STUDIES ON HISTONE FRACTION F2A1 IN MACRO- AND MICRONUCLEI OF TETRAHYMENA PYRIFORMIS

Histone fraction F2A1 has been isolated and purified from macronuclei of the ciliate Tetrahymena pyriformis. It migrates as a single species on sodium dodecyl sulphate-acrylamide gel electrophoresis, with a molecular weight indistinguishable from that of calf thymus F2A1. The solubility properties of Tetrahymena F2A1 are also similar to those of calf thymus F2A1. Electrophoretic analyses on urea-acrylamide gels indicate that Tetrahymena F2A1 consists of four or five subspecies, the two fastest having electrophoretic mobilities identical with those of the two major electrophoretically separable forms of calf thymus F2A1. High resolution (long gel) electrophoresis coupled with incorporation of radioactive acetate both in vivo and in vitro suggest that, as in the case of calf thymus F2A1, differentical acetylation of a parent molecule can explain the observed electrophoretic heterogeneity of Tetrahymena F2A1. Electrophoretic analysis of histones isolated from the micronucleus, which is genetically less active than the macronucleus, indicates that it contains largely the relatively unacetylated (parent) form of histone F2A1.     

An electrophoretic comparison of the histones of various strains of Tetrahymena pyriformis

Histones were extracted from isolated macronuclei of several strains of the ciliated protozoan Tetrahymena pyriformis and compared by electrophoresis on both urea-acrylamide and sodium dodecyl sulfate-acrylamide gels. High resolution urea-acrylamide-gel electrophoresis resolves Tetrahymena histones into five main classes. The lysine-rich histone H1 exhibits microheterogeneity within each strain, mostly due to phosphorylation, and varies extensively in electrophoretic mobility and apparent molecular weight among the strains. Both H3 and H4 are constant among Tetrahymena strains and consist of several secondarily modified subspecies. However, while the electrophoretic constancy of H4, observed in higher organisms, extends to this lower eukaryote, H3 of each Tetrahymena strain migrates faster than calf thymus H3 in both gel systems. This suggests that H3 is not as rigidly conserved as H4. Fraction HX has no electrophoretic counterpart in calf thymus histone. It consists of five subfractions, each of which displays a remarkably constant electrophoretic mobility among the various strains. H2B is electrophoretically variable among Tetrahymena strains. The intersyngen and interphenoset diversity of Tetrahymena histone is shown to be comparable to that found among vertebrate classes.     

Specific interaction of histone H1 with eukaryotic DNA.

The interaction of calf thymus histone H1 with homologous and heterologous DNA has been studied at different ionic strengths. It has been found that about 0.5 M NaCl histone H1, and its fragments N-H1 (residues 1-72) and C-H1 (residues 73-C terminal), precipitate selectively a small fraction of calf thymus DNA. This selective precipitation is preserved up to very high values (less than 2.0) of the input histone H1/DNA ratio. The percentage of DNA insolubilized by histone H1 under these ionic conditions is dependent upon the molecular weight of the nucleic acid, diminishing from 18% fro a Mw equals 1.0 x 10(7) daltons to 5% for a Mw equals 8.0 x 10(4) daltons. The base composition of the precipitated DNA is similar to that of the bulk DNA. Calf thymus histone H1 also selectively precipitates a fraction of DNA from other eukaryotes (herring, trout), but not from some prokaryotes (E. coli, phage gamma. On the other hand, at 0.5 M NaCl, the whole calf thymus DNA (but not E. coli DNA) presents a limited number of binding sites for histone H1, the saturation ratio histone H1 bound/total DNA being similar to that found in chromatin. A similar behavior is observed from the histone H1 fragments, N-H1 and C-H1, which bind to DNA in complementary saturation ratios. It is suggested that in eukaryotic organisms histone H1 molecules maintain specific interactions with certain DNA sequences. A fraction of such specific complexes could act as nucleation points for the high-order levels of chromatin organization.     

Purification by preparative electrophoresis and characterization of histone H2B from rat chloroleukaemia.

