Analytical techniques for cell fractions : XXVI. A two-dimensional electrophoretic analysis of basic proteins using phosphatidyl choline/urea solubilization

The ISO-DALT system of two-dimensional electrophoresis allows high-resolution separations of proteins and protein subunits. However, the conventional isoelectric focusing employed in this system does not give satisfactory resolution of the more basic proteins, such as histones. The BASO-DALT system was designed to obtain improved resolution of these basic proteins in the first dimension. In this system, phosphatidyl choline is used as the solubilization agent, and allows resolution of many low molecular weight basic proteins that were not seem with more conventional detergents. Using the BASO-DALT system, Novikoff hepatoma chromosomal proteins have been analyzed, and the five histones identified.     

Alterations of gene expression in Novikoff hepatoma cells induced by a factor in human urine

Proteins and protein subunits from Novikoff hepatoma cells have been mapped by two-dimensional polyacrylamide gel electrophoresis utilizing the BASO-DALT system to resolve the basic proteins. Utilizing this technique, it has been demonstrated that human urine contains proteins that retain biological activity and can stimulate synthesis of several new proteins in neoplastic cells. This stimulatory activity has been detected in urine from cancer patients and normal individuals.     

Rapid analysis of mitotic histone H1 phosphorylation by cationic disc electrophoresis at neutral pH in minigels.

A new method is described for analysis of histone H1 and other basic proteins by cationic disc electrophoresis in polyacrylamide gels at neutral pH. The multiphasic buffer (disc) system uses Na+ as leading ion, L-histidine as trailing ion, and Hepes as buffering counterion. These "Hepes/histidine gels" have three advantages over conventional acid-urea gels for studies of H1 phosphorylation and dephosphorylation: speed, convenience, and the need for only small amounts of cells or chromatin. Core histones and their acetylated forms can also be separated in gels containing 0.4% Triton X-100. The difference in electrophoretic mobility between mitotic (superphosphorylated) and interphase H1 from HeLa cells is approximately twice as great at neutral pH as at pH 4.5, making it possible to separate these two H1 forms rapidly and easily in Hepes/histidine "minigels" only 5-cm long. Total histones can be rapidly prepared by simply neutralizing 0.2 N HCl extracts, and the entire analysis, from harvesting cells to destaining gels, can be carried out in 1 day. The stacking effect of the disc system produces sharp bands and high resolution even with relatively dilute samples.     

Study of nuclear basic proteins of Physarum polycephalum: Differential synthesis during plasmodial cell cycle and spherule germination

An electrophoresis system providing a good resolution of all basic proteins and their variants or modified forms extracted from Physarum polycephalum nuclei has been used to study the synthesis of the basic nuclear proteins of this organism during three developmental stages: the S-phase and the G2-phase of the plasmodial cell cycle and the premitotic stage of germinating spherules. Differences have been seen in the synthesis of the different classes of histones and HMG like proteins during these three stages.     

Isolation and characterization of histones and other acid-soluble chromosomal proteins from Physarum polycephalum

Chromosomal basic proteins were isolated from amoebal and plasmodial stages of the acellular slime mold Physarum polycephalum. Polyacrylamide electrophoresis on high resolution acid-urea gels separated the five histone fractions in the sequence H1, H2A, H2B, H3, and H4. Under these electrophoretic conditions Physarum histones migrated more like plant (rye) than animal (calf) histones. Furthermore, Physarum histones H1, H2A, and H2B have higher molecular weights on sodium dodecyl sulfate (SDS) gels than the corresponding calf fractions. No differences were detected between amoebal and plasmodial histones on either acid-urea or SDS-polyacrylamide gel electrophoresis. Amoebal basic proteins were fractionated by exclusion chromatography. The five histone fractions plus another major acid-soluble chromosomal protein (AS) were isolated. The Physarum core histones had amino acid compositions more closely resembling those of the calf core histones than of rye, yeast, or Dictyostelium. Although generally similar in composition to the plant and animal H1 histones, the Physarum H1 had a lower lysine content. The AS protein was extracted with 5% perchloric acid or 0.5 M NaCl, migrated between histones H3 and H4 on acid-urea polyacrylamide gels, and had an apparent molecular weight of 15 900 on SDS gels. It may be related to a protein migrating near H1. Both somewhat resembled the high mobility group proteins in amino acid composition.     

