Identification of suberimidate cross-linking sites of four histone sequences in H1-depleted chromatin. Histone arrangement in nucleosome core

The arrangement of 8 histones in the nucleosome core has been investigated by identifying the sites of 4 histone sequences cross-linked with a bifunctional amino-group reagent, dimethyl suberimidate, selected from among 4 diimidoesters of various linker lengths examined. H1-depleted calf thymus chromatin was allowed to react with 14C-labeled suberimidate at pH 8.5 and 0 degrees C. The cross-linked chromatin was then digested exhaustively with trypsin. Almost all the histone fragments were released from the chromatin with 0.25 M HCl and chromatographed on several columns and on paper. Cross-linked peptides were detected by analyzing the content of radioactive suberimidoylbislysine after acid hydrolysis. The chromatographic procedure developed here showed that the whole histone fragments contained 29 mol% of the total linked reagent as suberimidoylbisylsine. The 5 finally purified cross-linked peptides were identified from the total and N-terminal amino acids of each pair of peptides separated by two-dimensional cellulose thin layer chromatography after cutting the linker by ammonolysis. Thus, intramolecular cross-linking was found between Lys-5 and Lys-9 of H2A, and Lys-34 and Lys-85 of H2B, while intermolecular cross-linking was found between Lys-24 (or 27) of H2B and Lys-74 of H2A, Lys-85 of H2B and Lys-91 of H4, and Lys-120 of H2B and Lys-115 of H3 and/or Lys-77 of H4. Most of these lysine residues are located in the DNA-binding segments of the 4 histone sequences identified previously [Kato, Y. & Iwai, K, (1977) J. Biochem. 81, 621--630]. All the 5 or 6 cross-links can be located in a heterotypic tetramer consisting of one molecule each of H2A, H2B, H3, and H4, and a model of the histone arrangement in the tetramer is proposed. Two such tetramers may compose to the histone octamer in the nucleosome core.     

Phosphorylated sites of calf thymus H2B histone by adenosine 3':5'-monophosphate-dependent protein kinase from bovine cerebellum.

Phosphorylated sites of calf thymus H2B histone were studied with adenosine 3′:5′-monophosphate-dependent protein kinase partially purified from bovine cerebellum. Amino acid analysis of the phosphopeptides which were obtained by proteolytic digestion revealed that the enzyme had the ability to phosphorylate Ser-32 as well as Ser-36. The evidence together with the previous results which were obtained with silkworm enzyme (Hashimoto,E., Takeda,M., Nishizuka,Y., Hamana,K. and Iwai,K. (1975) Biochem. Biophys. Res. Commun., 66, 547–555) seems to suggest that this class of enzymes lacks tissue- as well as species-specificities in their catalytic properties.     

A proposal for a coherent mammalian histone H1 nomenclature correlated with amino acid sequences.

Bio-Rex 70 chromatography was combined with reverse-phase (RP) HPLC to fractionate histone H1 zero and 4 histone H1 subtypes from human placental nuclei as previously described (Parseghian MH et al., 1993, Chromosome Res 1:127-139). After proteolytic digestion of the subtypes with Staphylococcus aureus V8 protease, peptides were fractionated by RP-HPLC and partially sequenced by Edman degradation in order to correlate them with human spleen subtypes (Ohe Y, Hayashi H, Iwai K, 1986, J Biochem (Tokyo) 100:359-368; 1989, J Biochem (Tokyo) 106:844-857). Based on comparisons with the sequence data available from other mammalian species, subtypes were grouped. These groupings were used to construct a coherent nomenclature for mammalian somatic H1s. Homologous subtypes possess characteristic patterns of growth-related and cAMP-dependent phosphorylation sites. The groupings defined by amino acid sequence also were used to correlate the elution profiles and electrophoretic mobilities of subtypes derived from different species. Previous attempts at establishing an H1 nomenclature by chromatographic or electrophoretic fractionations has resulted in several misidentifications. We present here, for the first time, a nomenclature for somatic H1s based on amino acid sequences that are analogous to those for H1 zero and H1t. The groupings defined should be useful in correlating the many observations regarding H1 subtypes in the literature.     

