Secondary and tertiary structural differences between histone H1 molecules from calf thymus and sea-urchin (Sphaerechinus granularis) sperm

DNA and nucleosomes direct distinct folding of a linker histone H1 C-terminal domain

We previously documented condensation of the H1 CTD consistent with adoption of a defined structure upon nucleosome binding using a bulk FRET assay, supporting proposals that the CTD behaves as an intrinsically disordered domain. In the present study, by determining the distances between two different pairs of sites in the C-terminal domain of full length H1 by FRET, we confirm that nucleosome binding directs folding of the disordered H1 C-terminal domain and provide additional distance constraints for the condensed state. In contrast to nucleosomes, FRET observed upon H1 binding to naked DNA fragments includes both intra- and inter-molecular resonance energy transfer. By eliminating inter-molecular transfer, we find that CTD condensation induced upon H1-binding naked DNA is distinct from that induced by nucleosomes. Moreover, analysis of fluorescence quenching indicates that H1 residues at either end of the CTD experience distinct environments when bound to nucleosomes, and suggest that the penultimate residue in the CTD (K195) is juxtaposed between the two linker DNA helices, proposed to form a stem structure in the H1-bound nucleosome.

DNA-bridging by a palindromic alpha-helix

The nucleosomal DNA repeat of 240 base pairs in the chromatin structure of sea urchin sperm is exceptionally long and is accompanied by the presence of a histone H1 molecule larger than is usual in most species of chromatin. I propose how these two features are correlated and how they fit into the solenoidal model for the 300-A-diameter fiber of chromatin. Comparison of the sequence of spermatogenous H1 with other H1 sequences reveals an insert of 55 amino acid residues (residues 122-176). A 37-residue sequence in the insert (residues 140-176) has a palindromic character. I propose that each half of the palindromic sequence constitutes an alpha-helical DNA-binding unit and that the continuous alpha-helix made up of the two halves, by virtue of its palindromic nature, stabilizes the formation of an extra superhelical turn by the long linker DNA between two nucleosome cores. The N-terminal-C-terminal "polarity" of each alpha-helical section of half the palindromic sequence indicates how the arginine/lysine-rich DNA-binding surface of the alpha-helical section is used. The polarity of the H1 insertion sequence supports the so-called "reverse-loop" model or a "figure-eight" model for the path of the DNA within the solenoid structure; i.e., the linker DNA forms a right-handed superhelical turn toward the center of the solenoid structure. This use of a pair of a palindromically related alpha-helical sections has a similarity with the "scissors-grip" model for the interaction of the leucine-zipper proteins with DNA.

The C-domain in the H1 histone is structurally conserved

The C-domain of H1 is conserved in composition and not in sequence. The following regularities have been identified: the distribution of lysine, alanine and proline is non-random; alanine occurs in doublets and at intervals of 4-6 significantly more often than expected for random sequences of equal composition; and lysine also deviates from random distribution in that doublets are under-represented and intervals of 2-7 are over-represented. Lysine preferentially occurs in singlets and alanine in doublets rather than triplets or quadruplets. This discourages the formation of helices without neutralization of lysine charges. When lysine residues are paired with DNA phosphate residues, helices are highly probable. Interproline spacing promotes short helical segments. The regularities arising from the conservation of composition and non-random residue distribution suggests that C-domains adopt similar structures and in fact are structurally conserved.

Analysis of the charge distribution in the C-terminal region of histone H1 as related to its interaction with DNA

We have studied the net positive charge distribution in the C-terminal region of histone H1. We find that it is not random, but rather uniform. In most histone H1 sequences, 4 +/- 1 positive charges are found in this region of the molecule in over 95% of all possible segments that are 10 amino acids long. Neither alternating sequences (basic-nonbasic) nor more complex repeating sequences are ever found. Clusters of three or more basic amino acids are seldom observed in somatic H1s, yet their presence increases in sperm histones and even more so in protamines. It is concluded that the C-terminal region of histone H1 has a remarkably uniform distribution of charge, in spite of its apparent variations in sequence in different proteins and within individual molecules. The functional significance of these findings is discussed, suggesting a purely electrostatic role for the C-terminal region of histone H1, which may be evenly wrapped around individual segments of DNA molecules, thus decreasing its net charge. A likely candidate for a long alpha-helical region in the C-terminal region of histone H1 from sea urchin spermatozoa also has been located. This region may contribute to the aggregating properties of this histone in sperm chromatin.

