Complete amino acid sequence of goose erythrocyte H5 histone and the homology between H1 and H5 histones

The occurrence of a mutant dimerizable histone H5 in Japanese quail erythrocytes

An allelic variant of linker histone H5 has been found in the erythrocytes of Japanese quail (Coturnix japonica) descended from a small group of feral birds captured on the island of Hawaii. This variant spontaneously forms protein dimers in vitro in the absence of reducing agents. That this depends upon the introduction of a sulfhydryl group (presumably because of a cysteine substitution) is indicated by its reaction with 2-nitro-5-thiocyanobenzoate and by its fluorescence after reaction with 4-aminosulfonyl-7-fluoro-2,1,3-benzoxadiazole. This is the first reported example of cysteine in a vertebrate linker histone and offers a specific reactive site for structural studies. A homozygous line for this form of H5 is being developed.

Histone H1t: a tissue-specific model used to study transcriptional control and nuclear function during cellular differentiation

One of the most prominent and best studied family of genes is the histone gene family. In recent years, histone gene regulation during the cell cycle of somatic cells has been studied extensively. This paper is intended to highlight and emphasize recent data concerning the tissue-specific expression of histone H1t using spermatogenesis as a model system. In this article we describe a unique DNA element within the proximal promoter of the histone H1t gene. This element has been shown to bind exclusively to nuclear proteins from pachytene spermatocytes and early spermatids. Thus, there is a strong temporal correlation between the appearance of the testis-specific DNA-binding protein and the onset of transcription of the testis-specific histone H1t gene.

Crystal structure of globular domain of histone H5 and its implications for nucleosome binding

The structure of GH5, the globular domain of the linker histone H5, has been solved to 2.5 A resolution by multiwavelength anomalous diffraction on crystals of the selenomethionyl protein. The structure shows a striking similarity to the DNA-binding domain of the catabolite gene activator protein CAP, thereby providing a possible model for the binding of GH5 to DNA.

Sequence differences between histones of procyclic Trypanosoma brucei brucei and higher eukaryotes

Four histones, a, b, c, d from procyclic Trypanosoma brucei brucei, which show similarities with the amino acid composition of the core histones H3, H2A, H2B and H4, were isolated and cleaved with Endoproteinase Glu-C. The fragments were separated by FPLC reversed phase chromatography and a subset of the fragments (a5, a9, b6, c8, d3, d9, d11) was subjected to sequence analysis. A 54-71% identity was found in the sequences of the fragment c8 and the C-terminal half of H2B and of three fragments of protein d covering the N-terminal half as well as the C-terminal region of H4. The amino acid sequence of the fragment a9 showed a 57 and 54% identity with H3 sequences of Saccharomyces cerevisiae and Xenopus laevis. Neither the a5 nor the b6 sequence could be aligned with histone sequences of other eukaryotes. The significant differences of 21-48% between the T.b. brucei histone sequences and those of calf thymus histones, which are more pronounced than the differences of Tetrahymena pyriformis and the higher eukaryote, resulted partially from replacements of amino acids with different properties and indicate specific patterns of histone-histone and/or histone-DNA contact sites in the nucleosome of T.b. brucei. These differences, together with the lack of a functional histone H1, may be sufficient to explain the lack of a salt-dependent formation of the nucleosome filament into the 30 nm fibre, which reflects alternative methods of organizing and processing the genetic information in the nucleus of the protozoan parasite and which may be of chemotherapeutic significance.

Structure analysis of purified histone H5 and of H5 in nuclei by limited proteolysis

The structure of purified histone H5 in 1 M-NaClO4 and of H5 in nuclei was analysed by digestion with either one of three endoproteinases, papain, subtilisin or elastase, which preferentially cleave unstructured protein regions (and additionally with trypsin). Digestion with papain and subtilisin produced 'limiting' resistant peptides (p1 and s1) that contain the central region between residues 18-20 and residue 114. Digestion of purified H5 with elastase generated resistant peptides e1 and e2, and that of H5 in nuclei, peptide e2. Peptides e1 and e2 contain the region from residues 22 to 114 and 109 respectively. These results show that a central region of H5 encompassing the sequence between residues 18-22 and residue 114 is folded into a compact structure. A central structured 'core' domain ranging from residues 22 to 100 is defined by the limit trypsin peptide t3, which is identical to the previously described fragment GH5 [Aviles et al. (1978) Eur. J. Biochem. 88, 363-371]. Generation of peptides e2 and t3, as well as of resistant peptides of lower abundance, shows that the sites near Lys-100 and Lys-109 exhibit some proteolytic sensitivity, which may result either from an exposed location or from a locally less compact conformation. Significantly, all these structural features of H5 are manifested in the purified form as well as in nuclei. A role of the structured region from residues 101 to 114 for the interaction with linker DNA and the determination of its path is discussed.

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.