Tetrahymena ubiquitin-histone conjugate uH2A. Isolation and structural analysis

The ubiquitin-histone H2A conjugate, uH2A, of the protozoan Tetrahymena pyriformis was isolated by gel chromatography and octadecylsilyl-silica chromatography, from the fractions on the chromatographic purification of histone H2A [Fusauchi, Y. & Iwai, K. (1983) J. Biochem. 93, 1487-1497]. The uH2A showed an amino acid composition corresponding to the sum of an equimolar mixture of two protozoan H2A variants and protozoan free ubiquitin. N- and C-terminal sequencing of the uH2A, by Edman degradation and carboxypeptidase P digestion, showed a branched structure having two N-terminals, those of the H2A and ubiquitin components, and one C-terminal, that of each H2A variant component. Further structural analyses of the uH2A, by tryptic digestion of citraconylated uH2A and of a ubiquitinated BrCN fragment, showed that the ubiquitin C-terminal Gly-Gly is linked to the epsilon-amino group of either Lys-123, 125, or 126 in the H2A sequence, and that the ubiquitin sequence is similar to that of calf thymus but differs at least in the sequence of residues 12-27. The deducted structure was compared with the only known uH2A structure, that of calf thymus, with special reference to the branched site.     

Sequence of histone 2B of Drosophila melanogaster.

The complete sequence of histone 2B of Drosophila has been determined by using an improved Beckman sequenator. Comparing these data with those previously published by other investigators on the histone 2B of calf [Iwai, K., Hayashi, H., & Ishikawa, K. (1972) J. Biochem. (Tokyo) 72, 357--367], trout [Koostra, A., & Bailey, G. S. (1978) Biochemistry 17, 2504--2510], and Patella (a limpet) [van Helden, P. D., Strickland, W. N., Brandt, W. F., & von Holt, C. (1979) Eur. J. Biochem. 93, 71--78], it is possible to assess the evolutionary stability of this protein. There is little conservation of sequence in the N-terminal portion of the molecule (residues 1--26 numbering according to calf H2B), while the remainder of the protein, which we designate the C-terminal portion, is highly conserved. In the region of 27--125 residues, there are 9 substitutions in the composite data among the 98 positions, 8 of them conservative. These data indicate that very different selective pressures operate on the two different portions of the H2B molecule, implying the existence of two well-defined regions. Studies on the structure of the nucleosome by others have suggested that the C-terminal portion of H2B is involved in histone-histone interactions while the N-terminal portion is a relatively free "tail" binding to DNA. The sequence data indicate that the function of the C-terminal region of H2B requires considerable sequence specificity while that of the N-terminal region does not.     

The histones of the sperm of Spisula solidissima include a novel, cysteine-containing H-1 histone

The histones remaining at the end of the spermiogenic differentiation, which are found associated with a highly basic protamine-like component [Ausio, J. and K.E. Van Holde (1987) Eur. J. Biochem. 165, 363-371] in the mature sperm of Spisula solidissima, have been isolated and characterized for the first time. All four core histones H2A, H2B, H3, H4, and the lysine-rich histone H1 are present. The core histones are found in equal stoichiometric amounts. As has been observed in other bivalve molluscs, the amino acid compositions of the core histones of S. solidissima sperm are very close to those of their counterparts in the calf thymus somatic histones. The spermatic histone H1 exhibits an amino acid composition and structural features similar to other histones of the histone H1 family. Yet this latter histone seems to be sperm-specific, and it contains at least two cysteine residues per molecule, which makes it unique in its class.     

