Characterization of nucleosome core particles containing histone proteins made in bacteria

Journal of Molecular Biology

Volumn 272, Issue 3, 1997, Pages 301-311

  Luger, Karolin ^a   Rechsteiner, Thomas J ^a   Flaus, Andrew J ^a   Waye, Mary M Y ^b   Richmond, Timothy J ^a  

^a ETH ZURICH   (Switzerland)

^b CHINESE UNIVERSITY OF HONG KONG   (Hong Kong)

Author keywords

Chromatin; Histone; Nucleosome core particle; Protein expression; Recombinant nucleosome

Indexed keywords

BACTERIAL PROTEIN; CELL PROTEIN; DEOXYRIBONUCLEASE I; DNA FRAGMENT; HISTONE; RECOMBINANT PROTEIN; RNA 5S;

ARTICLE; CHROMATIN; CONTROLLED STUDY; DENATURATION; ERYTHROCYTE; ESCHERICHIA COLI; GEL ELECTROPHORESIS; IONIC STRENGTH; NONHUMAN; NUCLEOSOME; PRIORITY JOURNAL; PROTEIN ASSEMBLY; PROTEIN DOMAIN; PROTEIN EXPRESSION; PROTEIN FOLDING; PROTEIN PURIFICATION; X RAY CRYSTALLOGRAPHY; XENOPUS LAEVIS;

BACTERIA (MICROORGANISMS); ESCHERICHIA COLI; GALLUS GALLUS; XENOPUS LAEVIS;

EID: 0031587289     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1997.1235     Document Type: Article

References (48)

