Extension of the Amino Acid Sequence of a Lysine-rich Histone

Characterization of the mitotic specific phosphorylation site of histone H1. Absence of a consensus sequence for the p34cdc2/cyclin B kinase

32P-Labeled histone H1 was isolated from synchronized Chinese hamster (line CHO) cells, subjected to tryptic digestion, and fractionated into 15 phosphopeptides by high performance liquid chromatography. These phosphopeptides were grouped into five classes having different cell cycle phosphorylation kinetics: 1) peptides reaching a maximum phosphorylation rate in S and then declining in G2 and M, 2) peptides reaching a maximum phosphorylation rate in G2 and then remaining constant or declining in M, 3) peptides with increasing phosphorylation throughout S and G2 and reaching a maximum in M, 4) one peptide that was phosphorylated only in M, and 5) peptides that had low levels of phosphorylation that remained constant throughout the cell cycle. Amino acid analysis and sequencing demonstrated that the mitotic specific H1 phosphopeptide was the 16-amino acid, N-terminal, tryptic peptide Ac-SETAPAAPAAAPPAEK of the H1-1 class. This peptide, which is phosphorylated on both the Ser and Thr, does not contain the consensus sequence (S/T)PXZ (where X is any amino acid and Z is a basic amino acid). This sequence is thought to be required by the p34cdc2/cyclin B kinase that has maximum phosphorylating activity in mitosis. These data indicate that this kinase either does not have an obligatory requirement for the consensus sequence in vivo as generally believed or that it is not the enzyme responsible for the mitotic specific H1 phosphorylation.

Antimicrobial proteins of murine macrophages

Three murine microbicidal proteins (MUMPs) were purified from cells of the murine macrophage cell line RAW264.7 that had been activated by gamma interferon. Similar proteins were also present in nonactivated RAW264.7 cells, in cells of the murine macrophage cell line J774A.1, and in resident and activated murine peritoneal macrophages. MUMP-1, MUMP-2, and MUMP-3 killed Salmonella typhimurium, Escherichia coli, Staphylococcus aureus, Listeria monocytogenes, Mycobacterium fortuitum, and Cryptococcus neoformans in vitro. MUMP-1 resembled an H1 histone but was unusual because its N-terminal residue (serine) was not N acetylated. Although MUMP-2 was N terminally blocked, its high lysine/arginine ratio and its reactivity with an antibody to H1 histones suggested that it also belonged to the H1 histone family. MUMP-3 was identical to histone H2B in 30 of 30 amino-terminal residues. Although the antimicrobial properties of histones have been recognized for decades, this is the first evidence that such proteins may endow the lysosomal apparatus of macrophages with nonoxidative antimicrobial potential. Other MUMPs, including some with a more restricted antimicrobial spectrum and one that appeared to be induced in RAW264.7 cells after gamma interferon stimulation, were noted but remain to be characterized.

Histone H1a subtype presents structural differences compared to other histone H1 subtypes. Evidence for a specific motif in the C-terminal domain

