Accessibility of histone oligomers to the action of trypsin in a solution or in chromatin with different degrees of compactness

The accessibility to trypsin of "core" histones within the dimer (H2A-H2B), tetramer (H3-H4)2, octamer (H2A-H2B-H3-H4)2 and in chromatin was studied. It was shown that the hydrolysis of histones H2A and H2B within the dimer and octamer occurs in essentially the same way. The tetramer (H2-H4)2 becomes more compact with an increase in the ionic strength. Some of the tetramer (H3-H4)2 sites within the octamer are protected against trypsin. It was demonstrated that in terms of the histone accessibility to trypsin chromatin can exist in three states, i.e., tightly packed (in the presence of histone H1 and bivalent cations), intermediate (in the absence of histone H1 or bivalent cations) and folded (in the absence of histone H1 and bivalent cations). The folding of histones in neither of these chromatin states coincides with that within the octamer in 2M NaCl.     

Characteristics of sulfhydryl groups of histone H3 from the calf thymus using mercury-containing nitroxyl radicals

The interaction between total histone and deoxyribonucleoprotein (DNP) preparations from calf thymus with mercury-containing nitroxyl radicals in low ionic strength solutions, 2 M NaCl and urea was investigated. It was found that the label is rapidly incorporated into the SH-groups of histone H3 to produce characteristic EPR signals. Titration of SH-groups within DNP demonstrated that in low ionic strength solutions only one SH-group (presumably, the SH-group of the cysteine residue in position 110) is accessible to the reagents. After dissociation by 2 M NaCl, two SH-groups become titrable; however, the EPR spectra point to differences in the conformational state of these two groups. In 4 M urea, these differences are compensated for by structural disintegration. The spin labels may be used for the analysis of SH-groups under different conditions and at different functional states of nucleoproteins.     

Spectropolarimetric analysis of the core histone octamer and its subunits

The secondary structure of the calf thymus core histone octamer, (H2A-H2B-H3-H4)2, and its two physiological subunits, the H2A-H2B dimer and (H3-H4)2 tetramer, was analyzed by ORD spectropolarimetry as a function of temperature and solvent ionic strength within the ranges of these experimental parameters where assembly of the core histone octamer exhibits pronounced sensitivity. While the secondary structure of the dimer is relatively stable from 0.1 to 2.0 M NaCl, the secondary structure of the tetramer exhibits complex changes over this range of NaCl concentrations. Both complexes exhibit only modest responses to temperature changes. ORD spectra of very high and very low concentrations of stoichiometric mixtures of the core histones revealed no evidence of changes in the ordered structure of the histones as a result of the octamer assembly process at NaCl concentrations above 0.67 M, nor were time-dependent changes detected in the secondary structure of tetramer dissolved in low ionic strength solvent. The secondary structure of the chicken erythrocyte octamer dissolved in high concentrations of ammonium sulfate, including those of our crystallization conditions, was found to be essentially unchanged from that in 2 M NaCl when examined by both ORD and CD spectropolarimetry. The two well-defined cleaved products of the H2A-H2B dimer, cH2A-H2B and cH2A-cH2B, exhibited reduced amounts of ordered structure; in the case of the doubly cleaved moiety cH2A-cH2B, the reductions were so pronounced as to suggest marked structural rearrangements.     

Electron spin resonance studies on the conformation and interactions of histories containing cysteine. Histones H3 from calf thymus and H4 from sea urchin sperm.

