Biophysical approach to the determination of the secondary structure of the histone H1 globular region

A possible secondary structure of the globular part of the histone H1 was obtained with a statistical approach based on the GOR method. The results of circular dichroism measurements on the protein were taken into account in order to choose between theoretically equivalent structures.     

The conformation of histone H5 bound to DNA. Maintenance of the globular structure after binding.

Trypsin digestion is used to investigate the conformation of histone H5 when bound to DNA. A central region of H5 comprising residues (22--100) is found to be resistant to digestion and it is concluded that this region is compacted whilst the remaining N- and C-terminal regions are more extended. Since this is the same result found previously for the free solution conformation of histone H5 it follows that a 3-domain structure is preserved on DNA binding. The binding of H5 and the central region (22--100) to DNA is also studied using proton magnetic resonance (270 MHz) and a precipitation approach. It is concluded that all 3 domains of H5 bind to DNA at low ionic strengths. The central domain (residues 22--100) is released at 0.3--0.4 M NaCl, but 0.7 M NaCl is required to release the N- and C-terminal regions. Comparison is made of H5 binding to DNA with that of the related histone H1.     

The globular region of histone H5 is equally accessible to antibodies in relaxed and condensed chromatin

The accessibility of histone H5 in chromatin was examined with monoclonal antibodies recognizing several epitopes of the globular region (GH5) of the histone (Rózalski, M., Lafleur, L., and Ruiz-Carrillo, A. (1985) J. Biol. Chem. 260, 14379-14385). The stoichiometry of the chromatin-antibody complexes indicated that while 0-86% of the H5 molecules were able to react, depending on the particular epitope, the extent of antibody binding to relaxed chromatin (in 5 mM KCl) and condensed chromatin (in 100 mM KCl or 0.35 mM MgCl2) was virtually identical. This indicates that the topography of H5 does not change during the conformational transition of chromatin. The data suggest that H5 is not completely internalized in the 30-nm fiber or that the fiber is flexible enough to allow full exposure of the GH5 epitopes. Several control experiments, including monoclonal antibody binding, sedimentation analysis, DNase II digestion, and glutaraldehyde cross-linking, showed that epitope accessibility is not due to H5 exchange or to perturbation of the chromatin fiber. The accessibility of GH5 suggests ways in which inactive chromatin may be unfolded in vivo.     

A minireview of microheterogeneity in H1 histone and its possible significance

Subtypes of H1 histone vary in primary structure, and the higher organisms that have been studied each seem to have about a half-dozen subtypes. The proportions of these subtypes vary with the progress of differentiation as seen in embryonic development, hormonally induced changes, spermatogenesis, and terminal differentiation. The H1 subtypes differ among themselves in their ability to condense DNA and small chromatin fragments. They have the potential, therefore, of causing different parts of the chromatin to be condensed to different degrees.     

The conformation of histone H5. Isolation and characterisation of the globular segment

Treatment of chicken erythrocyte histone H5 with trypsin in a high-ionic-strength medium results in very rapid initial digestion and the formation of a 'limiting' resistant product peptide. Under these solution conditions the H5 molecule is maximally folded by spectroscopic criteria and it is concluded that the resistant peptide, GH5, represents a globular folded region of the molecule whilst the rapidly digested parts are disordered. The peptide GH5 is shown to comprise the sequence 22-100. In support of this conclusion it is shown that whilst intact histone H5 is hydrodynamically far from being a compact globular shape, peptide GH5 is approximately spherical by hydrodynamic and scattering criteria. Further more, peptide GH5 retains all the alpha-helical structure of intact H5 (circular dichroism) and appears to also maintain all the tertiary structure (nuclear magnetic resonance). It follows that in solution at high ionic strength, histone H5 consists of three domains: an N-terminal disordered region 1-21, a compact globular central domain 22-100 and a long disordered C-terminal chain 101-185. Structural parallels are drawn with the three-domain structure of the histone H1 molecule.     

The primary structure of histone H3 from wheat

Wheat embryo histone H3 has been isolated and purified and the elucidation of the complete amino-acid sequence is described. Peptides were generated by cleavages with CNBr, S. aureus V8 proteinase, endoproteinase Lys-C and trypsin. The peptides were purified by HPLC and the sequence determined by solid-state and gas-phase sequencing methodology. The amino-acid sequence of the protein is identical to pea embryo histone H3 and the sequence deduced from the nucleotide sequence of a wheat embryo histone gene (Tabata T. et al. (1984) Mol. Gen. Genet. 196, 397-400).     

Infrared spectroscopic studies of solvent-induced conformational changes in globular proteins.