Structural differences between histone H1 molecules from sea urchin (Strongylocentrotus intermedius) sperm and calf thymus: hydrodynamic and c.d. studies

Comparative sedimentation, diffusion and circular dichroism (c.d.) measurements have been performed on two histones H1 from sperm of the sea urchin Strongylocentrotus intermedius (H1S) and from calf thymus (H1T), at a high salt concentration of M NaCl. Both the Stokes radius and the frictional ratio derived from the hydrodynamic parameters were found to be somewhat smaller for H1S than the corresponding values for H1T. In view of the considerably higher molar mass of H1S compared with that of H1T, this result indicates that H+S in 2 M NaCl has a more compact conformation than H1T, probably due to a higher degree of secondary structure in the flanking domains of H1S. The c.d. measurements likewise show that H1S has a higher content of ordered structures than H1T. Model considerations indicate that the C-terminal tail of H1S is the main candidate for accommodation of these additional secondary structure regions.

Differences in the binding of H1 variants to DNA. Cooperativity and linker-length related distribution

A study of the complexes formed between short linear DNA and three H1 variants, a typical somatic H1, and the extreme variants H5, from chicken erythrocytes, and spH1 from sea urchin sperm, has revealed differences between H1, H5 and spH1 that have implications for chromatin structure and folding. 1. All three histones bind cooperatively to DNA in 35 mM NaCl forming similar, but not identical, rod-like complexes. With sufficiently long DNA the complexes may be circular, circles forming more easily with H5 and spH1 than with H1. 2. The binding of H5 and spH1 to DNA is cooperative even in 5 mM NaCl, resulting in well-defined thin filaments that appear to contain two DNA molecules bridged by histone molecules. In contrast, H1 binds distributively over all the DNA molecules in 5 mM NaCl, but forms short stretches similar in appearance to the thin filaments formed with H5 and spH1. Rods appear to arise from the intertwining of regular thin filaments containing cooperatively bound histone molecules on raising the NaCl concentration to 35 mM. 3. The compositions of the rods correspond to one histone molecule for about every 47 bp (H1), 81 bp (H5) and 112 bp (spH1), suggesting average spacings of 24 bp (H1), 41 bp (H5) and 56 bp (spH1) in the component thin (double) filaments. Strikingly, these values are proportional to the linker lengths of the chromatins in which the particular H1 variant is the main or sole H1.

The chromatin of sea urchin sperm

Digestion of sea urchin sperm nuclei with micrococcal nuclease yields nucleosomal monomer fragments of 151 and 164 base pairs. Prior trypsin treatment of the sperm chromatin does not alter the size of these monomer DNA fragments despite the fact that the H1 histone is reduced to a limit globular peptide of about 83 residues. Heterologous reconstitution experiments show that this peptide is capable of protecting an extra 22 base pairs beyond the core particle in a chromatosome. Nuclease digestion of reconstitutes from DNA and sperm core histones yields a core monomer of about 141 base pairs. It is concluded that this sperm chromatin contains a chromatosome of 164 bp essentially similar to that observed in the more usual chromatins. Edman degradation of the H1 limit peptide shows its sequence to be closely analogous to the corresponding peptide of calf H1 and chicken H5. Circular dichroism studies of histone H1 from the sperm of three sea urchin species demonstrate the presence of trypsin-sensitive helical regions outside the globular domain that are absent in calf H1 and chicken H5.

Sequence of the amino terminal half of rat testis-specific histone variant H1t

H1t is a testis-specific H1 histone variant that appears during the meiotic phase of spermatogenesis in mammals. The sequence of the first 108 residues of rat H1t have been determined and compared to boar H1t and also to a consensus sequence characteristic of standard somatic H1 variants. The two versions of H1t share a common pattern of divergence from the standard somatic consensus. For example, they both share many substitutions within the H1 globular region (residues 40-110), a portion of the molecule that is virtually invariant among the common somatic variants. Within the entire region sequenced, there are 28 shared locations where both forms of H1t differ from the somatic consensus. However, identical substitutions occur at only 15 of these sites, and each protein also differs from the consensus at five (boar) or ten (rat) additional locations that are not shared. These results establish that H1t from diverse sources shows a characteristic pattern of divergence from the sequence of standard somatic H1 proteins. However, it is also clear that there is great tolerance for species-specific variation within this H1 class.