In this study the spin-label method has been used to obtain information about conformational properties of regions containing cysteine of histone H3 from calf thymus, histone H4 from sperm of the sea urchin Arbacia lixula, and the histone complex H3–H4. It has been found that the microenvironments of histone H3 causing immobilization of the spin labels are sensitive to variations in ionic strength of dilute solutions of phosphate buffer, are partially destroyed by urea, and fully destroyed by proteolytic enzymes. The interaction of spin-labeled histone H3 with histone H4 induces an increase of immobilization of the spin label, indicating an increase in rigidity at the cysteine region of histone H3. The use of a series of spin labels of variable length for histone H3 gives an estimate of 0.8–1.0 nm for the apparent depth of the spin label binding site, a value which does not change upon interaction of histone H3 with H4. Histone H4 from A. lixula sperm causes a similar immobilization of the spin label. As for histone H3, immobilization increases with the ionic strength, and the structures are destroyed by urea and proteolytic enzymes. Upon mixing with histone H3, however, the extent of immobilization appears only slightly changed, and together with sedimentation velocity results, these studies suggest that the spin label attached to histone H4 prevents the complex formation.     

An octamer of core histones in solution: central role of the H3-H4 tetramer in the self-assembly.

The association of histones H2A, H2B, H3, and H4 in solution has been studied. In 2 M NaCl and at neutral pH they can assemble in a complex in which each histone is present in equimolar amounts. The complex has a weight average molecular weight of 98,000 (+/- 3700) and a sedimentation coefficient (so20,w) of 4.8. The value of the weight average molecular weight and the histone stoichiometry indicate that the complex is an octamer. The pairs of histones H2A,H2B and H3,H4 studied separately under identical conditions only associated as equimolar complexes consistent with dimeric and tetrameric structures, respectively. The stability of the core histone octamer is a function of the ionic strength, pH, and concentration of protein. The octamer dissociates by losing dimers of H2A,H2B until the main complexes existing in solution are the H3.H4 tetramer and the H2A.H2B dimer. This process is reversible upon reestablishing the original conditions.     

The nature of forces stabilizing nucleosome structure. Dissociation of histone octamers from DNA

We have used the measurements of the histone fluorescence parameters to study the influence of the ionic strength on histone-DNA and histone-histone interactions in reconstructed nucleosomes. The ionic strength increase lead to the two-stage nucleosome dissociation. The dimer H2A-H2B dissociates at the first stage and the tetramer (H3-H4)2 at the second one. The dimer H2A-H2B dissociation from nucleosome is a two-stage process also. The ionic bonds between (H2A-H2B) histone dimer and DNA break at first and then the dissociation of dimer from histone tetramer (H3-H4)2 occurs. According to the proposed model the dissociation accompanying a nucleosome "swelling" and an increase of DNA curvature radius. It was shown that the energy of electrostatic interactions between histone dimer and DNA is sufficiently less than the energy of dimer-tetramer interaction. We propose that the nucleosome DNA ends interact with the dimer and tetramer simultaneously. The calculated number (approximately 30 divided by 40) of ionic bonds between DNA and histone octamer globular part practically coincides with the number of exposed cationic groups on the surface of octamer globular head. On this basis we have assumed that the spatial distribution of these groups is precisely determined, which explains the high evolutionary conservatism of the histone primary structure.     

Affinity labeling of rabbit skeletal muscle phosphorylase kinase by 5′-(p-fluorosulfonylbenzoyl)adenosine

Simple mixing of acid purified histones H₃ and H₄ in equimolar quantities at low ionic strength near pH 7 does not yield the tetramer but rather a high M_r aggregate. Dialysis of acid extracted total or core histones into 2 M NaCl 150 mM phosphate (pH 7.4) followed by fractionation of the histone complexes at lower ionic strength (150 mM NaCl) results in an H₃H₄ tetramer of a structure identical to that derived from salt-extracted histones. Dialysis of acid extracted total or core histones directly into the lower ionic strength buffer with subsequent fractionation, results in H₃H₄ tetramer of closely similar structure.     