Infrared absorption spectroscopy has been used to study the effect of organic solvents on the conformation of myoglobin, apomyoglobin, hemoglobin, lysozyme and ribonuclease. Beta structure can easily be induced by specific solvent effects. Films prepared from a 50% (v/v) mixture of alcohol, acetone, pyridine, tetrahydrofuran or dimethylsulfoxide/water mixtures show a high proportion of beta structure. The degree of induction of beta structure depends on the hydrocarbon content of the alcohol in the order methanol greater than ethanol greater than butanol. No beta structure was observed in films prepared from aqueous octanol solutions. Lyophilization tends to decrease secondary structure. The conformation of the proteins depends on the particular solvent system and the solvent composition. Solution studies of myoglobin in pure dimethylsulfoxide show that the conformation is a mixture of random and beta forms while in dimethylsulfoxide/2H2O mixtures the conformation is a mixture of alpha-helical and beta forms.     

Studies on the role and mode of operation of the very-lysine-rich histone H1 in eukaryote chromatin. The isolation of the globular and non-globular regions of the histone H1 molecule.

Digestion of calf thymus H1 histone with thrombin cleaves the molecule at the sequence -(Pro)-Lys-Lys-Ala-, corresponding to a point approximately 122 residues from the N-terminus (about 56% along the molecule). The N-terminal fragment is shown by proton nuclear magnetic resonance (NMR) to possess the globular structure of the intact histome H1 molecule, whereas the C-terminal fragment appears to possess little or no structure. The N-terminal fragment separates into two peaks on an ion-exchange column, one of which is shown to originate from a single subfraction of calf thymus histone H1 and the other to originate from the other subfractions, by detailed comparison of the NMR spectra. It thus seems that the structure of the H1 histone in solution under physiological conditions consists of a globular head with a highly basic random coil tail. It is suggested that the globular head has a specific binding site on the subunit structure of the chromosome.     

Free DNA stretches in histone H1-depleted chromatin and their possible relation to chromomere structure

Oligomers of chromatin subunits (oligonucleosomes) were prepared by a mild digestion of chromatin with staphylococcal nuclease followed by a purification of a high molecular weight material (hexanucleosomes and larger DNP particles) by gel chromatography. The main finding is that a mild removal of histone H1 from the oligonucleosome preparation by treatment with tRNA in the absence of any significant hydrodynamic shearing leads to the formation of free DNA molecules which constitute 5–6% of the total oligonucleosomal DNA.The size of nucleosome-free DNA stretches in H1-depleted hydrodynamically sheared chromatin is about 6000 base pairs and their content is apparently 10–12% of the total DNA. These and related findings are discussed in terms of the previously proposed asymmetric hairpin model of DNA packing in chromatin [1–4]. Different kinds of the asymmetric hairpin are considered and ambiguities in interpretations of experimental data are pointed out.     

The involvement of histone H1[0] in chromatin structure.

Micrococcal nuclease digestion and light scattering are used to compare native chromatins with various histone H1[0] contents. The experimental data show that the higher the H1[0] content, the greater the ability to form compact structures with increasing ionic strength, and the lower the DNA accessibility to micrococcal nuclease. On the contrary, reconstituted samples from H1-depleted chromatin and pure individual H1 fractions behave in such a way that samples reconstituted with pure H1 degree give rise to a looser structure, more accessible to nuclease than samples reconstituted with H1-1. This contradiction suggests that the effect of H1o on chromatin structure must originate from the interaction of this histone with other components in native chromatin among which other histone H1 subfractions are good candidates.     

Immunochemical studies of histone H5 from Halobatrachus didactylus.

1. Histone H5 from Halobatrachus didactylus was isolated by using perchloric acid (PCA) extraction of fish liver nuclei and trichloroacetic acid (TCA) precipitation. 2. A polyclonal antiserum was generated by immunizing rabbits with the antigen purified from SDS-PAGE. 3. By immunofluorescence the serum stains erythrocyte nuclei from H. didactylus but it does not react with mammalian cells. 4. By Western blotting, the anti-H5 antibody reacts with the isolated antigen at high titers. 5. Digestion of histone H5 with pepsin and cyanogen bromide suggests that the epitopes are located in the globular and C-terminal region of the H5 molecule excluding the N-terminal.     

The structure of ubiquitinated histone H2B.

Ubiquitinated histone H2B (uH2B) has been purified from both calf and pig thymus by exclusion chromatography in 7 M urea. Digestion of uH2B with Staphylococcus aureus V8 protease yielded the peptide 114-125 containing the ubiquitin moiety. Further digestion of this peptide with trypsin removed the ubiquitin and three H2B residues from the N-terminus. Edman degradations of both peptides established that ubiquitin is attached to the epsilon-amino group of lysine 120 in both calf and pig uH2B by an iso-peptide bond to the C-terminal glycine 76 of ubiquitin.     

The primary structure of histone H3 from cycad pollen

The complete primary structure of cycad pollen histone H3 has been established. Microheterogeneity in several positions revealed the presence of H3 variants. Various lysine residues in the N-terminus were found to be completely or partially methylated. The cycad H3 sequence is compared to that of pea and calf.     