Following a previous isolation by reverse-phase HPLC of five histone H1 subtypes from adult rat liver, purity of three of them, H1a, H1b and H1d (according to Lennox's nomenclature), was achieved. Structural features of these three subtypes were investigated. Partial cleavage of these subtypes by endoproteinase Glu-C showed a different behavior of the H1a subtype when compared to the H1b and H1d subtypes. Under the conditions used in this work, the H1b and H1d subtypes present three major sites accessible to the endoproteinase Glu-C, while the H1a subtype presents only one major site accessible to the proteinase. Partial N-terminal sequence of the different fragments obtained after proteolysis indicated that the two H1b and H1d subtypes were cleaved inside the globular domain (Glu-54,-75) and between the globular domain and the C-terminal one (Glu-116). The H1a subtype was only cleaved between the globular domain and the C-terminal tail (Glu-116), though Glu-54 and Glu-75 sites were present. These results would suggest some differences in the conformation of these proteins. Furthermore, the partial determined sequences of H1b and H1d showed 85% similarity to each other (the main differences were threonine residues instead of alanine residues in the C-terminal domain) while H1a was only 60% similar to H1b and H1d, for the sequences which aligned. The strongest differences between the H1a subtype and the two other subtypes were observed in the first amino acid residues of the C-terminal domain. The 117-126 amino acid residues (SKASTTKVTV) of H1a were quite different from those of H1b and H1d. This sequence, which showed a number of serine and threonine residues, was not found in any other histone sequence, after consultation with data bases. This H1a subtype was a minor component in adult liver (2.4%). As it was described in testis as a major component, testis histone H1 proteins were fractionated onto reverse-phase HPLC under the same conditions as those used for histone H1 proteins from liver. The pure testis H1a fraction was submitted to the endoproteinase Glu-C digestion. The pattern digestion was the same as that observed for liver H1a. The two 44-76 and 117-126 determined amino acid residues of H1a from testis were strictly identical to those of liver H1a. We demonstrate that H1a is the same protein in liver and testis and we give evidence for a specific motif SKASTTKVTV (117-126 residues) in the sequence of the C-terminal domain.(ABSTRACT TRUNCATED AT 400 WORDS)

Conformational calculations on the Ala14-Pro27 LC1 segment of rabbit skeletal myosin

In order to define the conformational characteristics of a singular Ala14-Pro27 segment in myosin LC1, conformational calculations were performed using the Simplex algorithm of Nelder and Mead (Computer J. 7 (1965) 308-313) in the ACME program proposed by Tournarie (J. Appl. Cryst. 6 (1973) 309-346). The (Ala-Pro) n = 1 unit was assigned a given conformation x; the conformation energy was then minimized for n = 1 to n = 7 by adjusting structural parameters (angle values). Similarly, 13 different possible conformations were optimized and compared, showing that a (beta 2R)7 conformation is favored by about 20 kcal per mol over the next most probable conformation (C7R)7. In the beta 2R conformation, the (Ala-Pro)7 segment is a wide helix, 15 A in length and 8.65 A in diameter, while the C7R conformation results in a semi-extended structure of 25 A long, with an approximate diameter of 6 A. These characteristics are in agreement with available experimental data and putative functions of the LC1 N-terminus.

Isolation and characterisation of five histone H1 subtypes from adult rat liver

A procedure is described for quantitative purification of H10 and five H1-1 subtypes--named H1-1a to e--from adult rat liver by reverse-phase high-pressure liquid chromatography. Milligram amounts of each fraction have been obtained. The H1-1a subtype shows a very high lysine content (34%) and H1-1d subtype has an amino-acid composition close to that of H10, but its electrophoretic mobility is different. Salt dependent folding of these subtypes has been studied by circular dichroism. In the presence of 2 or 10 mM sodium phosphate buffers at pH 7.5, H1-1a shows the lowest alpha-helix content. In phosphate-buffer containing 1 M NaCl the number of residues in alpha-helix for all the subtypes rises to 9-10%. Partial cleavage of these subtypes by endoproteinase Glu-C produce three main peptides arising from C-terminal domains. The interaction of the H1-1 subtypes with 196 basepairs linear DNA, purified from rat liver chromatin by high-pressure ion-exchange liquid chromatography, has for consequences a modification of the patterns of digestion: partial proteolysis of the H1-1a and H1-1b subtypes shows differences in the presence or in absence of DNA; on the contrary, H1-1c and H1-1d seem to have the same organization. So these subtypes may play a role in the differential packing of specific region of chromatin.

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.

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.