Structure of histone octamers in reconstituted polynucleosomes

The salt-dependent structural changes of the histone octamer in complex with high-molecular-weight DNA have been studied by fluorescent spectroscopy. Changes in both the spectra maximum position and anisotropy of the histone tyrosine fluorescence reveal structural transitions in nucleosome within the ranges of 0.5-3 mM and 20-30 mM NaCl. Comparison of the octamer fluorescent parameters in complex with DNA as well as in a free state permits to interpret the revealed structural transitions as a change in degree of contacts stability between (H2A-H2B) dimer and (H3-H4)2 tetramer. More pronounced conformational changes in histone octamer are observed under the conditions of polynucleosome fibers interaction within the range of physiological ionic strength (100-600 mM NaCl). As far as fluorescent parameters are concerned, the aforementioned changes are connected with entire destruction of (H2A-H2B) dimer specific contacts with (H3-H4)2 tetramer. The obtained results suggest the possibility of existence of different structural states of histone octamer in the chromatin composition including those which are quite dissimilar from the octamer structure in the 2M NaCl solution.     

Theoretical study of structural transition in a nucleosome at low ionic strength

The theoretical analysis of nucleosome stability at low ionic strength has been performed on the basis of consideration of different contributions to the free energy of compact state of the nucleosome DNA terminal regions. The proposed model explains: the fact of low-salt structural change; the transition point (approximately 1.7 mM NaCl) and width (approximately 1 mM); the shift of the transition to the higher salt concentrations in the case of histones tails removal by trypsin. According to the model the increase of electrostatic repulsion between neighbouring turns of DNA superhelix is the main cause of the unwinding of nucleosomal DNA terminal regions in the course of low-salt structural change. The interactions between histone (H2A-H2B) dimer and (H3-H4)2 tetramer provide the compact state of the nucleosomal DNA terminal regions. The existence of electrostatic interactions of nucleosomal DNA terminal regions with tetramer was suggested. These interactions can provide the compact state of nucleosomal DNA at physiological ionic strength even in the absence of (H2A-H2B) dimer.     

Peculiarities of the amino acid composition, spatial organization and interaction with DNA of histones H1 from calf thymus and carp spermatozoa

The amino acid composition of the H1-like histone isolated from carp spermatozoa (H1carp) is characterized by a high content of lysine (34.6%) and a low content of glycine (4.5%) as compared to that of its calf counterpart (H1calf). The Lys/Arg ratio is 21.6, which is much higher than that for the H1-like histones from other species spermatozoa (cf. echinodermata). It was shown that the fluorescence anisotropy and excitation spectra of histones H1carp and H1calf change synchronically. At the same time the final folding of the polypeptide chains of these histones within their ternary structure is different. These differences manifest themselves in a distinct quantum yield of both histones and different accessibility of the single tyrosine residue for fluorescence quenchers. In histone--DNA complexes the tyrosine fluorescence is quenched. An increase in the ionic strength gives rise to a formation of large-sized aggregates in a histone H1--DNA solution which contain structurally heterogenous histones H1 from different sources. Histone H1carp causes DNA aggregation at lower ionic strength values than its calf counterpart. The complexes are dissociated at 0.6 M NaCl.     

Expression and purification of recombinant human histones

Nucleosomes reconstituted from bacterially expressed histones are useful for functional and structural analyses of histone variants, histone mutants, and histone post-translational modifications. In the present study, we developed a new method for the expression and purification of recombinant human histones. The human histone H2A, H2B, and H3 genes were expressed well in Escherichia coli cells, but the human histone H4 gene was poorly expressed. Therefore, we designed a new histone H4 gene with codons optimized for the E. coli expression system and constructed the H4 gene by chemically synthesized oligodeoxyribonucleotides. The recombinant human histones were expressed as hexahistidine-tagged proteins and were purified by one-step chromatography with nickel-nitrilotriacetic acid agarose in the presence of 6 M urea. The H2A/H2B dimer and the H3/H4 tetramer were refolded by dialysis against buffer without urea, and the hexahistidine-tags of the histones in the H2A/H2B dimer and the H3/H4 tetramer were removed by thrombin protease digestion. The H2A/H2B dimer and the H3/H4 tetramer obtained by this method were confirmed to be proficient in nucleosome formation by the salt dialysis method. The human CENP-A gene, the centromere-specific histone H3 variant, contains 28 minor codons for E. coli. A new CENP-A gene optimized for the E. coli expression system was also constructed, and we found that the purified recombinant CENP-A protein formed a nucleosome-like structure with histones H2A, H2B, and H4.     