Molecular cloning and characterization of a late Tipula iridescent virus gene

Virions of the cytoplasmic, icosahedral insect virus, Tipula iridescent virus (TIV), contain two major DNA components (L, greater than 176 kb; and S1, 10.8 kb) and 25-30 proteins. We characterized a gene (L96) whose 3.6-kb transcript is expressed late in the course of TIV infection of cultured of Estigmene acrea (salt marsh caterpillar, permissive host) and Aedes albopictus (mosquito, semipermissive host) cells. The L96 gene has an open reading frame of 867 codons, predicting a protein of 96 kDa with a pI of 10.9. The C terminus of the L96 protein is rich in hydrophobic amino acids and contains a small region of homology spanning a proteolytic cleavage site within two mammalian viral (GAG) polyproteins. Additional identity with H5 lysine-rich histones in the same region and with other DNA-binding proteins suggests that this protein may be involved in TIV structure. The lengths of the 5'- and 3'-untranslated regions of the L96 transcript were determined to be 21 nucleotides (nt) and 700 nt, respectively. Comparison of the TIV L96- and capsid-encoding genes, both of which are expressed late in infection, revealed that their 5' and 3' regions are generally rich in A and T residues, and that their 3' ends encode at least one eukaryotic polyadenylation signal (AATAAA).

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.

Crystallization of the globular domain of histone H5

The globular domain of histone H1/H5 binds to the nucleosome and is crucial for the formation of chromatin higher order structure. We have expressed in Escherichia coli a gene that codes for the globular domain of H5. The protein produced in E. coli is functional in nucleosome binding assays. We have obtained crystals of the protein that diffract to beyond 2.5 A (1 A = 0.1 nm) resolution. The crystals are orthorhombic with unit cell dimensions of a = 80.1 A, b = 67.5 A and c = 38.0 A.

SPXX, a frequent sequence motif in gene regulatory proteins

A new DNA-binding unit, composed of four amino acid residues and common in gene regulatory proteins, is proposed. The occurrences of the sequences Ser-Pro-X-X (SPXX) and Thr-Pro-X-X (TPXX) in gene regulatory proteins are compared with those in general proteins. These sequences are found more frequently in gene regulatory proteins including homoeotic gene products, segmentation gene products, steroid hormone receptors and certain oncogene products, than they are in DNA-binding proteins that are not directly involved in gene regulation, such as the core histones, or in general proteins. It is therefore suggested that these sequences contribute to DNA-binding in a manner important for gene regulation. Amino acid residues characteristic of the types of proteins are found as the variable residues X: basic residues, Lys and Arg, in histones, H1 and sea urchin spermatogenous H2B; Tyr in RNA polymerase II; and Ser, Thr, Ala, Leu and Pro in other gene regulatory proteins S(T)PXX sequences are located on either side of other DNA-recognizing units such as Zn fingers, helix-turn-helices, and cores of histones. The structure of a S(T)PXX sequence is presumed to be a beta-turn I stabilized by two hydrogen bonds, and its potential mode of DNA-binding is discussed.

The phosphorylation site of Ca(2+)-dependent protein kinase from alfalfa

A 50 kDa, calcium-dependent protein kinase (CDPK) was purified about 1000-fold from cultured cells of alfalfa (Medicago varia) on the basis of its histone H1 phosphorylation activity. The major polypeptide from bovine histone H1 phosphorylated by either animal protein kinase C (PK-C) or by the alfalfa CDPK gave an identical phosphopeptide pattern. The phosphoamino acid determination showed phosphorylation of serine residues in histone H1 by the plant enzyme. Histone-related oligopeptides known to be substrates for animal histone kinases also served as substrates for the alfalfa kinase. Both of the studied peptides (GKKRKRSRKA; AAASFKAKK) inhibited phosphorylation of H1 histones by bovine and alfalfa kinases. The results of competition studies with the nonapeptide (AAASFKAKK), which is a PK-C specific substrate, suggest common features in target recognition between the plant Ca(2+)-dependent kinase and animal protein kinase C. We also propose that synthetic peptides like AAASFKAKK can be used as a tool to study substrates of plant kinases in crude cell extracts.

Reconstitution of chromatin higher-order structure from histone H5 and depleted chromatin

Reconstitution of the 30 nm filament of chromatin from pure histone H5 and chromatin depleted of H1 and H5 has been studied using small-angle neutron-scattering. We find that depleted, or stripped, chromatin is saturated by H5 at the same stoichiometry as that of linker histone in native chromatin. The structure and condensation behavior of fully reconstituted chromatin is indistinguishable from that of native chromatin. Both native and reconstituted chromatin condense continuously as a function of salt concentration, to reach a limiting structure that has a mass per unit length of 6.4 nucleosomes per 11 nm. Stripped chromatin at all ionic strengths appears to be a 10 nm filament, or a random coil of nucleosomes. In contrast, both native and reconstituted chromatin have a quite different structure, showing that H5 imposes a spatial correlation between neighboring nucleosomes even at low ionic strength. Our data also suggest that five to seven contiguous nucleosomes must have H5 bound in order to be able to form a higher-order structure.