Highly purified histone H2B from rat chloroleukaemia has been isolated by preparative electrophoresis at pH 2.7 in polyacrylamide slab gel, using the fraction F2b of Johns (Johns E. W. (1964) Biochem, J. 92, 55-59) as starting material. This histone was characterized by amino acid analysis and end groups determination. Comparative studies with homologous calf thymus histone show similarity of the amino acid compositions and of the amino terminal groups. the carboxyl terminal sequence presents two conservative substitutions.     

A study of histones in amoeba nuclei by indirect immunofluorescence method.

Nuclear proteins of four species of free-living Amoebidae (Amoeba proteus, A. discoides, Chaos carolinensis and Polychaos dubia) have been studied by indirect immunofluorescence technique using specific antisera to H1, H2A, H2B, H3 and H4 histone fractions from the calf thymus. It has been shown that the nuclei of the species examined have all these five histone fractions. However, the degree of similarity between homologous fractions from amoebae and the calf thymus varies and can be expressed in terms of immunological distance. Immunological differences between amoebic and calf thymus histones are the most pronounced in H1, being least in H3 and H4. Judged by its immunochemical characteristics, the histone fraction H2A from P. dubia is closer to the corresponding fraction from the calf thymus than is H2A from the other three amoeba species.     

Binding of thymus histone F1 and E. coli RNA polymerase to DNA of Polytene Chromosomes of Drosophila

Polytene chromosomes of Drosophila melanogaster can bind large quantities of calf thymus histone F1 and E. coli RNA polymerase. This shows that a substantial fraction of chromosomal DNA is accessible for interaction with extra-chromosomal proteins.     

A study of calf thymus histone fraction F2(b) by gel filtration

The gel-filtration behaviour of calf thymus histone fraction F2(b) was studied at three different salt concentrations (0.01m-, 0.10m- and 1.00m-sodium chloride) and two different pH ranges (pH3–4 and pH6.7–7.1). Other histone fractions [F1, F2(a) and F3] were also utilized to assist interpretation of the data. It was found that the Stokes radius of histone fraction F2(b) was not significantly changed when the salt concentration was increased, implying that the aggregation of the individual histone molecules (Edwards & Shooter, 1969) resulted in only relatively minor changes in the hydrodynamic volume. Aggregation would appear to be due to the salting out of hydrophobic regions giving rise, in the aggregate, to a compact core of hydrophobic groups from which protrude the remaining basic parts of the molecule. Repulsion between charged groups on the basic regions of individual histone molecules would give the aggregate approximately spherical symmetry, the diameter of the aggregate approximating to the length of a single histone molecule.     

The isolation of nuclei and basic nucleoproteins from the cellular slime mold Dictyostelium discoideum.

A method is described for the isolation of nuclei from an axenic strain of Dictyostelium discoideum using a sorbitol/Ficoll solution and low concentration of Triton X-100. Basic proteins have been extracted from the nuclei and on polyacrylamide gel electrophoresis yield a consistent pattern in which five major groups or bands predominate. Four of these five fractions comigrate with calf thymus histones and one fraction seems to be unique to D. discoideum. The slowest moving of the five fractions is soluble in 0.5 M perchloric acid and comigrates with calf thymus histone F1. After recovery from the perchloric acid solution by precipitation with acetone this fraction yielded one major band on electrophoresis.     

Generation and characterization of novel antibodies highly selective for phosphorylated linked histone H1 in Tetrahymena and HeLa cells

Phosphorylated forms of Tetrahymena macronuclear histone H1 were separated from each other and from dephosphorylated H1 by cation-exchange HPLC. A homogeneous fraction of hyperphosphorylated macronuclear H1 was then used to generate novel polyclonal antibodies highly selective for phosphorylated H1 in Tetrahymena and in human cells. These antibodies fail to recognize dephosphorylated forms of H1 in both organisms and are not reactive with most other nuclear or cytoplasmic phosphoproteins including those induced during mitosis. The selectivity of these antibodies for phosphorylated forms of H1 in Tetrahymena and in HeLa argues strongly that these antibodies recognize highly conserved phosphorylated epitopes found in most H1s and from this standpoint Tetrahymena H1 is not atypical. Using these antibodies in indirect immunofluorescence analyses, we find that a significant fraction of interphase mammalian cells display a strikingly punctate pattern of nuclear fluorescence. As cells enter S-phase, nuclear staining becomes more diffuse, increases significantly, and continues to increase as cells enter mitosis. As cells exit from mitosis, staining with the anti-phosphorylated H1 antibodies is rapidly lost presumably owing to the dephosphorylation of H1. These immunofluorescent data document precisely the cell cycle changes in the level of H1 phosphorylation determined by earlier biochemical studies and suggest that these antibodies represent a powerful new tool to probe the function(s) of H1 phosphorylation in a wide variety of eukaryotic systems. Received: 3 August 1993; in revised form: 9 November 1993 / Accepted: 23 November 1993     