Influence of histone H1 on chromatin structure

Removal of histone H1 produces a transition in the structure of chromatin fibers as observed by electron microscopy. Chromatin containing all histone proteins appears as fibers with a diameter of about 250 A. The nucleosomes within these fibers are closely packed. If histone H1 is selectively removed with 50-100 mM NaCl in 50 mM sodium phosphate buffer (pH 7.0) in the presence of the ion-exchange resin AG 50 W - X2, chromatin appears as "beads-on-a-string" with the nucleosomes separated from each other by distances of about 150-200 A. If chromatin is treated in the presence of the resin with NaCl at concentrations of 650 mM or more, the structural organization of the chromatin is decreased, yielding fibers of irregular appearance.     

Site-directed mutagenesis studies on the binding of the globular domain of linker histone H5 to the nucleosome.

The globular domain of the linker histone H5 has been expressed in Escherichia coli. The purified peptide is functional as it permits chromatosome protection during micrococcal nuclease digestion of chromatin reconstituted with the peptide, indicating that it binds correctly at the dyad axis of the nucleosomal core particle. The globular domain residue lysine 64 is highly conserved within the linker histone family, and site-directed mutagenesis has been used to assess the importance of this residue in the binding of the globular domain of linker histone H5 to the nucleosome. Recombinant peptides mutated at lysine 64 are unable to elicit chromatosome protection to the same degree as the wild-type peptide, and since they appear to be fully folded, these observations confirm a major role for this residue in determining the effective interaction between the globular domain of histone H5 and the nucleosome.     

The primary structure of the major isoform (H1.1) of histone H1 from the nematode Caenorhabditis elegans.

The complete primary structure of the major isoform (H1.1) of histone H1 from the nematode Caenorhabditis elegans was determined. The amino acid chain consists of 207 amino acids and has a blocked N-terminus. The nematode histone shows rather little sequence identity when compared with proteins of the H1 family derived from other organisms. However, the main characteristic features of H1 molecules have been well conserved: a tripartite domain structure consisting of a central hydrophobic core of about 80 residues, flanked by an N-terminal domain which is somewhat acidic at the very N-terminus, but very basic further on, and a long C-terminal domain very rich in lysine, alanine and proline. Several repeat structures, including a twice (with modification)-repeated and well-conserved phosphorylation site, can be recognized in this region. The presence of O-phosphoserine at these sites could not be demonstrated, however.     

The primary structure of a minor isoform (H1.2) of histone H1 from the nematode Caenorhabditis elegans.

The complete amino acid sequence of a minor isoform (H1.2) of histone H1 from the nematode Caenorhabditis elegans was determined. The amino acid chain consists of 190 residues and has a blocked N-terminus. Histone subtype H1.2 is 17 residues shorter than the major isoform H1.1, mainly as the result of deletions of short peptide fragments. Considerable divergence from isoform H1.1 has occurred in the N-terminal domain and the very C-terminus of the molecule, but the central globular domain and most of the C-terminal domain, including two potential phosphorylation sites, have been well conserved. Secondary-structure predictions for both H1 isoforms reveal a high potential for helix formation in the N-terminal region 1-33 of isoform H1.1 whereas the corresponding region in isoform H1.2 has low probability of being found in alpha-helix. No major differences in secondary structure are predicted for other parts of both H1 subtypes. The aberrant conformation of isoform H1.2 may be indicative of a significantly different function.     

Co-operative binding of the globular domain of histone H5 to DNA.

The globular domain of histone H5 (GH5) was prepared by trypsin digestion of H5 that was extracted from chicken erythrocyte nuclei with NaCl. Electron microscopy, sucrose gradient centrifugation, native agarose gel electrophoresis and equilibrium density gradient ultracentrifugation show that GH5 binds co-operatively to double-stranded DNA. The electron microscopic images suggest that the GH5-DNA complexes are very similar in structure to co-operative complexes of intact histone H1 (or its variants) with double-stranded DNA, studied previously, which have been proposed to consist of two parallel DNA double helices sandwiching a polymer of the protein. For complexes with GH5 or with intact H1, naked DNA co-sediments with the protein-DNA complexes through sucrose gradients, and DNA also appears to protrude from the ends and sides of the complexes; measurements of the protein-DNA stoichiometry in fractionated samples may not reflect the stoichiometry in the complexes. An estimate of the stoichiometry obtained from the buoyant density of fixed GH5-DNA complexes in CsCl suggests that sufficient GH5 is present in the complexes for the GH5s to be in direct contact, as required by a simple molecular mechanism for the co-operative binding. Chemical crosslinking demonstrates that GH5s are in close proximity in the complexes. In the absence of DNA, GH5-GH5 interactions are weak or non-existent.