Generation of different nucleosome spacing periodicities in vitro. Possible origin of cell type specificity

We have been able to generate ordered nucleosome arrays that span the physiological range of spacing periodicities, using an in vitro system. Our system (a refinement of the procedure previously developed) uses the synthetic polynucleotide poly[d(A-T)], poly[d(A-T)], core histones, purified H1, and polyglutamic acid, a factor that increases nucleohistone solubility and greatly promotes the formation of ordered nucleosome arrays. This system has three useful features, not found in other chromatin assembly systems. First, it allowed us to examine histones from three different cell types/species (sea urchin sperm, chicken erythrocyte, and HeLa) as homologous or heterologous combinations of core and H1 histones. Second, it allowed us to control the average packing density (core histone to polynucleotide weight ratio) of nucleosomes on the polynucleotide; histone H1 is added in a second distinct step in the procedure to induce nucleosome alignment. Third, it permitted us to study nucleosome array formation in the absence of DNA base sequence effects. We show that the value of the spacing periodicity is controlled by the value of the initial average nucleosome packing density. The full range of physiological periodicities appears to be accessible to arrays generated using chicken erythrocyte (or HeLa) core histones in combination with chicken H5. However, chromatin-like structures cannot be assembled for some nucleosome packing densities in reactions involving some histone types, thus limiting the range of periodicities that can be achieved. For example, H1 histone types differ significantly in their ability to recruit disordered nucleosomes into ordered arrays at low packing densities. Sea urchin sperm H1 is more efficient than chicken H5, which is more efficient than H1 from HeLa or chicken erythrocyte. Sea urchin sperm core histones are more efficient in this respect than the other core histone types used. These findings suggest how different repeat lengths arise in different cell types and species, and provide new insights into the problems of nucleosome linker heterogeneity and how different types of chromatin structures could be generated in the same cell.

A new h.p.l.c. isolation procedure for chicken and goose erythrocyte histones

Total chicken erythrocyte histones were separated by reversed-phase h.p.l.c. using a multi-step acetonitrile gradient in a very short time (35 min). The proteins were eluted in the following order: H1, H5, H2B, H2A.2, H4, H2A.1 and H3.2. Applying a special gradient system adapted for the separation of very-lysine-rich histones, chicken erythrocyte H5 was resolved into two subfractions. Their electrophoretic mobilities were identical in both SDS and acetic acid/urea/Triton polyacrylamide-gel electrophoresis, but different in free-flow electrophoresis. Amino-acid-sequence analyses revealed that the two components only differ with respect to position 15, one having glutamine in that position and the other arginine. A separation of histones prepared from goose erythrocytes disclosed no H5 subfractionation. Furthermore, histones obtained from anaemic-chicken blood were analysed by the above-mentioned h.p.l.c. conditions. An alteration in the relation of H1 to H5 was detected, but no further differences in the number and quantity of the histones and histone variants were observed as compared with the corresponding proteins processed from normal-chicken blood.

Histone H1 heterogeneity in the midge, Chironomus thummi. Structural comparison of the H1 variants in an organism where their intrachromosomal localization is possible

1. Seven subfractions of histone H1 have been isolated and purified from larvae of Chironomus thummi (Diptera). They have been denominated I-1, II-1, II-2, II-3, III-1, III-2, and III-3, according to the order of migration in two steps of preparative electrophoresis. 2. The amino acid compositions are similar to those of other H1 histones. Subfractions I-1 and II-1 were found to contain one methionine and two tyrosine residues, II-2 contained two methionine and three tyrosine residues, and III-1 one methionine and three tyrosine residues. The other subfractions contained one or two methionine and two or three tyrosine residues. For subfractions I-1 and II-1 a chain length of about 252 amino acids was estimated. 3. Peptide pattern analyses after chemical cleavage at the methionine and tyrosine residues, and enzymatic cleavage with thrombin and chymotrypsin, respectively, showed that all subfractions have different individual primary structures. A comparison of peptide sizes and of the positions in the peptide patterns of epitopes recognized by monoclonal antibodies was made to check whether some of the subfractions could arise by proteolytic degradation of others. This possibility can be excluded for five of the subfractions and is very improbable for the two others. Treatment of C. thummi H1 with alkaline phosphatase did not change the pattern of subfractions, while the phosphorylated subfraction of histone H2A disappeared after this treatment. Most and very probably all subfractions are thus H1 sequence variants. 4. Inbred strains and individual larvae of C. thummi were found to comprise all seven variants. The H1 heterogeneity can therefore not be due to allelic polymorphism. Salivary gland nuclei were found to contain variant I-1 and at least some of the other variants. 5. H1 from Drosophila melanogaster and from calf thymus were used as reference molecules in all cleavage experiments and yielded the peptide patterns expected from the sequence. The comparison discriminates the group of C. thummi H1 histones clearly from Drosophila and calf thymus H1. Limited trypsin digestion yielded a protected peptide of uniform size in six of the seven variants which was considerably smaller than the protected central domain of calf thymus H1. 6. Two other species of Chironomidae, C. pallidivittatus and Glyptotendipes barbipes were found to contain five and three H1 subfractions, respectively.(ABSTRACT TRUNCATED AT 400 WORDS)