A study on histones in amoeba nuclei by indirect immunofluorescence method

Nuclear proteins of four species of free-living Amoebidae (Amoeba proteus, A. discoides, Chaos carolinensis and Polychaos dubia) have been studied by indirect immunofluorescence technique using specific antisera to H1, H2A, H2B, H3 and H4 histone fractions from the calf thymus. It has been shown that the nuclei of the species examined have all these five histone fractions. However, the degree of similarity between homologous fractions from amoebae and the calf thymus varies and can be expressed in terms of immunological distance. Immunological differences between amoebic and calf thymus histones are the most pronounced in H1, being least in H3 and H4. Judged by its immunochemical characteristics, the histone fraction H2A from P. dubia is closer to the corresponding fraction from the calf thymus than is H2A from the other three amoeba species.     

Distribution of histone F1 on calf thymus nucleohistone DNA.

A method of large-scale preparation of the histone F1-DNA complex by removing all other proteins from calf thymus nucleohistone was established. This involved gel filtration of nucleohistone through a column containing a band of sodium dodecyl sulfate. The F1-DNA complex obtained had the original amount of F1 and no other. The F1-DNA complex exhibited distinct two-step melting on thermal denaturation. The first step was apparently attributable to naked DNA regions and the second step, about 30 deg. C higher than the first step, to the regions covered with F1. Buoyant density experiments with the complex after fixation with formalin revealed that F1 was distributed fairly evenly over DNA fragments of an average molecular weight of about 4 × 10⁶. Electron microscopic examination of the complex after various degrees of denaturation with formalin indicated that the longest stretch of unbound DNA was about 0·3 μm.     

Electrophoretic analysis of liver and testis histones of the frog Rana pipiens

Histones were extracted from frog livers and testes and analyzed by electrophoresis on long polyacrylamide gels and on sodium dodecyl sulfate (SDS)-containing polyacrylamide gels. Frog histones were found to be similar to those of calf thymus except that frog histone fraction F2A2 showed a marked dependence on the temperature at which the long gels were run, and frog histone fraction F3 could be separated from frog F2B on SDS-containing gels. Comparisons between frog liver and frog testis histones indicated that the testis contains as its major F1 component a fast migrating species not found in liver. Testis histones also showed less microheterogeneity of fractions F3 and F2A1 than liver histones. These were the only differences observed between liver and testis histones, even when testis histones were prepared from sperm suspensions that were rich in cells in the late stages of spermiogenesis. Thus it seems that, in Rana, the electrophoretic properties of the basic proteins of sperm differ from those of somatic cells only in the nature of histone F1 and in the degree of microheterogeneity of fractions F2A1 and F3.     

Histone-like protein in the prokaryote Thermoplasma acidophilum.

The DNA of the prokaryote Thermoplasma acidophilum is associated with a histone-like protein that has the following properties: it has a high content (23%) of basic amino acids, is positively charged at neutral pH, is soluble in acid, and can stabilize DNA against thermal denaturation. In polyacrylamide gel electrophoresis, in the presence of either sodium dodecylsulfate or urea, it migrates at the same rate as histone IV (F2a1) of calf thymus. The amino acid composition, however, it unusually rich in the amides of acidic amino acids (16-20%), and it does not appear to be closely homologous to any of the classes of eukaryotic histones. Escherichia coli DNA, on the other hand, was associated with no detectable acid-soluble proteins, and the nucleoprotein thermally denatured at a lower temperature than pure DNA.     

Changes sperm culei during sperimogensis and epidymal maturation.