Lability to acid hydrolysis in some different DNA-protein complexes of spermatozoa

The Feulgen hydrolysis kinetics was investigated in spermatozoa with different composition in DNA-protein complexes. The species used were: Bos taurus (arginine rich nuclear protein also containing cystine residues), Pichroplus bergi, Triatoma infestans (arginine-rich nuclear protein), Lytechinus variegatus and Apis mellifera (lysine-rich nuclear protein). The spermatozoa were subjected to Feulgen's reaction, after varying the fixative type and the hydrolysis times. Feulgen-DNA values were obtained with an automatic scanning cytophotometric procedure. Differences were demonstrated in the hydrolysis kinetics as a function of differences in composition of the DNA-protein complexes being present in the spermatozoon chromatin. Differences in the profiles of Feulgen hydrolysis curves, having for basis the fixation, were rather clear for bull, grasshopper, and blood-sucking insect spermatozoa than for the sea-urchin and bee spermatozoa. The different hydrolysis kinetics of chromatin of blood-sucking insect spermatozoa compared to that of grasshopper, sea-urchin, and bee sperm cells suggests that, although the first 2 materials contain an arginine-rich "germinative" protein and the latter 2 ones contain a lysine-rich protein, these differ to each other. The DNA depurination was obtained more quickly for T. infestans (20 min) and P. bergi (10 min) spermatozoa when they were fixed in the ethanol-acetic acid (EA) mixture. Morphologically anomalous bull spermatozoa fixed in the EA mixture presented a quicker depurination (30 min) as compared to the normal cells (1 h). The fast lability to acid hydrolysis in the abnormal cells is certainly due to anomalies in their basic nuclear "germinative" protein. In the formalin fixed materials the maximal depurination was obtained earlier in bull spermatozoa (30 min) followed by sperm cells of P. bergi, T. infestans, L. variegatus (all of them one-hour hydrolysis) and finally Apis mellifera (2 h hydrolysis). The presence of secondary peaks at the descending branch of the hydrolysis curves of grasshopper and sea-urchin spermatozoa, indicates for these, more than 1 kind of apurinic-acid protein complexes. The spermatozoa bearing arginine-and/or cystine-rich nuclear protein contain a more easily soluble apurinic acid protein complex. Due to the differences in hydrolysis kinetics of chromatin in spermatozoa containing different nuclear "germinative" proteins, this cellular type does not appear indicated as a haploid control for evaluation of Feulgen-DNA contents of diploid and polyploid somatic cells.

Physical studies by NMR and circular dichroism determining three structurally different domains in Physarum polycephalum histone H1

Combined studies which include, NMR spectroscopy, circular dichroism, amino acid analysis and polyacrylamide gel electrophoresis together show that the protein designated as histone H1 from Physarum polycephalum has many of the features of histone H1 derived from other sources. The molecular masses of the globular peptide and the whole molecule were found to be 9000 +/- 1000 Da and 33000 +/- 3000 Da respectively. NMR melting experiments showed that the half-melt temperature was 53 +/- 1 degree C and the enthalpy of melting was 100 kJ . mol-1. Unusual facets of the molecule are the relatively large numbers of histidine residues (6 or 7) and the mono, di and trimethylation of some of the lysines, the major type of modification being trimethylation of 9 +/- 2 residues. The conditions necessary for structuring Physarum H1 are not the same as the histone H1 from calf thymus. It is suggested that titration of the histidine residues is the most decisive step for the development of tertiary folding of the globular unit.

Interaction of histone H1 from sea urchin sperm with superhelical and relaxed DNA

Complexes of histone H1 from sea urchin sperm (H1S) and calf thymus (H1T) with superhelical DNA I and relaxed circular DNA II have been analyzed by analytical sedimentation. Similar to H1T, the highly basic and relatively arginine-rich histone H1S preferentially interacts with DNA I compared to DNA II under competition conditions. However, H1S induces a stronger aggregation of both forms of DNA than H1T. Below 0.05 M NaCl, the soluble complexes formed by both histones have similar properties, but aggregation proceeds in a different manner: H1S induces a stronger aggregation of DNA II as compared to DNA I, whereas H1T fails to aggregate DNA I. The results are explained on the basis of differences in amino acid sequence and structure of the two histones and related to the special chromatin condensing ability of histone H1S.