Homology of histone H1 variants with adenine nucleotide-binding proteins

Significant homology was observed between the adenine nucleotide-binding domain in the catalytic subunit of bovine protein kinase A and the carboxy-terminal half of the globular domain of histone H1. A consensus sequence deducible from several previously characterized adenine nucleotide-binding sites is totally conserved in H1. In addition, several putative phosphate binding-sites were observed within the carboxyterminal tail and one in the cluster of basic amino acids in the aminoterminal tail. Both the putative adenine and phosphate-binding sites are well conserved through evolution in various species and in different H1 variants. The present data thus suggest that histone H1 variants may bind to adenine derivatives and imply that they may recognize a specific nucleotide sequence in DNA.

Monoclonal autoantibodies recognizing histone variants

Balb/c mice were immunized with affinity purified Ro(SS-A) from human origin in order to allow the preparation of monoclonal anti-Ro(SS-A) antibodies. After fusion of mouse myeloma cells (line Sp2/0 A914) with spleen cells from one of these mice, anti-Ro(SS-A) monoclonals were not obtained, but, instead, two IgM producing hybridomas reactive with histone H1 and one with histone H2B. The specificity of the anti-H1 monoclonals was investigated by means of immunoblotting of very lysine-rich histone variants from mouse which were separated by two-dimensional gelelectrophoresis. One of them (CLB-ANA 105) has H1(0) specificity with respect to the histone variants of mouse and man, but recognizes H5 as well as H1 from Xenopus laevis. Another monoclonal (CLB-ANA 108) reacts with the variant H1c from mouse, exclusively. From the way these monoclonals were produced, we postulate that they were not the result of immunization, but comprise specificities of naturally occurring autoantibodies.

Immunological relationships among vertebrate lysine-rich histones

1. The relationship between sequence homology and immunological cross-reaction was investigated by enzyme-linked immunosorbent assay and immunoblotting using polyclonal antisera against lysine-rich histones (LRH) of known sequence, chicken H1 and H5, trout Hl and Xenopus H1s. 2. The order of immunological relatedness was consistent with known homologies among these LRH and goose H5, but quantitative correlations reflected varied locations of antigenic determinants. 3. When immunoblotting was extended to LRH from eight more vertebrates, it was evident that avian H5, mammalian H1o and anuran H1s form a sub-class, to which turtle H1s may belong, that urodele erythrocytes contain no H5-like histone and that fish "H5" is more like H1 than the H5/H1s/H1o subclass.

Genes for chromosomal proteins expressed before and after meiosis

Cloned gene sequences have been isolated for two testis-specific chromosomal proteins, one of which, histone (H1t), appears during meiosis, whereas the other, transition protein 1 (TP1), appears only during the later steps of spermatid development. Aspects of the regulation of each gene have been examined. In the case of H1t, analysis of its promoter region shows that it contains excellent matches to each of the four sequence homologies identified for the usual somatic H1 variants, so that the factor(s) that restrict H1t expression to spermatocytes remain a mystery. In the case of TP1, a cDNA clone allowed identification of its message by Northern blots as well as by in situ hybridization. The message appears postmeiotically in late round spermatids but is translationally repressed until the spermatid nucleus begins to condense.

Use of protein blotting to study the DNA-binding properties of histone H1 and H1 variants

Sub-types of histone H1 have been observed in a variety of tissues from several organisms. One of the best characterized H1 variants is H5 from avian erythrocytes. Several lines of evidence suggest that H5 has a greater affinity for DNA than H1 and is thus thought to account, in part, for the highly condensed and transcriptionally repressed state of avian erythrocyte chromatin. In trout there is an analogous erythrocyte-specific H1 variant, previously termed 'H5' [B.L.A. Miki and J.M. Neelin (1975) Can. J. Biochem. 53, 1158-1169). Using a sensitive and rapid protein-blotting procedure which is specific amongst the histones for histone H1 and its variants, we compared DNA-binding properties of the trout erythrocyte histone 'H5' and chicken H5. By increasing the NaCl concentration of the binding buffer, a gradual decrease in the amount of DNA that bound to chicken H1, trout H1 and trout erythrocyte 'H5' variant was observed, such that at concentrations above 0.37 M, negligible amounts of DNA were bound. By contrast, chicken H5 bound a significantly greater amount of DNA even at a concentration of 0.4 M NaCl. Based on the DNA-binding, properties, we conclude that the trout erythrocyte variant 'H5' is more closely related to H1 than to H5. By assaying the DNA-binding affinity of calf thymus H1 DNA-binding affinity of calf thymus H1 peptide fragments, generated by protease and chemical cleavage, and the sperm-specific H1 variants of the annelid, Platynereis dumerilii, which possess greatly shortened C-terminal tails, we conclude that a domain that includes a very small portion of the C-terminal tail and part of the globular domain is sufficient for the binding of H1 to DNA.