Spin-label study of histone H1-DNA interaction. Involvement of the central part of the molecule in reconstituted chromatin

As shown in a previous paper [J. J. Lawrence et al. (1980) Eur. J. Biochem. 107, 263-269], covalent spin labeling of basis residues in histone H1 allows the study of the interaction of this protein with DNA. Using a step gradient dialysis procedure to reconstitute chromatin from labeled H1 and stripped chromatin, it is shown that the process of interaction of the lysine residues and DNA is the same whether histone H1 is bound to linear purified DNA or to H1-depleted chromatin. In contrast, spin labeling of the unique tyrosine of histone H1 located in the globular part of the molecule shows that this part is more involved in the interaction with chromatin than it is with linear DNA (as judged from the lengthening of the rotational correlation time). These data are interpreted as reflecting different roles for the N and C termini of the molecule of H1 and the central globular part. A model, based on these observations together with examination of the primary structures of histones H1, is proposed which accounts for the H1 involvement in the chromatosome structure.     

Ubiquitin carrier protein-catalyzed ubiquitin transfer to histones. Mechanism and specificity

Ubiquitinated derivatives of histones H2A and H2B, in which the carboxyl terminus of ubiquitin is joined to epsilon-amino groups of specific lysine residues of each histone, occur in vivo. Certain ubiquitin carrier proteins (E2s) catalyze ubiquitin transfer to histones (Pickart, C. M., and Rose, I. A. (1985) J. Biol. Chem. 260, 1573-1581). The catalytic activities of these purified ubiquitin carrier proteins have been quantitatively characterized with purified histones, in order to determine if one or more of them exhibits specificity for H2A over other histones (H3,H4) which are not known to be ubiquitinated in vivo. The results show the following. 1) No E2 exhibits strong specificity for H2A over the other histones. 2) For a given histone, kinetics of formation of its monoubiquitinated adduct do not differ strongly among the E2s; sigmoid kinetics (nH = 2) are generally observed, with values of K 0.5 ranging from 2-6 microM. 3) E214K catalyzes primarily monoubiquitination. 4) E220K catalyzes multiple ubiquitination (up to three ubiquitin/histone) by a processive mechanism that involves joining of ubiquitin carboxyl termini to multiple histone lysine residues. 5) E235K also catalyzes processive ubiquitination, with formation of polyubiquitinated products exhibiting a lag phase. Many of the polyubiquitinated adducts produced at low histone concentration are larger than expected for monoubiquitination of every histone-lysine residue, and polyubiquitination is selectively inhibited by substitution of reductively methylated ubiquitin for ubiquitin. These results suggest that E235K uniquely catalyzes ubiquitin transfer to lysine residues of previously conjugated ubiquitin molecule(s). The implications of these results for biological mechanisms of histone ubiquitination are discussed.     

Enzymatic Sialylation of N-Linked Oligosaccharides Using an α-(2,3)-Specific trans-Sialidase from Trypanosoma cruzi: Structural Identification Using a Three-Dimensional Elution Mapping Technique

α-(2,3)-Sialylated biantennary and triantennary oligosaccharides were enzymatically prepared from pyridyl-2-amino-oligosaccharides with terminal Gal residues, using an α-(2,3)-specific trans-sialidase from Trypanosoma cruzi (Lee, K. B., and Lee, Y. C. (1994) Anal. Biochem. 216, 358-364). From the pyridyl-2-amino-derivatives of neutral and α-(2,6)-monosialylated biantennary oligosaccharides from human fibrinogen, 5 different sialyl biantennary oligosaccharides were obtained. From two different asialo-triantennary oligosaccharides from fetuin, 35 sialyl oligosaccharides were obtained. The trans-sialidase transferred sialic acids effectively and indiscriminately to different galactosyl residues in the different positions on the substrates. Since the starting materials are neutral oligosaccharide of established structure, and the only α-(2,3)-sialyl residues are added to the nonreducing Gal terminal residues, the structures of these oligosaccharides could be identified unambiguously by using the three-dimensional mapping technique (Takahashi, N., Nakagawa, H., Fujikawa, K., Kawamura, Y., and Tomiya, N. (1995) Anal. Biochem. 226, 139-146.) in combinations with strategic digestion with β-galactosidase, β-N-hexosaminidase, and sialidase L.     