Study by the spin-label method of relaxation properties of protein kinase, its subunits and the catalytic subunit--histone H1 complex

Using the spin label method, the rotational relaxation in solution of adenosine 3',5'-monophosphate-dependent protein kinase and its subunits as well as the complexes of the enzyme with the substrate, histone H1, was studied. The rotational correlation time of the spin labeled macromolecules was measured on the basis of the quantitative estimation of the label mobility in relation to the protein globule. The holoenzyme molecule was found to be a rigid sphere. Whereas the complex of the globular catalytic subunit of the enzyme with a specific protein substrate, the spin labeled histone H1, appeared a flexible formation. The relaxation properties of the histone H1 molecule selectively labeled by the spin label in its globular part were investigated.     

Histone interactions in solution and susceptibility to denaturation.

Histone interactions in solution may depend upon treatments used for purification. Optical rotatory dispersion and sedimentation-velocity measurements have been made in a reference solvent, before and after exposure to various treatments, to investigate histone susceptibility to irreversible denaturation. Some acid conditions and urea and guanidine solutions may denature. Interaction studies performed on nondenatured histones indicate that the dimer, (H4)(H3), and tetramer, (H4)2(H3)2, dissociate to monomers at low ionic strength. Sedimentation-velocity experiments suggest a model for the (H4)2(H3)2 tetramer, with a compact semispherical center and four protruding amino-terminal regions. Fractions H2a and H2b interact to form the mixed dimer in equilibrium with monomers. Fraction H2a self-associates readily to dimers, tetramers, and octamers, while fraction H1 associates only weakly to form dimers.     

Equilibrium folding of the core histones: the H3-H4 tetramer is less stable than the H2A-H2B dimer

To compare the stability of structurally related dimers and to aid in understanding the thermodynamics of nucleosome assembly, the equilibrium stabilities of the recombinant wild-type H3-H4 tetramer and H2A-H2B dimer have been determined by guanidinium-induced denaturation, using fluorescence and circular dichroism spectroscopies. The unfolding of the tetramer and dimer are highly reversible. The unfolding of the H2A-H2B dimer is a two-state process, with no detected equilibrium intermediates. The H3-H4 tetramer is unstable at moderate ionic strengths (mu approximately 0.2 M). TMAO (trimethylamine-N-oxide) was used to stabilize the tetramer; the stability of the H2A-H2B dimer was determined under the same solvent conditions. The equilibrium unfolding of H3-H4 was best described by a three-state mechanism, with well-folded H3-H4 dimers as a populated intermediate. When compared to H2A-H2B, the H3-H3 tetramer interface and the H3-H4 histone fold are strikingly less stable. The free energy of unfolding, in the absence of denaturant, for the H3-H4 and H2A-H2B dimers are 12.4 and 21.0 kcal mol(-)(1), respectively, in 1 M TMAO. It is postulated that the difference in stability between the histone dimers, which contain the same fold, is the result of unfavorable tertiary interactions, most likely the partial to complete burial of three salt bridges and burial of a charged hydrogen bond. Given the conservation of these buried interactions in histones from yeast to mammals, it is speculated that the H3-H4 tetramer has evolved to be unstable, and this instability may relate to its role in nucleosome dynamics.     