Microheterogeneity in H1 histones and its consequences

The extent of microheterogeneity of H1 histones in individual higher organisms, without considering post-translational modifications, is such that five to eight molecular species can be recognized. The H1 variants differ among themselves in their ability to condense DNA and chromatin fragments, and they are non-uniformly distributed in chromatin. This review assembles data that support the notion that the differences in chromatin condensation (heterochromatization) observed through the microscope are maintained by the non-uniform distribution of H1 variants, and that this pattern of chromatin condensation may determine the dynamics of chromatin during replication and may represent the commitment aspect of differentiation. The differential response of the multiple H1 variants with regard to their synthesis and turnover is consistent with this notion.

Molecular cloning of a pea H1 histone cDNA

A pea (Pisum sativum, var. Little Marvel) H1 histone cDNA has been isolated from a lambda gt11 expression vector library. This cDNA has been sequenced and shown to represent the entire protein-coding region of the mRNA. The deduced protein sequence is 265 amino acids long (28018 Da) and contains 70 lysines and 3 arginines. The structure of the encoded protein is comparable to animal lysine-rich histones. The central region, which has an amino acid composition similar to that found in the globular domains of animal lysine-rich histones, is flanked by an amino-terminal region rich in lysine, glutamic acid and proline and by a carboxyl-terminal region rich in lysine, alanine, valine and proline. Despite the structural similarities, the protein has little sequence homology with animal lysine-rich histones. This H1 protein is unusual because 12 of the first 40 amino acids are glutamic acid.

Predictability of sequence homologies among lysine-rich histones by immunological distance

The relationship between immunological distance (I.D.) measured by microcomplement fixation and amino acid sequence difference for lysine-rich histones was tested using antisera to lysine-rich histones of known sequence, chicken H1 and H5, goose H5, and trout H1 as well as to trout H5. The best relationship between I.D. (y) and percent sequence difference (x) for lysine-rich histones, y = 2x, applies as well to other histones of known sequence but it differs from y = 5x, reported for other proteins and often used for histones. Although deviations indicate that I.D. is a poor predictor of primary sequence differences among histones, it suggests that trout H5 is more closely related to H1 than to chicken H5.

Characterization of mouse H3.3-like histone genes

We designed a strategy to select genomic clones of mouse replication-independent H3.3 histone genes. We obtained three clones which met our selection criteria for being H3.3 genes. Upon sequencing two of these clones we found that they were unlike previously isolated chicken H3.3 clones: they code for several unpredicted amino acid substitutions and contain no introns in the coding regions. We showed by S1 nuclease assays that these genes are protected by mRNAs that have expression characteristics of H3.3 mRNA. The protection data and nucleotide sequence analysis show that the H3.3 transcripts can be processed at one of four cleavage/polyadenylation sites. We show that these genes probably evolved through reverse transcription intermediates, and are processed pseudogenes which are no longer under selective pressure. The 5' and 3' transcribed, nontranslated sequences show extensive homology to those of a human cDNA clone, and we suggest that these sequences may be required for appropriate regulation of expression of H3.3 genes.

H1(0) histones of normal and cancer human cells. Amino acid composition of H1 purified by polyacrylamide gel electrophoresis

H1 histones were purified by preparative sodium dodecyl sulfate polyacrylamide gel electrophoresis from human lung carcinoma (line DMS79), human hepatoblastoma (HepG2), human adult lung and human adult and fetal liver. The purified human H1 histones were analyzed for their amino acid composition and terminal residues. The comparative analysis of the amino acid compositions of the different human H1 histones showed that: all the H1 preparations have the characteristically high lysine content associated with a low arginine content, which distinguishes outer histones from core histones; H1 is distinguishable from other H1 histones by the presence of methionine and histidine; H1 histones from human adult, fetal and cancer cells are very similar in amino acid composition, and in cancer cells the level of the H1 histone is not inversely related with cell growth rate nor with the expression of the alpha-fetoprotein gene.

Effect of exogenous histone H5 on integration of histone H1 in rat liver chromatin. Correlations with aberrant epsilon-N-methylation of histone H1