Action of mercurials on activity of partially purified soluble protein kinase C from mice brain

The enzymatic activity of soluble protein kinase C from mice brain was inhibited by mercuric chloride (II) (HgCl2) and organic mercurials, i.e. methyl mercury, phenyl mercury and p-chloromercuribenzoic acid (PCMB). The IC50 was 0.08 microM for HgCl2 and about 1 microM for organic mercurials. Sulfhydryl blocking reagents such as 5,5'-dithiobis-2-nitrobenzoic acid (DTNB) and N-ethylmaleimide (NEM) were less potent but nevertheless inhibited the enzymic activity of protein kinase C. The Hill coefficients of HgCl2, DTNB and NEM were close to unity whereas the values for organic mercurials were 1.3 to 1.5. The inhibition was of a non-competitive type with respect to H1 histone. 3H-PDBu binding activity was also inhibited by all of the reagents in a non-competitive manner. Mercurials apparently bind to sulfhydryl groups of protein kinase C to inhibit the enzymatic activity.

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.

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.

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.

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.

Codon-level analysis of histone primary sequence: evidence of a repeat tetrapeptide origin and later inclusion of transcribed sequence

This work is directed to the question of protein sequence conservation. By reference to the genetic code the aminoacyl sequence of histones H2A, H4, H3, H2B and H1 (fragment) were rewritten as the codon sequences. The N-terminal regions were set aside on the grounds of different composition and sequence. The remainder of the molecule could be referred to simple repeat-tetrapeptide proteins by codon composition (high Gxy, low xGy content) and by sequence. Random segments of three to six residues occur characterized by composition and sequence as originating from the complimentary DNA strand, i.e. as codon "transcript". Ancestral features are probably best seen in H3, point mutations appear to be more extensive in H2B and H1. Segments in reverse order in H2A and in "transcript" in H4 distinguish these two from the other three histones. There is a tenuous possibility the N-terminals also originated as repeat-tetrapeptide now intensively modified. At codon-level the 50S ribosomal protein (L7/L12) of E. coli has features in common with histones (including a palindrome-containing N-terminal). It has the composition and sequence of a well-conserved tetrapeptide-repeat strand (statistical support). If interpretations made here are substantially correct, the 50S r-protein illustrates a significant stage in evolution of histone codon strands.

Structural studies on histones H1. Circular dichroism and difference spectroscopy of the histones H1 and their trypsin-resistant cores from calf thymus and from the fruit fly Ceratitis capitata

A peptide containing the globular region of the histone H1 from the fruit fly Ceratitis capitata has been isolated after limited tryptic digestion of insect H1. The composition of this trypsin-resistant core resembles that of the homologous peptide from calf thymus H1, although the insect H1 core possesses one cysteine, two tyrosines, one histidine, and more isoleucine and less glycine and leucine than the calf thymus H1 core. Circular dichroism measurements indicate that all the fragments that possess an ordered secondary structure (approximately 11% in both calf thymus H1 and Ceratitis H1) are present in the trypsin-resistant cores. Both calf thymus and Ceratitis H1 and their trypsin-resistant cores fold cooperatively on titration with NaOH, though the folding of the cores is less cooperative than that for the parentmolecules. On the other hand, salt-induced folding of both cores and intact molecules is noncooperative. The environment of the tyrosyl residues in both calf thymus and Ceratitis H1 has been studied by circular dichroism in the region 250-300 nm and by difference spectroscopy; their pKa' values have also been determined. The results suggest that one of the tyrosyl residues of Ceratitis H1 is buried in the hydrophobic core, in an environment similar to that of calf thymus tyrosine-72, while the second tyrosyl residue of the insect H1 molecule, which titrates with a lower pKa' value (approximately 9.30 in the absence of salt and approximately 9.80 in the presence of 0.3 M KF), is on the surface of the trypsin-resistant core. Due to the limited number of aromatic residues in the histone molecules, the above-mentioned techniques proved to be useful tools to study conformational transitions.