An antibody specific to histone F2b of calf thymus was prepared by using the highly purified histone fraction in addition to antibodies against histones F1 and F2a1, as reported previously. The nuclear staining pattern obtained with anti-histone F2b antibody was compared to those obtained with anti-histone Fl and F2a1 antibodies in cultured hamster fibroblasts, both by immunofluorescence and immunoperoxidase. The nuclear staining patterns with each anti-histone antibody obtained by immunoperoxidase were almost completely the same as those obtained by immunofluorescence. Nuclear staining patterns with anti-F2b antibody were speckled in appearance with a faint staining of the nuclear membrane. These findings were different from the results obtained with anti-F1 antibody and with anti-F2a1 antibody. These results suggest the possibility that these three histones are located in different chromatin states.     

The synthesis of diacetylated histone H4-(1–37) for studies on the mechanism of histone deacetylation

The heptatriacontapeptide [Lys([¹⁴C]Ac)¹², Lys([³H]Ac)¹⁶]histone H4-(1–37) was synthesized by the automated solid phase method. This dual-labeled peptide was designed for studies on the mechanism of histone deacetylation. The synthesis was monitored by an automated picrate method; and the product, purified by affinity chromatography and ion exchange chromatography, was homogeneous by polyacrylamide gel electrophoresis and gave excellent amino acid and radiolabel ratios. A purified calf thymus histone deacetylase released acetyl groups from this synthetic peptide at essentially the same rate as from a diacetylated 1–37 peptide derived from native calf thymus histone H4. The relative rate of release of [¹⁴C]acetyl from Lys¹² and of [³H]acetyl from Lys¹⁶ was 1.03 ± 0.03 throughout the time course of the enzymatic assay. Based on these results, possible mechanisms of histone deacetylation are proposed.     

Iodination of Xenopus laevis histone F2a1 in chromatin.

The reaction of calf thymus and Xenopus laevis histones with radioactive iodine has been studied under various conditions that affect chromatin structure. All histones from both species contain at least one tyrosine residue and, in a denaturing solvent, all the the histones react with iodine. Histone F2a1 has been studied in detail. Calf thymus F2a1 is known to contain four tyrosyls and all four react with iodine. In high voltage paper electrophoresis, the tyrosine-containing peptides from calf co-migrate with those from Xenopus F2a1, suggesting that the amino acid sequence is strongly conserved between these two species. Therefore, the published calf thymus F2a1 sequence has been used to order the Xenopus F2a1 peptides within the molecules. When gently isolated native chromatin is iodinated in a low ionic strength medium 60% of the radioactivity in F2a1 is in tyrosyl 88, 30% in tyrosyl 51, and tyrosyl 72 and 98 have almost no radioactivity. Reagents which remove the protein from the DNA (2 M NaCl) or partially disrupt protein tertiary structure (5 M urea) increase the reactivity of each of the four tyrosyls five- to tenfold, suggesting that all four are protected about equally by the overall folding of the chromatin. Isolated F2a1 iodinated in the presence of 10 M urea shows uniform labeling in each of the four peptides, suggesting that tyrosyl 72 and 98 are afforded some protection solely by protein-protein interactions. The stepwise removal of histones in increasing NaCl concentrations differentially increases the availability of each F2a1 tyrosyl. The preferential exposure of tyrosyl 88 coincides with the removal of the majority of F1 histones at 0.5 M NaCl while the gradual and stepwise increase in reactivity of tyrosyl 51, 72, and 98 correlates with the gradual removal of histones other than F1. Radioactive iodination of chromatin has been shown to be a sensitive probe for detecting changes in the association state (or conformation) of histone F2a1.     