Binding modes of histones H1 and H5, and their competition for chromatin-binding sites in rat liver nuclei, were correlated with aberrant N-methylation of H1 histone lysine residues, induced by chicken erythrocyte histone H5, in order to gain more insight into the integration of lysine-rich histones in chromatin. Addition of approx. 2.5 molecules of histone H5 per nucleosome to rat liver nuclei increases the ratio of total basic residues in histones to DNA nucleotides (BR/NT) in the nuclear chromatin from 1.0 to 1.5. At this concentration, approx. 0.7 molecule of histone H5 is bound per nucleosome, and there is no displacement of histone H1 from the nuclear chromatin. If S-adenosyl[Me-3H]methionine is present in the incubation mixture, the aberrant incorporation of labeled methyl groups into histone H1 reaches a maximum at this concentration of histone H5. The radioactivity present in histone H1 from nuclei incubated with labeled AdoMet at a total BR/NT ratio of 1.5: resides mainly in a histone H1 subfraction tentatively identified by Bio-Rex 70 chromatography and acrylamide gel electrophoresis as histone H1c; presents as a single spot upon peptide mapping of tryptic hydrolysates by means of two-dimensional thin-layer chromatography; and elutes in the position of mono-N-methyllysine upon ion-exchange chromatography of histone H1 hydrolysates. Upon further increase of the BR/NT ratio, the following changes are produced: a gradual decrease in radioactive methyl uptake into histone H1; a gradual displacement of histone H1 from the chromatin; increased binding of histone H5 in chromatin, up to a maximum of 3.4 residues per nucleosome; and a slowly increasing uptake of label into histone H5. The combined data from histone H1/H5 binding and histone H1 methylation studies suggest that upon addition of exogenous histone H5 to rat liver nuclei the binding of two lysine-rich histones per nucleosome plays a significant role in the induction of specific changes in chromatin structure, which in vivo may have important functional implications in terms of chromatin condensation and suppression of transcription.

Differential distribution of lysine and arginine residues in the closely related histones H1 and H5. Analysis of a human H1 gene

A human H1 histone gene and its flanking sequences were isolated from a human gene library using a fragment of the duck H5 histone gene as a hybridization probe. The primary structure of this human H1 histone (as deduced from the nucleotide sequence of the gene) reveals a close homology of H1 and H5 histones and fits the three-domain organization of all members of the H1 histone family. Within this protein organization, the C-terminal domain of H1 differs from the arginine-rich H5 in its distribution of the basic amino acids: the C-terminal domain of the human H1 shows only one arginine and most of the H5 specific arginine positions show lysine instead.

Histones and their modifications

Histones constitute the protein core around which DNA is coiled to form the basic structural unit of the chromosome known as the nucleosome. Because of the large amount of new histone needed during chromosome replication, the synthesis of histone and DNA is regulated in a complex manner. During RNA transcription and DNA replication, the basic nucleosomal structure as well as interactions between nucleosomes must be greatly altered to allow access to the appropriate enzymes and factors. The presence of extensive and varied post-translational modifications to the otherwise highly conserved histone primary sequences provides obvious opportunities for such structural alterations, but despite concentrated and sustained effort, causal connections between histone modifications and nucleosomal functions are not yet elucidated.

Homologies and anomalies in primary structural patterns of nucleotide binding proteins

In searches for homology among nucleotide binding proteins, recent reports have described primary structure alignments for stretches of 30 or so amino acid residues among a variety of proteins including the ras and src oncogene products. The significance of these sequence matches has been tested by searching in available data banks for certain conserved residue patterns resulting from the alignments. The tests suggest that alignments over these limited stretches are not necessarily justifiable and any implications for residues involved in nucleotide binding must be viewed with caution.

Involvement of the histidine residues in the pH-induced conformational change of histone H5

Comparative studies on the conformational stability of histones H1 and H5 have been carried out by monitoring the pH-induced conformational transitions of the proteins by CD and 1H NMR spectroscopies. The transition point of H1 agrees with the pKa of the carboxyl groups of the acidic residues. In contrast, the transition of H5 is associated with the ionization of the histidine residues which exist exclusively in H5, as well as the deionization of the acidic residues. These observations, combined with the result of the deuterium exchange rates of the histidine C-2 protons, led us to conclude that His-25 and His-62, which are buried in the globular domain, play an important role in the conformational stability of histone H5.

Modification of the lysine residues of histones H1 and H5: effects on structure and on the binding to chromatin

The extensive modification of histone H1 from calf thymus with the amino-group reagent dimethylmaleic anhydride (over 35 lysine residues modified per molecule) produces no effect on its secondary structure detectable by circular dichroism (far UV). Fluorescence and circular dichroism (near-UV) of the modified histone show variations in the local environment of its sole tyrosine residue. These changes are reversed on regeneration of the modified amino groups. While histone H1 is easily dissociated with this reagent from calf thymus or chicken erythrocyte chromatin, a much stronger treatment is needed to liberate histone H5 from erythrocyte chromatin. This difference appears to be related to the higher arginine content of histone H5.

Phosphorylation of sea urchin sperm H1 and H2B histones precedes chromatin decondensation and H1 exchange during pronuclear formation

Immediately following fertilization in the sea urchin, sperm-specific histones Sp H1 and Sp H2B are phosphorylated. Then, in parallel with chromatin decondensation, nearly all phosphorylated Sp H1 is lost from the pronuclear chromatin, with the concurrent assimilation of the egg phosphoprotein CS H1. Chemical cleavage of in vivo labeled Sp H1 and Sp H2B shows that serine phosphorylation occurs in the unusually long N-terminal region of these proteins. These regions contain tandemly repeated tetra- and pentapeptide units each containing serine, proline, and two basic amino acids. It is proposed that sperm chromatin decondensation may require prior phosphorylation of these unusual N-terminal regions, whose function in the mature sperm may be to condense or stabilize its highly compact chromatin.

