Distinct properties of the two putative "globular domains" of the yeast linker histone, Hho1p

Journal of Molecular Biology

Volumn 337, Issue 5, 2004, Pages 1123-1135

  Ali, Tariq ^a   Thomas, Jean O ^a  

^a UNIVERSITY OF CAMBRIDGE   (United Kingdom)

Author keywords

CD, circular dichroism; Chromatin; Chromatosome; DTT, dithiothreitol; Four way junction; Intrinsically unstructured domain; Linker histone; PCR, polymerase chain reaction; PMSF, phenylmethylsulphonyl fluoride

Indexed keywords

HISTONE; HISTONE H1; HISTONE H5; HISTONE HHO1P; PERCHLORATE; PHOSPHATE; SODIUM DIHYDROGEN PHOSPHATE; SULFATE; UNCLASSIFIED DRUG;

ARTICLE; BINDING AFFINITY; BINDING SITE; CHROMATIN; DNA BINDING; NONHUMAN; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN FOLDING; SACCHAROMYCES CEREVISIAE; SEQUENCE HOMOLOGY;

EUKARYOTA; SACCHAROMYCES; SACCHAROMYCES CEREVISIAE;

EID: 1842523300     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2004.02.029     Document Type: Article

References (53)

1. Bates D.L., Thomas J.O. Histone H1 and H5: one or two molecules per nucleosome? Nucl. Acids Res. 9:1981;5883-5893.
2. Simpson R.T. Structure of the chromatosome, a chromatin particle containing 160 base pairs of DNA and all the histones. Biochemistry. 17:1978;5524-5531.
3. Thoma F., Koller T., Klug A. Involvement of histone H1 in the organization of the nucleosome and of the salt-dependent superstructure of chromatin. J. Cell Biol. 83:1979;403-427.
4. Butler P.J.G., Thomas J.O. Changes in chromatin folding in solution. J. Mol. Biol. 140:1980;505-529.
5. Carruthers L.M., Bednar J., Woodcock C.L., Hansen J.C. Linker histones stabilize the intrinsic salt-dependent folding of nucleosomal arrays: mechanistic ramifications for higher-order chromatin folding. Biochemistry. 37:1998;14776-14787.
6. Allan J., Hartman P.G., Crane-Robinson C., Aviles F.X. The structure of histone H1 and its location in chromatin. Nature. 288:1980;675-679.
7. Allan J., Mitchell T., Harborne N., Böhm L., Crane-Robinson C. Roles of H1 domains in determining chromatin higher order structure and H1 location. J. Mol. Biol. 187:1986;591-601.
8. Thoma F., Losa R., Koller T. Involvement of the domains of histones H1 and H5 in the structural organization of soluble chromatin. J. Mol. Biol. 167:1983;619-640.
9. Thomas J.O., Rees C., Finch J.T. Cooperative binding of the globular domains of histones H1 and H5 to DNA. Nucl. Acids Res. 20:1992;187-194.
10. Draves P.H., Lowary P.T., Widom J. Cooperative binding of the globular domain of histone H5 to DNA. J. Mol. Biol. 225:1992;1105-1121.
11. Ramakrishnan V., Finch J.T., Graziano V., Lee P.L., Sweet R.M. Crystal structure of globular domain of histone H5 and its implications for nucleosome binding. Nature. 362:1993;219-223.
12. Goytisolo F.A., Gerchman S.E., Yu X., Rees C., Graziano V., Ramakrishnan V., Thomas J.O. Identification of two DNA-binding sites on the globular domain of histone H5. EMBO J. 15:1996;3421-3429.
13. Zhou Y.-B., Gerchmann S.E., Ramakrishnan V., Travers A., Muyldermans S. Position and orientation of the globular domain of linker histone H5 on the nucleosome. Nature. 395:1998;402-405.
14. Clark K.L., Halay E.D., Lai E., Burley S.K. Co-crystal structure of the HNF-3γ fork head DNA-recognition motif resembles histone H5. Nature. 364:1993;412-420.