H2a-specific proteolysis as a unique probe in the analysis of the histone octamer

We have utilized the H2a-specific protease as a unique probe to investigate the nature of the interactions between the protein subunits which form the core histone octamer. Upon incubation in high ionic strength media this protease, normally found tightly associated with isolated calf thymus chromatin, releases the 15 COOH-terminal amino acids of histone H2a by specifically cleaving the H2a polypeptide between Val114 and Leu115, yielding cleaved H2a (cH2a) and a free pentadecapeptide (Eickbush, T. H., Watson, D. K., and Moudrianakis, E. N. (1976) Cell 9, 785-792). We find that removal of this pentadecapeptide results in a marked dissociation of the octamer into its H2a:H2b dimer and H3:H4 tetramer subunits. Reconstitution experiments indicate that cH2a is capable of forming a dimer with H2b, but this cH2a:H2b dimer has a substantially lower affinity for the H3:H4 tetramer than native H2a:H2b dimer. Kinetic studies of H2a cleavage in high ionic strength solutions demonstrate that H2a molecules in the octamer are relatively resistant to proteolytic attack compared to H2a molecules in the dimer. The extent of this resistance, in response to various experimental parameters, is directly correlated to the strength of interaction between the H2a:H2b dimer and H3:H4 tetramer subunits. These reconstitution and kinetic experiments suggest that the histone domains proximal to the H2a cleavage site have an important function in maintaining the association of the histone octamer subunits.     

Interactions between arginine-rich histones and deoxyribonucleic acids. I. Thermal denaturation.

Physical properties of histone-DNA complexes very often depend upon the method of complex formation. In an attempt to make the studies of histone-DNA interactions more relevant to biological systems, results from thermal denaturation of native chromatin were used as references for determining how closely a given histone-DNA complex approaches its native state in chromatin. In the case of arginine-rich histones H3 (III or f3) and H4 (IV or f2a1), four methods were used for making complexes with calf thymus DNA: (A) NaCl gradient dialysis with urea; (B) NaCl gradient dialysis without urea; (C) direct mixing in 2.5 x 10(-4) EDTA, pH 8.0; and (D) direct mixing in 0.01 M sodium phosphate, pH 7.0. It was observed that a complex made by direct mixing in phosphate (method D) is closer to the native than is one made by direct mixing in EDTA (method C) than the one made by gradient dialysis with urea (method A) or without urea (method B). Regardless of the method used for complex formation, no substantial differences were observed between complexes with histone H3 dimer with disulfide bond(s) and a reduced H3 without disulfide bond, implying that perhaps a dimer with or without disulfide bond is a natural fundamental subunit in our experimental conditions. When the method of direct mixing in EDTA is used, the melting properties of the complexes vary only slightly with any one of the following H3 histones: from calf thymus, H3 without disulfide bond, H3 dimer, and H3 oligomer with disulfide bonds, also, from duck erythrocyte, H3 monomer and dimer. The complexes formed between DNA and a mixture of H3 and H4 by method D have melting properties similar to those of native chromatin. Since an equimolar mixture of histone H3 and H4 in 0.01 M phosphate, pH 7.0, was shown to form a tetramer (D'Anna, J.A., and Isenberg, I. (1974), Biochem. Biophys. Res. Commun. 61, 343), our results suggest that, a tetramer of H3 and H4, likely to be (H3)2(H4)2, formed from one H3 dimer and one H4 dimer, can bind DNA in a manner similar to that in native chromatin.     

Deposition of newly synthesized histones: new histones H2A and H2B do not deposit in the same nucleosome with new histones H3 and H4

We have developed procedures to study histone-histone interactions during the deposition of histones in replicating cells. Cells are labeled for 60 min with dense amino acids, and subsequently, the histones within the nucleosomes are cross-linked into an octameric complex with formaldehyde. These complexes are sedimented to equilibrium in density gradients and octamer and dioctamer complexes separated by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. With reversal of the cross-link, the distribution of the individual density-labeled histones in the octamer is determined. Newly synthesized H3 and H4 deposit as a tetramer and are associated with old H2A and H2B. Newly synthesized H2A and H2B deposit as a dimer associated with old H2A, H2B, H3, and H4. The significance of these results with respect to the dynamics of histone interactions in the nucleus is discussed. Control experiments are presented to test for artifactual formation of these complexes during preparative procedures. In addition, reconstitution experiments were performed to demonstrate that the composition of these octameric complexes can be determined from their distribution on density gradients.     