The amino terminal sequence of sea urchin sperm histone H1 and its phosphorylation by egg cytosol

1. The amino acid sequence of the first 34 residues of sperm histone H1 (SpH1) from Strongylocentrotus purpuratus shows striking similarity with sequences from three South African species. 2. Five contiguous repeats of the tetrapeptide SPBB (where B is R or K) occur between positions 10 and 29. 3. SpH1 was phosphorylated in vitro using egg cytosol as the source of protein kinase and approximately 4.2 mol phosphate were incorporated per mol H1. 4. Sequences of five phosphopeptides of SpH1 show the egg possesses protein kinase activity capable of phosphorylating multiple seryl residues including SPBB in the NH2-, and BBSP in the COOH-end of the protein.     

Studies on amino acid sequences of two isoforms of 17-kDa essential light chain of smooth muscle myosin from porcine aorta media.

Amino acid sequences were analyzed for two isoforms of myosin essential light chain, LC17a and LC17b [Hasegawa, Y., Ueno, H., Horie, K., & Morita, F. (1988) J. Biochem. 103, 15-18] from porcine aorta smooth muscle. Both LC17a and LC17b consisted of 150 amino acid residues and their N-terminal Cys residues were blocked by an acetyl group. The amino acid sequences of LC17a and LC17b were common from the N-terminal to Glu-141 and five amino acid substitutions were observed within the remaining C-terminal 9 residues. The amino acid sequences of LC17a and LC17b were identical to those deduced from the nucleotide sequences of bovine aortic cDNAs encoding the two isoforms [Lash, J. A., Helper, D.J., Klug, M., Nicolozakes, A.W., & Hathaway, D.R. (1990) Nucleic Acids Res. 18, 7176].     

Tetrahymena contain two distinct and unusual high mobility group (HMG)- like proteins

Previous studies have described the existence of high mobility group (HMG)-like proteins in macronuclei of the ciliated protozoan, Tetrahymena thermophila (Hamana, K., and K. Iwai, 1979, J. Biochem. [Tokyo], 69:1097-1111; Levy-Wilson, B., M. S. Denker, and E. Ito, 1983, Biochemistry, 22:1715-1721). In this report, two of these proteins, LG- 1 and LG-2, have been further characterized. Polyclonal antibodies raised against LG-1 and LG-2 fail to cross react with each other or any other macronuclear polypeptide in immunoblotting analyses. As well, LG- 1 and LG-2 antibodies do not react with calf thymus, chicken, or yeast HMG proteins. Consistent with these results, a 47 amino-terminal sequence of LG-1 has been determined that shows limited homology to both calf thymus HMGs 1 and 2 and HMGs 14 and 17. Two internal sequences of V8 protease-generated peptides from LG-2 have been determined, and these do not share any homology to the LG-1 sequence or any other sequenced HMG proteins. Comparison of the partial sequences of LG-1 and LG-2 with the complete amino acid sequence of the Tetrahymena histone H1 (Wu, M., C. D. Allis, R. Richman, R. G. Cook, and M. A. Gorovsky, 1986, Proc. Natl. Acad. Sci. USA, 83:8674-8678) rules out the possibility that LG-1 and LG-2 are proteolytically derived from H1, the other major macronuclear perchloric acid-soluble protein. Interestingly, however, both LG-1 and LG-2 are efficiently extracted from macronuclei by elutive intercalation (Schroter, H., G. Maier, H. Ponsting, and A. Nordheim, 1985, Embo (Eur. Mol. Biol. Organ.) J., 4:3867-3872), suggesting that both may share yet undetermined properties with HMGs 14 and 17 of higher eukaryotes. Examination of the pattern of LG-1 and LG-2 synthesis during the sexual phase of the life cycle, conjugation, demonstrates that the synthesis of LG-1 and LG-2 is coordinately increased from basal levels during the differentiation of new macronuclei (7-13 h), suggesting that both of these proteins play a role in determining a macronuclear phenotype. However, a specific induction of LG-2 synthesis is detected in early stages of conjugation (meiotic prophase, 1-4 h), leading to maximal synthesis of LG-2 at 3 h. Interestingly, the early induction of LG-2 synthesis closely parallels the hyperphosphorylation of histone H1. Taken together, these data suggest that LG-1 and LG-2 are not strongly related to each other or to higher eukaryotic HMG proteins.(ABSTRACT TRUNCATED AT 400 WORDS)     