The primary structure of histone H1 from sperm of the sea urchin Parechinus angulosus. 1. Chemical and enzymatic fragmentation of the protein and the sequence of amino acids in the four N-terminal cyanogen bromide peptides

The primary structure of the amino-terminal 84 residues of sperm histone H1Parechinus has been determined. The sequence is: Pro-Gly-Ser-Pro-Gln-Lys-Arg-Ala-Ala-Ser-Pro-Arg-Lys-Ser-Pro-Arg-Lys-Ser-Pro-Lys-Lys-Ser-Pro-Arg-Lys-Ala-Ser-Ala-Ser-Pro-Arg-Arg-Lys-Ala-Lys-Arg-Ala-Arg-Ala-Ser-Thr-His-Pro-Pro-Val-Leu-Glu-Met-Val-Gln-Ala-Ala-Ile-Thr-Ala-Met-Lys-Glu-Arg-Lys-Gly-Ser-Ser-Ala-Ala-Lys-Ile-Lys-Ser-Tyr-Met-Ala-Ala-Asn-Tyr-Arg-Val-Asp-Met-Asn-Val-Leu-Ala-Pro-.

Advances in chromatin research

Recent results in chromatin research are reviewed. The nucleosomal arrangement is described and the roles of DNA, histones and non-histones are discussed in connection with their functions.

Isolation and partial sequence of the cyanogen bromide peptides from calf thymus non-histone chromosomal protein HMG 1

Peptides produced by cyanogen bromide cleavage of non-histone chromosomal protein HMG 1 have been isolated and characterized, and their partial sequences determined. The sequence data presented here account for over half of the sequence of the HMG 1 molecule and, together with previously published results, provide interesting information on the charge distribution within the molecule.

On the interaction of histone Hl and Hl peptides with DNA. Sedimentation, thermal denaturation and solubility studies

The interactions in buffered 0.14 M NaCl (pH 7.0) of DNA, native or sonicated, with histone Hl and with its fragments N-Hl (residues 1-72) and C-Hl (residues 73-COOH), have been studied by using the techniques of sedimentation, thermal denaturation and solubility. Histone Hl shows a preferential affinity for high molecular weight DNA in comparison with sonicated DNA. The binding of histone Hl to sonicated DNA in 0.14 M NaCl is reversible and the reversibility decreases with time. These findings are consistent with the view that Hl is cooperatively distributed along DNA molecules and that this distribution is energetically more favoured for long DNA than for sonicated DNA. It has been found that under conditions of moderate salt concentration, the C-terminal region is the main one responsible for the interaction of Hl with DNA, and also for a cooperative distribution of the histone along the DNA molecules. Addition of urea to the solution produces a decrease of solubility of Hl-DNA complexes. This effect reflects an additional condensation of the complex, which is probably related to the unfolding of the globular part of the histone. It is suggested that this globular region does not play a substantial role in the condensation of Hl-DNA complexes. A model which takes into account the presence of free lysyl and phosphate groups within the complex is discussed.

Genes and spacers of cloned sea urchin histone DNA analyzed by sequencing

A cloned histone gene cluster of the highly reiterated type from the sea urchin Psammechinus miliaris was analyzed by DNA sequencing. More than half of the 6 kb repeat was sequenced, including coding regions of all five histones, some prelude and trailing sequences lying adjacent to the structural gense, and segments of the AT-rich spacer DNA. The gene cluster does not code for gonad-specific histone variants but may instead be active in early sea urchin development, as indicated by comparison to reference histones. The encoded histones seem not to be derived from longer precursor proteins, not is there any evidence for insert sequences within the coding regions. Sequence similarities exist among the putative ribosome-binding sites adjacent to the initiator codons of individual genes. The AT-rich spacer segments between the genes differ from each other, are made up from relatively simple nucleotide arrangements, but are not repetitious, and apparently do not code for additional large proteins.