15. Varga-Weisz P., Zlatanova J., Leuba S.H., Schroth G.P., van Holde K. Binding of histones H1 and H5 and their globular domains to four way junction DNA. Proc. Natl Acad. Sci. USA. 91:1994;3525-3529.
16. Bussey H., Storms R.K., Ahmed A., Albermann K., Allen E., Ansorge W., et al. The nucleotide sequence of Saccharomyces cerevisiae chromosome XVI. Nature. 387:1997;103-105.
17. Landsman D. Histone H1 in Saccharomyces cerevisiae - a double mystery solved. Trends Biochem. Sci. 21:1996;287-288.
18. Ushinsky S.C., Bussey H., Ahmed A.A., Wang Y., Friesen J., Williams B.A., Storms R.K. Histone H1 in Saccharomyces cerevisiae. Yeast. 13:1997;151-161.
19. Srebreva L., Zlatanova J., Miloshev G., Tsanev R. Immunological evidence for the existence of H1-like histone in yeast. Eur. J. Biochem. 165:1987;449-454.
20. Spellman P.T., Sherlock G., Zhang M.Q., Iyer V.R., Anders K., Eisen M.B., et al. Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization. Mol. Biol. Cell. 9:1998;3273-3297.
21. Patterton H.G., Landel C.C., Landsman D., Peterson C.L., Simpson R.T. The biochemical and phenotypic characterization of Hho1p, the putative linker histone H1 of Saccharomyces cerevisiae. J. Biol. Chem. 273:1998;7268-7276.
22. Waterborg J.H. Steady-state levels of histone acetylation in Saccharomyces cerevisiae. J. Biol. Chem. 275:2000;13007-13011.
23. Thomas J.O., Furber V. Yeast chromatin structure. FEBS Letters. 66:1976;274-280.
24. Lohr D., Kovacic R.T., Van Holde K.E. Quantitative analysis of the digestion of yeast chromatin by staphylococcal nuclease. Biochemistry. 16:1977;463-471.
25. Duggan M.M., Thomas J.O. Two DNA-binding sites on the globular domain of histone H5 are required for binding to both bulk and 5S reconstituted nucleosomes. J. Mol. Biol. 304:2000;21-33.
26. Cerf C., Lippens G., Ramakrishnan V., Muyldermans S., Segers A., Wyns L., et al. Homo- and heteronuclear two-dimensional NMR studies of the globular domain of histone H1: full assignment, tertiary structure, and comparison with the globular domain of H5. Biochemistry. 33:1994;11079-11086.
27. Varga-Weisz P., van Holde K., Zlatanova J. Preferential binding of histone H1 to four-way helical junction DNA. J. Biol. Chem. 268:1993;20699- 20700.
28. De Petrocellis L., Quagliarotti G., Tomei L., Geraci G. Structuring of H1 histone. Evidence of high affinity binding sites for phosphate ions. Eur. J. Biochem. 156:1986;143-148.
29. Clark D.J., Hill C.S., Martin S.R., Thomas J.O. α-Helix in the C-terminal domain of histone H1. EMBO J. 7:1988;69-75.
30. Hill C.S., Martin S.R., Thomas J.O. A stable α-helical element in the carboxy-terminal domain of free and chromatin-bound histone H1 from sea urchin sperm. EMBO J. 8:1989;2591-2599.
31. Wright P.E., Dyson H.J. Intrisically unstructured proteins: re-assessing the protein structure-function paradigm. J. Mol. Biol. 293:1999;321-331.
32. Ali T., Coles P., Stevens T.J., Stott K., Thomas J.O. Two homologous domains of similar structure but different stability in the yeast linker histone, Hho1p. J. Mol. Biol. 2004;. In the press.
33. Ono K., Kusano O., Shimotakahara S., Shimizu M., Yamazaki T., Shindo H. The linker histone homolog Hho1p from Saccharomyces cerevisiae represents a winged-helix-turn-helix fold as determined by NMR spectroscopy. Nucl. Acids Res. 312:2003;7199-7207.