Proteins from the sperm of the bivalve mollusc Ensis minor. Co-existence of histones and a protamine-like protein

Analysis of the total protein of the mature sperm of the bivalve mollusc Ensis minor (razor shell) using gel electrophoresis, amino acid analysis, nuclear magnetic resonance, circular dichroism and trypsin digestion, show it to contain all five histones plus a protamine-like protein. The histones H3, H4 and probably H2A are similar to those from calf thymus or sea urchin sperm, but the putative H2B appears to have a very high molecular mass (about 20 kDa). The histone H1 molecule is unusual, having little or no proline and 8-10 residues of histidine. The protamine-like species is rich in both lysine as well as arginine and is of much higher molecular mass than fish sperm protamines. Nucleosomes containing the four core histones have been prepared and the nucleosomal repeat shown to be 200 +/- 5 base pairs. Checks for the absence of contaminating cells reinforce the conclusion that a histone-containing nucleosomal structure co-exists with a protamine-like protein in this sperm chromatin.

Isolation of a 167 basepair chromatosome containing a partially digested histone H5

A test has been made of the proposal that protection of the 167 basepair DNA length in the 'chromatosome' is due only to the central globular domain of the lysine-rich histones. Chicken erythrocyte chromatin was treated with trypsin to leave only the limit peptide from histones H1 and H5. Nucleosome monomers were then isolated on sucrose gradients following micrococcal nuclease digestion and were found to contain the 167 basepair DNA band as in intact chromatin. The presence of the limit peptide from H5 on the monomers was confirmed using an antibody to H5. It is concluded that the trypsin-susceptible domains of the lysine-rich histones are not involved in the protection of the 2-turn 167 basepair length of DNA in the nucleosome.

Histone H1 and chromatin higher order structure. Does histone H1 exhibit specific self-association?

1. Histones H1 and H5 in chromatin and in free solution can be cross-linked to higher multimers. Is this due to a specific protein/protein interaction? If so, this interaction might be the structural basis of the condensation of the chromosomal nucleofilament, known to be mediated by histones H1 and H5. 2. Since only the central domain of H1 and H5 exhibits tertiary folding and globular structure, this is the most likely site of specific interaction. 3. Formaldehyde has been used to test whether the central domains of histone H1 from calf thymus or from sea urchin sperm or histone H5 from chicken erythrocytes self-interact. 4. The cross-linking shown by each globular peptide was compared with that of its parent histone. 5. In all three cases the peptide cross-linked to a much lower extent than its intact parent histone and the observed cross-linked rates were roughly in proportion to the relative number of lysine residues parent histone and peptide. 6. It is concluded that there is no specific self-interaction between the globular domains of either H1 or H5 molecules in free solution. 7. This result suggests that specific H1/H1 protein/protein interactions are not the basic cause of chromatin condensation.

Precise elimination of the N-terminal domain of histone H1

The proteinase from mouse submaxillary gland was used to cleave total calf thymus histone H1 between residues 32 and 33. The C-terminal peptide, comprising residues 33 to the C-terminus, was purified and identified by amino acids analysis and Edman degradation. Spectroscopic characterization by n.m.r. for tertiary structure and by c.d. for secondary structure shows the globular domain of the parent histone H1 to be preserved intact in the peptide. It has therefore lost only the N-terminal domain and is a fragment of histone H1 comprising the globular plus C-terminal domains only. Precise elimination of only the N-terminal domain makes the fragment suitable for testing domain function in histone H1.

The central tryptic fragment of histones H1 and H5 is a fully compacted domain and is the only folded region in the polypeptide chain. A thermodynamic study

Scanning microcalorimetry has been used to show that the globular structure in histones H1 and H5 melts reversibly over a relatively narrow temperature range as a single domain with enthalpy of melting very close to the van't Hoff enthalpy. These proteins therefore exhibit macroscopic cooperativity like that of many well-studied small proteins. For histone H5 the observed melting temperature and melting enthalpy coincide with those previously obtained [Eur. J. Biochem. 67, 379-388 (1976)] using intrinsic Cotton effects in the circular dichroism spectrum, but not with those from extrinsic Cotton effects or NMR chemical shifts. Calorimetric measurements on a central tryptic fragment from histones H1 and H5 show these fragments to have the same molar melting enthalpy as the parent histones. The folded structures of H1 and H5 are therefore located only within these fragments. For histone H1 this conclusion is supported by the finding that the C-terminal fragment (residues 122-213) shows no peak in the specific heat curve.