The evolution of histones

The amino acid sequences of bovine histones H2A, H2B, H3, and H4 and the first 107 residues of rabbit thymus histone H1 were examined using newly developed procedures designed to detect and evaluate weak similarities (de Haën et al., 1976). Using the McLachlan scoring system, regions of statistically significant similarity were found between several pairs of the four smallest histones. The probability that this set of similarities could result simply from chance was estimated to be less than 10(-5). No similarity was found between the H1 sequence and the other histones. The results are interpreted to indicate that at least the C-terminal portions of the core histones evolved from a common ancestral protein.

The amino-acid sequence of trout-testis histone H1

The complete amino-acid sequence of 194 residues of trout testis histone H1 has been elucidated by automated Edman degradation of large peptides derived from specific cleavages at infrequent amino-acid residues. Trout testis histone H1 has a molecular weight of 19314, is only slighly microheterogeneous, and possesses pentapeptide sequences related to Ala-Ala-Ala-Lys-Lys repeated six times in the complete sequence. Although the N-terminus of histone H1 is known to be blocked, some 10% of intact trout testis H1 contains a free N-terminal alanine residue. Three seryl residues in the C-terminal half (97-194) of the molecule occur in the sequence Lys-Ser-Pro-Lys known to be phosphorylated in trout testis H1. The sequence has been compared to the known partial sequence of rabbit thymus H1. The results are consistent with a role for histone H1 in the maintenance of the higher-order structure of chromatin.

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

Limited digestion with trypsin of both calf thymus H1 histone and the fragment 1--120 of the H1 molecule has resulted in the isolation of the fragment 35--120. This fragment assumes a globular structure under physiological conditions of pH and ionic strength. The variable N-terminal portion of the molecule, up to residue 34, is not required for the formation of the H1 globular structure. Proton nuclear magnetic resonance (NMR) and ultracentrifugation studies show that the H1 histone molecule consists of three distinct structural domains under structuring conditions: a random coil 'nose' consisting of 35 to 40 residues from the N-terminal end; a globular 'head' involving the next approximately 80 residues; and a random-coil 'tail' of the remainder of the molecule.

Interaction of DNA with poly(L-Lys-L-Ala-Gly) and poly(L-Lys-L-Ala-L-Pro). Circular dichroism and thermal denaturation studies

Complexes of DNA with polypeptides composed of Lys, Ala, and Gly in both a sequential order, poly(L-lysine-L-alanine-glycine), and a statistical distribution, poly(L-lysine36-L-alanine28-glycine), were prepared using gradient dialysis. These polypeptide-DNA complexes were studied using ultraviolet absorption (UV) and circular dichroism (CD) to probe the conformation, binding, and melting behavior of DNA in the complex. Complexes with the sequential polypeptide showed no structural change in the DNA; however, the complexes with the random polypeptide yield CD spectra similar to phi DNA [Maniatis, T., Venable, Jr., J.S., and Lerman, L.S. (1974), J. Mol. Biol. 84, 37]. A second sequential polypeptide, poly(L-Lys-L-Ala-L-Pro)n, -DNA complex was also studied. It was found to exhibit pronounced structural changes as a function of ionic strength and poly-peptide-DNA ratio, more similar to the random sequence that the ordered sequence of the Lys, Ala, Gly polymer. Thus the importance of the composition and amino acid sequence in polypeptides which bind to DNA, even in such simple systems, is demonstrated. Evidence from thermal denaturation, employing simultaneous monitoring of CD and UV changes, supports a model in which specific polypeptides cause condensation of the DNA in the complex into an asymmetric tertiary structure. The relevance of these model systems to chromatin is discussed.

Tyrosine fluorescence of two tryptophan-free proteins: histones H1 and H5

The fluorescence intensity of the single tyrosine residue in histone H1 increases from RTYR = 0.3 to RTYR = 1.3 as the protein undergoes a conformational change from the random coil state to a folded form. Enhanced fluorescence in the folded state has not been observed before in ap protein. Histone H5 shows no change in fluorescence intensity on folding. This is interpreted as a result of compensation between enhanced and reduced fluorescence in the three tyrosine residues.