34. Nelson P.P., Albright S.C., Wiseman J.M., Garrard W.T. Reassociation of histone H1 with nucleosomes. J. Biol. Chem. 254:1979;11751-11760.
35. Downs J., Kosmidou E., Morgan A., Jackson S.P. Suppression of homologous recombination by the Saccharomyces cerevisiae linker histone. Mol. Cell. 11:2003;1685-1692.
36. Freidkin I., Katcoff D.J. Specific distribution of the Saccharomyces cerevisiae linker histone homolog HHO1p in the chromatin. Nucl. Acids Res. 29:2001;4043-4051.
37. Lowary P.T., Widom J. Higher-order structure of Saccharomyces cerevisiae chromatin. Proc. Natl Acad. Sci. USA. 86:1989;8266-8270.
38. Escher D., Schaffner W. Gene activation at a distance and telomeric silencing are not affected by yeast histone H1. Mol. Gen. Genet. 256:1997;456-461.
39. Barra J.L., Rhounim L., Rossignol J.L., Faugeron G. Histone H1 is dispensable for methylation-associated gene silencing in Ascobolus immersus and essential for long life span. Mol. Cell. Biol. 20:2000;61-69.
40. Hellauer K., Sirard E., Turcotte B. Decreased expression of specific genes in yeast cells lacking histone H1. J. Biol. Chem. 276:2001;13587-13592.
41. Thomas J.O. Histone H1: location and role. Curr. Opin. Cell Biol. 11:1999;312-317.
42. Shen X., Gorovsky M.A. Linker histone H1 regulates specific gene expression but not global transcription in vivo. Cell. 86:1996;475-483.
43. Hayashi T., Hayashi H., Iwai K. Tetrahymena histone H1 - isolation and amino acid sequence lacking the central hydrophobic domain conserved in other H1 histones. J. Biochem. 102:1987;369-376.
44. Bouvet P., Dimitrov S., Wolffe A.P. Specific regulation of Xenopus chromosomal 5S rRNA gene transcription in vivo by histone H1. Genes Dev. 8:1994;1147-1159.
45. Puig S., Matallana E., Pérez-Ortín J.E. Stochastic nucleosome positioning in a yeast chromatin region is not dependent on histone H1. Curr. Microbiol. 39:1999;168-172.
46. Pennings S., Meersseman G., Bradbury E.M. Linker histones H1 and H5 prevent the mobility of positioned nucleosomes. Proc. Natl Acad. Sci. USA. 91:1994;10275-10279.
47. Studier F.W., Moffatt B.A. Use of bacteriophage T7 RNA polymerase to direct selective high-level expression of cloned genes. J. Mol. Biol. 113:1986;130.
48. Thomas J.O., Kornberg R.D. The study of histone-histone associations by chemical cross-linking. Methods Cell Biol. 18:1978;429-440.
49. Clark D.J., Thomas J.O. Salt-dependent cooperative interaction of histone H1 and linear DNA. J. Mol. Biol. 187:1986;569-580.
50. Teo S.H., Grasser K.D., Thomas J.O. Differences in the DNA-binding properties of the HMG-box domains of HMG1 and the sex-determining factor SRY. Eur. J. Biochem. 230:1995;943-950.
51. Grasser K.D., Teo S.H., Lee K.B., Broadhurst R.W., Rees C., Hardman C.H., Thomas J.O. DNA-binding properties of the tandem HMG boxes of high-mobility-group protein 1 (HMG1). Eur. J. Biochem. 253:1998;787-795.
52. Webb M., Thomas J.O. Structure-specific binding of the two tandem HMG boxes of HMG1 to four-way junction DNA is mediated by the A domain. J. Mol. Biol. 294:1999;373-387.
53. Thomas J.O. Isolation and fractionation of chromatin and linker histones. Gould H.J. Chromatin. A Practical Approach. 1998;1-34 Oxford University Press, Oxford.