Conserved dyad symmetry structures at the 3' end of H5 histone genes. Analysis of the duck H5 gene

The duck H5 histone gene and its flanking DNA have been isolated and sequenced. S1 nuclease mapping reveals that transcription starts 149 nucleotides upstream of the initiation codon and that the site of polyadenylation is located 200 nucleotides downstream of the termination codon. A comparison with the chicken H5 gene demonstrates that the 3' non-translated segment of the polyadenylated H5 mRNA carries two conserved dyad symmetry sequences. The first potential hairpin is located directly after the termination codon of the H5 gene and is highly conserved, whereas the second stem and loop structure maps shortly upstream of the polyadenylation site and shows a homology block at the central part of this inverted DNA repeat.

Involvement of the globular domain of histone H1 in the higher order structures of chromatin

We have attacked H1-containing soluble chromatin by alpha-chymotrypsin under conditions where chromatin adopts different structures. Soluble rat liver chromatin fragments depleted of non-histone components were digested with alpha-chymotrypsin in NaCl concentrations between 0 mM and 500 mM, at pH 7, or at pH 10, or at pH 7 in the presence of 4 M-urea. alpha-Chymotrypsin cleaves purified rat liver histone H1 at a specific initial site (CT) located in the globular domain and produces an N-terminal half (CT-N) which contains most of the globular domain and the N-terminal tail, and a C-terminal half (CT-C) which contains the C-terminal tail and a small part of the globular domain. Since in sodium dodecyl sulfate/polyacrylamide-gel electrophoresis CT-C migrates between the core histones and H1, cleavage of chromatin-bound H1 by alpha-chymotrypsin can be easily monitored. The CT-C fragment was detected under conditions where chromatin fibers were unfolded or distorted: under conditions of H1 dissociation at 400 mM and 500 mM-NaCl (pH 7 and 10); at very low ionic strength where chromatin is unfolded into a filament with well-separated nucleosomes; at pH 10 independent of the ionic strength where chromatin never assumes higher order structures; in the presence of 4 M-urea (pH 7), again independent of the ionic strength. However, hardly any CT-C fragment was detected under conditions where fibers are observed in the electron microscope at pH 7 between 20 mM and 300 mM-NaCl. Under these conditions H1 is degraded by alpha-chymotrypsin into unstable fragments with a molecular weight higher than that of CT-C. Thus, the data show that there are at least two different modes of interaction of H1 in chromatin which correlate with the physical state of the chromatin. Since the condensation of chromatin into structurally organized fibers upon raising the ionic strength starts by internucleosomal contacts in the fiber axis (zig-zag-shaped fiber), where H1 appears to be localized, it is likely that in chromatin fibers the preferential cleavage site for alpha-chymotrypsin is protected because of H1-H1 contacts. The data suggest that the globular part of H1 is involved in these contacts close to the fiber axis. They appear to be hydrophobic and to be essential for the structural organization of the chromatin fibers.(ABSTRACT TRUNCATED AT 400 WORDS)

A survey of H1o-and H5-like protein structure and distribution in higher and lower eukaryotes

A survey of H1o and H5-like proteins has been conducted through a range of higher and lower eukaryotic species. All mammals examined possessed H1o proteins, although in variable amounts, and the protein's structure was well conserved, though not invariant. The testis-specific histone Hlt (from rat) did not have an H1o-like structure and it appears that H1o does not occur in spermatocytes in any form. The results also show that Xenopus laevis contains H1o-like proteins, but lower, non-vertebrate eukaryotes (a crustacean, two fungi and a plant tissue) do not possess H1o or H5 proteins. The evidence suggests that H1o and H5 proteins may be considered as belonging to one family, distinct from H1 types. This H1o/H5 family may well be 'replacement histone' variants of H1. The results do not support suggestions of roles such as repression of DNA synthesis or of transcription for H1o/H5 proteins.

Isolation from trout liver of a methionine-containing H1 subfraction, THImet

A trout H1 subfraction, THImet, which contains one residue of methionine and a blocked N-terminal amino acid, has been isolated from trout liver. Cyanogen bromide cleavage of THImet and amino acid analysis and polyacrylamide gel electrophoresis of the cleavage products show that it contains a residue of methionine at about the same distance from the N terminus as mammalian H1o and avian H5. THImet is shown to be similar to, but not identical with, the protein derived from trout erythrocytes generally accepted as the equivalent in fish of avian H5.