Pig gastric (H+ + K+)-ATPase. Lys-497 conserved in cation transporting ATPases is modified with pyridoxal 5'-phosphate

Pig gastric (H+ + K+)-ATPase can be covalently modified with pyridoxal 5'-phosphate (PLP) (about 1 mol/mol enzyme), and this modification is not observed in the presence of ATP, suggesting that PLP binds to a specific Lys residue in the ATP binding site or the region in its vicinity (Maeda, M., Tagaya, M., and Futai, M. (1988) J. Biol. Chem. 263, 3652-3656). The peptides labeled with radioactive PLP could be released from the gastric membrane vesicles quantitatively by chymotrypsin treatment, and two peptides were purified by high performance liquid chromatographies. These peptides were not obtained from vesicles incubated with PLP in the presence of ATP. The sequences of the two peptides were NH2-Asn-Ser-Thr-Asn-Lys-Phe-COOH and NH2-Ser-Thr-Asn-Lys-Phe-COOH, exactly corresponding to residues 493-498 and 494-498, respectively, of pig gastric (H+ + K+)-ATPase sequenced recently (Maeda, M., Ishizaki, J., and Futai, M. (1988) Biochem. Biophys. Res. Commun. 157, 203-209). Lys-497 was concluded to be the binding site of PLP, as pyridoxyl-Lys was identified at the corresponding position. This Lys residue is conserved in (Na+ + K+)- and Ca2+-ATPases. The possible amino acid residues in the catalytic site of gastric (H+ + K+)-ATPase are discussed.     

Purification and properties of a histone acetyltransferase from Artemia salina, highly efficient with H1 histone.

An histone acetyltransferase has been purified from nuclei of 40-h-old Artemia salina larvae. The enzyme is very unstable at 0 degrees C, requires free -SH groups for activity and is rapidly inactivated at 40 degrees C. The optimal pH for activity is 8.5 and the activity is half inhibited by millimolar concentrations of Mn2+, Ca2+ or Mg2+ or decimolar concentrations of Na+ and K+. The molecular weight of the enzyme, determined by gel filtration chromatography, changed with the ionic strength of the medium (280,000 in 10 mM Tris . HCl, 170,000 in 0.2 M KCl). The very-lysine-rich histone H1 is a better substrate acceptor than the arginine-rich histones H3 or H4. Under proper conditions, the enzyme can modify all the internal lysyl residues in histones H1 and H4. The acetylation of H1 is inhibited when all the other histone fractions are present in the assay mixture.     

The accessibilities of histones in nucleosome cores to an arginine-specific protease

Submaxillaris protease, reportedly specific for arginine residues, was used to probe accessible arginines of chicken erythrocyte nucleosome cores. The relative rates of digestion of histones in nucleosome cores by this protease were H3 greater than H2b greater than H4 much greater than H2a. At most, 8 of 52 total arginines among the four core histones were reasonably accessible to attack. Sites most rapidly cleaved were Arg-26 in H3, a site approximately 13 residues from the NH2 terminus of H2b, and Lys-12 or Arg-17 in H4. Five sites attacked more slowly were Arg-8, -128, or -129 and Arg-49, -52, or -53 in H3; Arg-3 and Arg-17 or -19 in H4; and a site near one terminus of H2b or H3. H2a and fragments resulting from the above cleavages were highly resistant to attack, even after prolonged incubation. Similar results were obtained upon digestion of histones in intact chromatin. H1 and H5 in whole chromatin were attacked at rates comparable to H3. Seven of the eight accessible sites lie outside of structure-forming histone sequences, i.e. sequences that are immobilized in histone complexes, indicating that these sequences are inaccessible in nucleosome cores. The single exceptional site noted, approximately 50 residues from the NH2 terminus of H3, is consistent with previous observations that Glu-51 and Glu-60 of H3 in nucleosomes are accessible to attack by S. aureus protease (Rill, R. L., and Oosterhof, D. K. (1981). J. Biol. Chem. 256, 12687-12691). The relationships of these protease accessibilities to NMR assignments of mobile histone tails in nucleosome cores are discussed.     