1. Ausio J., Dong F., van Holde K. E. Use of selectively trypsinized nucleosome core particles to analyse the role of the histone 'tails' in the stabilization of the nucleosome. J. Mol. Biol. 206:1989;451-463.
2. Bode J., Wagner K. G. Cooperative exposure of histones H3 thiols in core particles. Int. J. Biol. Macromol. 2:1980;129-136.
3. Böhm L., Crane-Robinson C. Proteases as structural probes for chromatin: the domain structure of histones. Biosci. Reports. 4:1984;365-386.
4. Boyer H. W., Roulland-Dussoix D. A complementation analysis of the restriction and modification of DNA in E. coli. J. Mol. Biol. 41:1969;459-472.
5. Carr S. A., Hemling M. E., Bean M. F., Roberts G. D. Integration of mass spectrometry in analytical biotechnology. Anal. Chem. 63:1991;2802-2824.
6. Dao-Pin S., Alber T., Bell J. A., Weaver L. H., Matthews B. W. Use of site-directed mutagenesis to obtain heavy atom derivatives for protein crystallography: cysteine-containing mutants of phage T4 lysozyme. Protein Eng. 2:1987;115-123.
7. Dillon P. J., Rosen C. A. A rapid method for the construction of synthetic genes using the polymerase chain reaction. BioTechniques. 9:1990;298-300.
8. Dong F., Hansen J. C., van Holde K. E. DNA and protein determinants of nucleosome positioning on sea urchin 5S rRNA gene sequences in vitro. Proc. Natl Acad. Sci. USA. 87:1990;5724-5728.
9. Eickbush T. H., Moudrianakis E. N. The histone core complex: an octamer assembled by two sets of protein-protein interaction. Biochemistry. 17:1978;4955-4964.
10. Flaus A., Luger K., Tan S., Richmond T. J. Mapping nucleosome position at single base-pair resolution using site-directed hydroxy radicals. Proc. Natl Acad. Sci. USA. 93:1996;1370-1375.
11. Frank G. New aspects in isocratic HPLC separation of phenyl thiodantoin amino acids through the application of ionic detergents. Methods in Protein Sequence Analysis. 1989;Springer Verlag, Berlin.
12. Gibson, T. J. 1984, Studies on the Epstein-Barr virus genome. PhD thesis, Cambridge University.
13. Gill S. C., von Hippel P. H. Calculation of protein extinction coefficients from amino acid sequence data. Anal. Biochem. 182:1989;319-326.
14. Harp J. M., Uberbacher E. C., Roberson A. E., Palmer E. L., Gewiess A., Bunick G. J. X-ray diffraction analysis of crystals containing twofold symmetric nucleosome core particles. Acta Crystallog. sect. D. 52:1996;283-288.
15. Hayes J. J., Clark D. J., Wolffe A. P. Histone contributions to the structure of DNA in the nucleosome. Proc. Natl Acad. Sci USA. 88:1991;6829-6833.
16. Helliger W., Lindner H., Hauptlorenz S., Puschendorf B. A new h.p.l.c. isolation procedure for chicken and goose erythrocyte histones. Biochem. J. 255:1988;23-27.
17. Kleinschmidt A. M., Martinson H. G. Role of histone tyrosines in nucleosome formation and histone-histone interaction. J. Biol. Chem. 259:1984;497-503.
18. Kunkel T. A., Roberts J. D., Zakour D. A. Rapid and efficient site-specific mutagenesis without phenotypic selection. Methods Enzymol. 154:1987;367-382.
19. Läemmli U. K. Cleavage of structural proteins during the assembly of the head of bacteriophage T4. Nature. 227:1970;681-685.
20. Lennox R. W., Cohen L. H. Analysis of histone subtypes and their modified forms by polyacrylamide gel electrophoresis. Methods Enzymol. 170:1989;532-549.
21. Lewis P. Fluorescently labeled histones as probes of nucleosome structure. Eur. J. Biochem. 99:1979;315-322.
22. Liew C. C., Haslett G. W., Allfrey V. G. N -Acetyl-seryl-tRNA and polypeptide chain initiation during histone biosynthesis. Nature. 226:1970;414-417.
23. Lindsey G. G., Thompson P., Pretorius L., Purves L. R., von Holt C. Octamer reconstitution from acid-extracted chicken erythrocyte histones. FEBS Letters. 155:1983;301-305.
24. Luger K., Maeder A. W., Richmod R. K., Sargent D. F., Richmond T. J. Structure of the nucleosome core particle at 2.8 Å resolution. Nature. 1997;in press-?
25. Marston F. A. O. The purification of eukaryotic polypeptides synthesized in E. coli. Biochem. J. 240:1986;1-12.
26. Martinez C., de Geus P., Stanssens P., Lauvereys M., Cambillau C. Engineering cysteine mutants to obtain crystallographic phases with a cutinase from Fusarium solani pisi. Protein Eng. 6:1993;157-165.
27. Maxam A. M., Gilbert W. Sequencing end-labelled DNA with base-specific chemical cleavage. Methods Enzymol. 65:1980;499-560.
28. Messing J. New M13 vectors for cloning. Methods Enzymol. 101:1983;20-78.
29. Moehs C. P., Baxevanis A. D., Moudrianakis E. N., Spiker S. Enhanced stability of histone octamers from plant nucleosomes: role of H2A and H2B histones. Biochemistry. 31:1992;10844-10851.
30. Nagai K., Thoegerson H. C. Generation of gamma-globin by sequence-specific proteolysis of a hybrid protein produced in E. coli. Nature. 309:1984;810-812.
31. Old R. W., Woodland H. R., Ballantine J. E. M., Aldridge T. C., Newton C. A., Bains W. A., Turner P. C. Organization and expression of cloned histone gene clusters from Xenopus laevis and Xenopus borealis. Nucl. Acids Res. 23:1982;7561-7580.
32. Oohara I., Wada A. Spectroscopic studies on histone-DNA interactions. II. Three transitions in nucleosomes resolved by salt-titration. J. Mol. Biol. 196:1987;399-411.
33. Pennings S., Meersseman G., Bradbury E. M. Mobility of positioned nucleosomes on 5 S rDNA. J. Mol. Biol. 220:1991;101-110.
34. Perry M., Thomsen G. H., Roeder R. G. Genomic organization and nucleotide sequence of two distinct histone gene clusters from Xenopus laevis. J. Mol. Biol. 185:1985;479-499.
35. Richmond T. J., Finch J. T., Rushton B., Rhodes D., Klug A. Structure of the nucleosome core particle at 7 Å resolution. Nature. 311:1984;532-537.
36. Richmond T. J., Searles M. A., Simpson R. T. Crystals of a nucleosome core particle containing defined DNA-sequences. J. Mol. Biol. 199:1988;161-170.
37. Ridsdale J. A., Davie J. R. Chicken erythrocyte polynucleosomes which are soluble at physiological ionic strength and contain linker histones are highly enriched in β-globin gene sequences. Nucl. Acids Res. 15:1987;1081-1096.
38. Ruiz-Carillo A., Wangh L. J., Allfrey V. G. Processing of newly synthesized histone molecules. Science. 190:1975;117-128.
39. Simon R. H., Felsenfeld G. A new procedure of purifying histone proteins H2A+H2B and H3+H4 from chromatin using hydroxylapatite. Nucl. Acids Res. 6:1979;689-696.
40. Stein A. DNA folding by histones: the kinetics of chromatin core particle reassembly and the interaction of nucleosomes with histones. J. Mol. Biol. 130:1989;103-134.
41. Stüber D., Ibrahimi I., Cutler D., Dobberstein B., Bujard H. A novel in vitro transcription-translation system: accurate and efficient synthesis of single proteins from cloned DNA sequences. EMBO J. 3:1989;3143-3148.
42. Studier W. F., Rosenberg A. H., Dunn J. J., Dubendorff J. W. Use of T7 RNA polymerase to direct expression of cloned genes. Methods Enzymol. 185:1990;60-89.
43. Thomas J. O., Butler P. J. G. Characterization of the octamers of histones free in solution. J. Mol. Biol. 116:1977a;769-781.
44. Thomas J. O., Butler P. J. G. The nucleosome core protein. Cold Spring Harbor Symp. Quant. Biol. 42:1977b;119-125.
45. Urban M., Franklin S. G., Zweidler A. Isolation and characterization of the histone variants in chicken erythrocytes. Biochemistry. 18:1979;3952-3960.
46. Waye M. M. Y., Verhoeyen M. E., Jones P. T., Winter G. EcoK selection vectors for shotgun cloning into M13 and deletion mutagenesis. Nucl. Acids Res. 13:1985;8561-8571.
47. Wood M. J., Yau P., Imai B. S., Goldberg M. W., Lambert S. J., Fowler A. G., Baldwin J. P., Godfrey J. E., Moudrianakis E. N., Koch M. H. J., Ibel K., May R. P., Bradbury E. M. Neutron and X-ray scatter studies of the histone octamer and amino and carboxyl domain trimmed octamers. J. Mol. Biol. 266:1991;5696-5702.
48. Zweidler A. Role of individual histone tyrosines in the formation of the nucleosome complex. Biochemistry. 31:1992;9205-9211.