Involvement of the domains of histones H1 and H5 in the structural organization of soluble chromatin

We have studied in reconstitution experiments the conditions under which peptides derived from histones H1 and H5 are bound in chromatin and to what extent they are involved in the organization of chromatin fibers. The fragments of rat liver histone H1 (rH1) and chicken erythrocytes H1 (cH1) and H5 (cH5) used were the globular domains (rG-H1, cG-H1, cG-H5), the globular domain and the N-terminal tail (rCT-N), about half of the globular domain and the C-terminal tail (rNBS-C) and the C-terminal tail (rCT-C). Fragments containing the C-terminal tail (rNBS-C and rCT-C) dissociate from H1-depleted rat liver chromatin at 300 mM-NaCl and above (similar to uncleaved H1) and fragments lacking the C-terminal tail (rG-H1 and rCT-N) dissociate between 100 and 200 mM-NaCl. This suggests that at putative physiological ionic strengths the binding of rH1 is dominated by its C-terminal tail, whereas the globular region and the N-terminal tail might only be loosely bound or not bound at all and by this modulate chromatin structure. The globular domain of cH5 binds more tightly than that of the chicken and rat H1 and is only partially released at 200 mM. Since in the transcriptionally silent erythrocytes of birds H5 replaces H1 to a large extent, we suggest that the globular domain of H1 serves as a temporary seal and that of H5 as a permanent seal of the nucleosome. All the H1 and H5 peptides tested condensed and precipitated chromatin and H1-depleted chromatin: rNBS-C and rCT-C at lower peptide per nucleosome ratios than rG-H1, cG-H1 and rCT-N. At about one peptide per nucleosome none of the H1 fragments induced condensation similar to that of native chromatin. At a peptide per nucleosome ratio close to the point of precipitation, all H1 fragments, but not poly-L-lysine, induced similar compact forms which were fiberlike, although more irregular than the compact fibers of native chromatin. These reconstitution experiments suggest that both halves of H1 as well as the globular domain by itself are involved and capable in forming higher-order chromatin structures. Details of these structures are not known.

Nucleotide sequences of H1 histone genes from Xenopus laevis. A recently diverged pair of H1 genes and an unusual H1 pseudogene

Four clones containing H1 histone gene sequences were previously isolated from a Xenopus laevis genomic library (1) and we now present the complete nucleotide sequences of these H1 genes and their flanking regions. Two of these genes code for minor H1 proteins, probably H1C, when expressed in the oocyte transcription/translation system and are present on clones with almost identical overall organization. However, at the nucleotide level these genes differ in showing base insertions and deletions, as well as substitutions. A third gene sequence which is more related to the major X. laevis H1A, corresponds to the 3' two thirds of an H1 gene. This gene has in place of a 5' coding region at least 1800 bp of apparently noncoding sequence, some of which is A-T rich. The junction does not correspond to the consensus sequence of an intron/exon boundary and therefore this H1 sequence is more likely to represent a pseudogene. Comparisons of the coding and flanking regions of these X. laevis H1 genes indicate the kind of differences which can occur among H1 subtypes within a species. A region of homology noted in the 3' noncoding portion of vertebrate histone genes is discussed in relation to the mechanism of termination of transcription.

Coomassie Blue R-250 metachromatic staining of histone 5 from goose and chicken erythrocytes

1. Histone 5 stains metachromatically with Coomassie Blue R-250, a property shared only with collagens and procollagens, histones 1 and 2B, and possibly certain proline-rich salivary gland proteins. 2. Coomassie Blue-stained goose and chicken H5 induce the same degree of metachromasia, which is intermediate between that induced by H1 and H2b. 3. The absorption spectra of all Coomassie Blue-stained gel bands consist of a primary maximum at 555 nm, but the absorption spectra of H5 gel bands also include a prominent shoulder in the vicinity of 525 nm, a region in which H1 gel bands display a secondary maximum. 4. The possible role of proline-rich sequences in the induction of metachromasia is discussed.

Localization of histone H5 in the subunit organization of chromatin using immunoelectron microscopy

In avian erythroid cells the erythrocyte-specific histone H5 is involved, like H1, in the packing of nucleosomes in the 25-nm chromatin fibers. In this study the distribution of histone H5 along the polynucleosomal chains was visualized by immunoelectron microscopy. Trinucleosomes from chicken erythrocytes and liver were used in order to test the specificity of the reaction with purified rabbit anti-H5 antibodies at various ionic strengths (5-80 mM). Long-chain chromatin was then reacted with anti-H5 antibodies and with sorted monomeric ferritin conjugate under chosen conditions. The antigenic determinants of histone H5 in the 25-nm fiber of long-chain chromatin (at 80 mM NaCl) are as accessible to the specific antibodies as in trinucleosomes. When the immunocomplexes were examined by electron microscopy in a low-ionic-strength buffer, permitting maximum extension of the chromatin structure on the grid, clusters of compacted nucleosomes were seen, separated by short regions of relaxed nucleosomes. Single nucleosomes enlarged by the antibodies are sometimes visible in the extended domains. We conclude that histone H5 is located primarily on series of adjacent nucleosomes but it can also be found on single nucleosomes located in the H1-enriched extended domains.