Molecular cloning of a novel chaperone-like protein induced by rhabdovirus infection with sequence similarity to the bacterial extracellular solute-binding protein family 5

Previously we demonstrated that a novel stress protein is induced in fish cells by the infection of a fish rhabdovirus (Cho W. J., Cha, S. J., Do, J. W., Choi, J. Y., Lee, J. Y., Jeong, C. S., Cho, K. J., Choi, W. S., Kang, H. S., Kim, H. D., and Park, J. W. (1997) Biochem. Biophys. Res. Commun. 233, 316-319). In this paper, we present the molecular cloning and characterization of a gene encoding this protein named virus-inducible stress protein (VISP). The VISP was purified partially by immunoprecipitation using a monoclonal antibody against the VISP and further purified by the electroelution from a SDS-PAGE gel. The protein was subjected to internal protein sequencing, and the sequence of three peptides was determined. Degenerate oligonucleotides based on the three peptide sequences were used to screen a cDNA library from rhabdovirus-infected CHSE-214 fish cells, and a cDNA of a 2193-bp open reading frame encoding the VISP with 730 amino acid residues (M(r) = 79.84) was identified. Whereas the nucleotide sequence of VISP shows no similarity with other genes in the GenBank(TM), the amino acid sequence of the VISP has similarity with the bacterial extracellular solute-binding protein family 5 (SBP_bac_5) that is proposed to have chaperone activity. Thus, we explored whether the VISP also had chaperone-like activity. Purified recombinant VISP expressed in Escherichia coli promoted the functional folding of alpha-glucosidase after urea denaturation and also prevented thermal aggregation of alcohol dehydrogenase. These results suggest that the VISP has amino acid sequence similarity with SBP_bac_5 and that it has chaperone activity that may play a role in virus infection.     

Effects of DNA and urea on the specificity for H1 histone of the neutral protease B partially-purified from rat liver chromatin

A neutral protease, named protease B in the previous report (Tsurugi, K. & Ogata, K. (1982) J. Biochem. 92, 1369-1381), was partially purified from rat liver chromatin by gel filtration through Sepharose 6B followed by DE-Sephadex column chromatography. The proteolytic activity on total histones of the partially-purified protease B was increased about two fold by addition of DNA and again increased by further addition of 2 M urea. Analysis of the hydrolysed products showed that out of five species of histones, only H1 was degraded in the presence of an amount of DNA equivalent to the amount of histones, whereas core histones were also degraded in the absence or presence of one-tenth amount of DNA. Urea accelerated the selective degradation of H1 histone because H1 histone was preferentially degraded in the presence of even a low amount of DNA. In contrast, core histones became resistant to the protease B in the presence of DNA and/or urea. Heat-denatured DNA stimulated the degradation of H1 histone even in the absence of urea to almost the same extent that native DNA did in the presence of urea. Thus, protease B efficiently degrades H1 histone when its association with DNA is destabilized by either addition of urea or pretreatment of DNA with heat.     

Identification of the phosphorylation sites of H2B histone by a catalytic fragment of p72syk from porcine spleen.

Phosphorylated sites of calf thymus H2B histone were investigated with a catalytic fragment of 72 kDa protein-tyrosine kinase (p72syk). Three of five tyrosine residues in H2B histone can be phosphorylated by this kinase. In this analysis, H2B histone was thoroughly phosphorylated in vitro with [gamma-32P]ATP and the kinase, and then digested with a lysylendopeptidase. The resulting radioactive phosphopeptides were separated by a reverse-phase column on high performance liquid chromatography. Subsequent sequential Edman degradation of the purified phosphopeptides revealed that 40Y, 83Y and 121Y were phosphorylated. 121Y is the major phosphorylated residue in H2B histone. No phosphorylation was detected in 37Y and 42Y. Although the consensus sequence was not defined from these analyses, our data suggest that higher-order structure(s) in addition to primary one may participate in recognition of H2B histone by this protein kinase.