Nematode chromosomal proteins--III. Some structural properties of the histones of Caenorhabditis elegans

The histones of Caenorhabditis elegans (Nematoda) have been identified by correlating criteria of electrophoresis and amino acid composition with the five main histones from calf thymus. C. elegans H1(1) consists of at least two subtypes with approximate molecular weights of 20,000 and 18,500 daltons as resolved by SDS polyacrylamide gel electrophoresis. They are some 10% smaller than the two subtypes of calf histone H1. The differences are also corrobated by the amino acid composition of the nematode and calf H1 complements. Nematode H2A resembles calf H2A in chromatographic and electrophoretic properties and in the amino acid composition, although it lacks histidine, which seems to be replaced by lysine. Like calf H2A, it is dimorphic as shown by Triton/acid/urea polyacrylamide gel electrophoresis. The H2B complement from C. elegans consists of two proteins with a molecular weight of approximately 12,500. They can be separated by ion-exchange chromatography, but they are very analogous to each other and to calf H2B in amino acid composition. Each form is also resolved into two more subtypes by Triton/acid/urea polyacrylamide gel electrophoresis. Nematode H3 resembles calf thymus H3 in its electrophoretic behaviour; three subfractions can be distinguished in Triton/acid/urea gels. C. elegans H4 is very similar to calf H4 in its chromatographic, electrophoretic and solubility properties, but differs significantly in composition. The meaning of this difference is discussed with regard to the generally observed stringent conservation of H4 sequences between distantly related species.     

Separation and properties of an H2B histone variant from the sperm chromatin of the sea urchin Sphaerechinus granularis

The purification and the physico-chemical characterization of one of the two H2B histone variants from the sperm of the sea urchin Sphaerechinus granularis are reported. The molecule shows, in addition to a distinctive molecular weight value, an amino acid composition different both from that of calf thymus H2B histone and from those of H2B histones from chromatin of sperm and embryos of other sea urchins. Circular dichroism and fluorescence data are discussed in comparison to those of calf thymus H2B.     

FURTHER CHARACTERIZATION OF THE F1-HISTONE PHOSPHOKINASE OF METAPHASE-ARRESTED ANIMAL CELLS

Exponentially growing Chinese hamster cells are found to contain two major phosphokinase activities with specificity for the phosphorylation of F1 (lysine-rich) histone. These two activities, designated KI and KII, were extracted with 0.35 M NaCl and fractionated in 0.2 M NaCl by Sephadex G-200 gel filtration. KI, which is similar to the ubiquitous cyclic 3',5'-adenosine monophosphate (cAMP)-dependent phosphokinase, differs from KII by several criteria. KII is mol wt 90,000, cAMP independent, rapidly turned over in vivo, low K_m for ATP, and phosphorylates F1 histone at several unique sites. Comparative examination of metaphase-arrested (M) and counterpart interphase (I) cells for these two activities reveals that KII is responsible for the overall high activity in M-arrested cells. Pulse labeling of cells with ³²P during traverse of the G₂-M phase of the cell cycle reveals an in vivo tryptic-phosphopeptide pattern in whole unfractionated F1 which is unique to M cells. Seven major phosphopeptides derived by in vitro phosphorylation of F1 with the KII enzyme correspond to these M cell-specific phosphorylation sites observed in vivo. It is suggested that KII activity predominates during the G₂-M transition and that F1 is its natural in vivo substrate.     

A Nuclear Protein Involved in Apoptotic-like DNA Degradation in Stylonychia: Implications for Similar Mechanisms in Differentiating and Starved Cells

Ciliates are unicellular eukaryotic organisms containing two types of nuclei: macronuclei and micronuclei. After the sexual pathway takes place, a new macronucleus is formed from a zygote nucleus, whereas the old macronucleus is degraded and resorbed. In the course of macronuclear differentiation, polytene chromosomes are synthesized that become degraded again after some hours. Most of the DNA is eliminated, and the remaining DNA is fragmented into small DNA molecules that are amplified to a high copy number in the new macronucleus. The protein Pdd1p (programmed DNA degradation protein 1) from Tetrahymena has been shown to be present in macronuclear anlagen in the DNA degradation stage and also in the old macronuclei, which are resorbed during the formation of the new macronucleus. In this study the identification and localization of a Pdd1p homologous protein in Stylonychia (Spdd1p) is described. Spdd1p is localized in the precursor nuclei in the DNA elimination stage and in the old macronuclei during their degradation, but also in macronuclei and micronuclei of starved cells. In all of these nuclei, apoptotic-like DNA breakdown was detected. These data suggest that Spdd1p is a general factor involved in programmed DNA degradation in Stylonychia.