomal arrays. EMBO J. 23, 3815-3824.
10. Gautier, T., Abbott, D. W., Molla, A., Verdel, A., Ausio, J., and Dimitrov, S. (2004) Histone variant H2ABbd confers lower stability to the nucleosome. EMBO Rep. 5, 715-720.
11. Jin, C., and Felsenfeld, G. (2007) Nucleosome stability mediated by histone variants H3.3 and H2A.Z. Genes Dev. 21, 1519-1529.
12. Boulard, M., Bouvet, P., Kundu, T. K., and Dimitrov, S. (2007) Histone variant nucleosomes: Structure, function and implication in disease. Subcell. Biochem. 41, 71-89.
13. Becker, P. B. (2002) Nucleosome sliding: Facts and fiction. EMBO J. 21, 4749-4753.
14. Langst, G. L., and Becker, P. B. (2004) Nucleosome remodelling: One mechanism, many phenomena? Biochim. Biophys. Acta 1677, 58-63.
15. Wang, G. G., Allis, C. D., and Chi, P. (2007) Chromatin remodeling and cancer, Part II: ATP-dependent chromatin remodeling. Trends Mol. Med. 13, 373-380.
16. Cairns, B. R., Lorch, Y., Li, Y., Zhang, M., Lacomis, L., Erdjument-Bromage, H., Tempst, P., Du, J., Laurent, B., and Kornberg, R. D. (1996) RSC, an essential, abundant chromatin-remodeling complex. Cell 87, 1249-1260.
17. Asturias, F. J., Chung, W. H., Kornberg, R. D., and Lorch, Y. (2002) Structural analysis of the RSC chromatin-remodeling complex. Proc. Natl. Acad. Sci. U.S.A. 99, 13477-13480.
18. Smith, C. L., Horowitz-Scherer, R., Flanagan, J. F., Woodcock, C. L., and Peterson, C. L. (2003) Structural analysis of the yeast SWI/SNF chromatin remodeling complex. Nat. Struct. Biol. 10, 141-145.
19. Chaban, Y., Ezeokonkwo, C., Chung, W. H., Zhang, F., Kornberg, R. D., Maier-Davis, B., Lorch, Y., and Asturias, F. J. (2008) Structure of a RSC-nucleosome complex and insights into chromatin remodeling. Nat. Struct. Biol. 15, 1272-1277.
20. Bustin, M. (1999) Regulation of DNA-dependent activities by the functional motifs of the high-mobility group chromosomal proteins. Mol. Cell. Biol. 19, 5237-5246.
21. Travers, A., and Thomas, J. O. (2004) Chromosomal HMG-box proteins. In Chromatin Structure and Dynamics: State-of-the-Art (Zlatanova, J., and Leuba, S. H., Eds.) pp 103-1134, Elsevier B.V., Amsterdam.
22. Bonaldi, T., Langst, G., Strohner, R., Becker, P. B., and Bianchi, M. E. (2002) The DNA chaperone HMGB1 facilitates ACF/CHRAC-dependent nucleosome sliding. EMBO J. 21, 6865-6873.
23. Ugrinova, I., Pasheva, E. A., Armengaud, J., and Pashev, I. G. (2001) In vivo acetylation of HMGB1 protein enhances its binding affinity to distorted DNA structures. Biochemistry 40, 14655-14660.
24. Ugrinova, I., Mitkova, E., Moskalenko, C., Pasherv, I. G., and Pasheva, E. A. (2007) DNA bending versus DNA end-joining activity of HMGB1 protein is modulated by in vitro by acetylation. Biochemistry 46, 2111-2117.
25. Schroter, H., and Bode, J. (1982) The binding sites for large and small high-mobility-group (HMG) proteins. Studies on HMG-nucleosome interactions in vitro. Eur. J. Biochem. 127, 429-436.
26. Nightingale, K., Dimitrov, S., Reeves, R., and Wolffe, A. P. (1996) Evidence for a shared structural role for HMG1 and linker histones B4 and Hi in organizing chromatin. EMBO J. 15, 548-561.
27. An, W., van Holde, K., and Zlatanova, J. (1998) The non-histone chromatin protein HMG1 protects linker DNA on the opposite to the protected by linker histones. J. Biol. Chem. 273, 26289-26291.
28. Lowary, P. T., and Widom, J. (1998) New DNA sequence rules for high affinity binding to histone octamer and sequence-directed nucleosome positioning. J. Mol. Biol. 276, 19-42.
29. Luger, K., Rechsteiner, T. J., and Richmond, T. J. (1999) Expression and purification of recombinant histones and nucleosome reconstitution. Methods Mol. Biol. 119, 1-16.
30. Cote, J., Quinn, J., Workman, J. L., and Peterson, C. L. (1994) Stimulation of GAL4 derivative binding to nucleosomal DNA by the yeast SWI/SNF complex. Science 265, 53-60.
31. Mutskov, V., Gerber, D., Angelov, D., Ausio, J., Workman, J., and Dimitrov, S. (1998) Persistent interactions of core histone tails with nucleosomal DNA following acetylation and transcription factor binding. Mol. Cell. Biol. 18, 6293-6304.
32. Angelov, D., Molla, A., Perche, P. Y., Hans, F., Cote, J., Khochbin, S., Bouvet, P., and Dimitrov, S. (2003) The histone variant Macro-H2A interferes with transcription factor binding and SWI/SNF nucleosome remodeling. Mol. Cell 11, 1033-1041.
33. Ueda, T., Chou, H., Kawase, T., Shirakawa, H., and Yoshida, M. (2004) Acidic C-tail of HMGB1 is required for its target binding to nucleosome linker DNA and transcription stimulation. Biochemistry 43, 9901-9908.
34. Cote, J., Peterson, C. L., and Workman, J. L. (1998) Perturbation of nucleosome core structure by the SWI/SNF complex persists after its attachment, enhancing subsequent transcription factor binding. Proc. Natl. Acad. Sci. U.S.A. 95, 4947-4952.
35. Gregory, P. D., Schmid, A., Zavari, M., Lui, L., Berger, S. L., and Hörz, W. (1998) Absence of Gcn5 HAT activity defines a novel state in the opening of chromatin at the PHO5 promoter in yeast. Mol. Cell 1, 495-505.
36. Gregory, P. D., Schmid, A., Zavari, M., Muunsterkötter, M., and Horz, W. (1999) Chromatin remodeling at the PHo8 promoter requires SWI/SNF and SAGA at a step subsequent to activator binding. EMBO J. 18, 6407-6417.
37. Syntichaki, P., Topalidou, I., and Thireos, G. (2000) The Gcn5 bromodomain co-ordinates nucleosome remodeling. Nature 404, 414-417.
38. Sterner, R., Vidali, G., and Allfrey, V. G. (1979) Studies of acetylation and deacetylation in high mobility group proteins. Identification of the sites of acetylation in HMG-1. J. Biol. Chem. 254, 11577-11583.
39. Pasheva, E. A., Sarov, M., Bidjekov, K., Ugrinova, I., Sarg, B., Lindner, H., and Pashev, I. G. (2004) In vitro acetylation of HMGB-1 and -2 proteins by CBP: The role of the acidic tail. Biochemistry 43, 2935-2940.
40. Travers, A. (2003) Priming the nucleosome: A role for HMGB proteins? EMBO Rep. 4, 131-136.
41. Gregory, P. D., Wagner, K., and Horz, W. (2001) Histone acetylation and chromatin remodeling. Exp. Cell Res. 265, 195-202.