Archaeal histone tetramerization determines DNA affinity and the direction of DNA supercoiling

DNA binding and the topology of DNA have been determined in complexes formed by >20 archaeal histone variants and archaeal histone dimer fusions with residue replacements at sites responsible for histone fold dimer:dimer interactions. Almost all of these variants have decreased affinity for DNA. They have also lost the flexibility of the wild type archaeal histones to wrap DNA into a negative or positive supercoil depending on the salt environment; they wrap DNA into positive supercoils under all salt conditions. The histone folds of the archaeal histones, HMfA and HMfB, from Methanothermus fervidus are almost identical, but (HMfA)(2) and (HMfB)(2) homodimers assemble into tetramers with sequence-dependent differences in DNA affinity. By construction and mutagenesis of HMfA+HMfB and HMfB+HMfA histone dimer fusions, the structure formed at the histone dimer:dimer interface within an archaeal histone tetramer has been shown to determine this difference in DNA affinity. Therefore, by regulating the assembly of different archaeal histone dimers into tetramers that have different sequence affinities, the assembly of archaeal histone-DNA complexes could be localized and used to regulate gene expression.     

Associative behavior of the histone (H3-H4)2 tetramer: dependence on ionic environment

Mixtures of histones H3 and H4 were examined by analytical ultracentrifugation and circular dichroism to determine their association behavior and secondary structure content in high and low ionic strength solvents containing chloride, phosphate, or sulfate. H3 and H4 were also cross-linked by using DSP in order to directly trap any intermolecular interactions occurring in solution. While H3 and H4 can exist as an H3-H4 dimer under limited conditions, they behave as a stable (H3-H4)2 tetramer under most conditions, particularly those which are physiologically relevant. In chloride-containing solutions, the equilibrium between H3-H4 and (H3-H4)2 is responsive to changes in ionic strength and paralleled by large changes in alpha-helicity. In sulfate- and phosphate-containing solutions, the equilibrium is again governed by ionic strength, but there are no significant changes in secondary structure accompanying shifts in the equilibrium. Small oligomers can be formed in the presence of sulfate and phosphate and trapped by the cross-linking reagent; these oligomers are much smaller than those formed in chloride-containing solutions. However, addition of the H2A-H2B dimer into the system prevents aggregation of the (H3-H4)2 tetramer by acting as a "molecular cap" and thus regulating the assembly pathway toward the formation of tripartite octamers. The observed assembly of H3 and H4 into a stable, tetrameric complex supports the concept of the core histone octamer having a tripartite organization in solution rather than being organized as two heterotypic tetramers.     

Intermolecular histone H4 interactions in core nucleosomes

Chicken histone H4, labeled at methionine-84 with 1-N-pyrenyliodoacetamide, has been incorporated into a nucleosome-like particle with core length DNA and unmodified histones H2A, H2B, and H3. These synthetic nucleosomes exhibit properties very similar to those displayed by native particles and those labeled with other fluors. The emission spectrum of the pyrene-labeled nucleosome was characteristic of excited dimer (excimer) fluorescence, indicating that the single pyrene groups on the two H4 molecules are in close proximity in the reconstituted particle. Histone H4 was also labeled randomly at lysines with a group that contains two pyrene moieties separated by 12 A at most. Incorporation of this histone into nucleosome-like particles provides an excimer standard which does not depend on intermolecular interactions. The properties of the pyrene-containing nucleosome were examined as a function of ionic strength. It was found that the H4-H4 pyrene excimer fluorescence exhibited a cooperative disruption centered at 0.1 M NaCl which preceded increases in accessibility and environment polarity revealed by other fluors attached at the same site.