典型涡鞭毛虫(Zooxanthella microadriatica)含有多种染色质碱性蛋白

以往的研究都表明涡鞭毛虫类不含真核细胞普遍具有的组蛋白,而仅含1—2种分子量较小、含量较低和碱性较弱的染色质碱性蛋白。但我们采用自己建立的先固定后抽提的方法从典型涡鞭毛虫Zooxanthella microadriatica获得了多种碱性蛋白成分。经SDS-PAGE分析,其中有六条带的迁移率分别十分接近地对应着小牛胸腺的五种组蛋白(H1有两条亚带)。另外迁移率在H1与H3之间的三条互相靠近的电泳带,据其分子量(17—19KDa)分析极可能来自于此细胞中含量极为丰富的叶绿体类核体的染色质,由于碱性性质相似而被一同提取出来。既然我们利用先固定后抽提的方法提取小牛胸腺组蛋白和提取涡鞭毛虫(Crypthecodinium cohnii)的染色质碱性蛋白获得了良好的提取效果和很好地重复了前人的结果,我们认为本工作首次报道了在典型涡鞭毛虫类中也有含有多种染色质碱性蛋白并且很相似于组蛋白(至少在分子量上)的情形,为揭示和澄清组蛋白的起源进化问题提供了新的实验依据。     

Heterogeneity of the histone-containing chromatin in sea cucumber spermatozoa. Distribution of the basic protein phi 0 and absence of non-histone proteins

Nuclei of spermatozoa of the sea cucumber Holothuria tubulosa contain the five somatic-type histones plus a sperm-specific histone H1 and a unique basic protein phi 0, which is related to H1 in amino acid composition. No proteins of the High Mobility Group (HMG) type have been detected. The structure of this chromatin has been probed nuclease digestion. Its behaviour is anomalous, since two distinct fractions of chromatin are recovered from these spermatozoa, which differ either in the presence or absence of the sperm-specific proteins H1 and phi 0. This heterogeneous distribution is not found in conventional materials, such as calf thymus or chicken erythrocytes. Proteins H1 and phi 0 are not uniformly distributed and may be localized in special regions of chromatin. Fragments containing long stretches of nucleosomes lacking both proteins can be recovered. At the same time, the chromatin fractions which contain these two proteins are shown to be less soluble. When an extensive digestion of chromatin is carried out yielding only nucleosomes and small oligomers, the H1 and phi 0 proteins redistribute themselves on chromatin, the two proteins acting in a cooperative fashion in this process. Cross-linking experiments carried out in whole cells indicate a proximity of phi 0 and H1, whereas no crosslinks have been detected between phi 0 and any of the four nucleosomal histones. The phi 0 protein may thus play a role similar to histone H1 and be only loosely associated with nucleosomal histones, but contribute to the structuration of chromatin during spermiogenesis.     

Hormonal control of meiosis reinitation in starfish oocytes. New evidence for the absence of efficient intracellular receptors for l-methyladenine recognition.

Nuclei isolated from testes of the house cricket were centrifuged in a gradient of colloidal silica with a density range of about 1.12 to 1.18 g/ml. Fractions were collected from the bottom to the top of the gradient, and the types of nuclei in them were classified by phase microscopy. The distribution of nuclear types in the gradient indicated relatively large increases in nuclear density during spermatogenesis, and that silica-gradient centrifugation can readily yield fractions enriched for nuclei of specific developmental stages needed to study basic protein changes during sperm development. Basic proteins could be extracted from nuclei spun through silica if they were washed with polyvinylpyrrolidone. The histones in different fractions of nuclei were analysed electrophoretically. Fractions of spermatocyte and early spermatid nuclei contained histones of the somatic types as their only basic proteins. Fractions with mixtures of mid-spermatid and earlier nuclei also yielded somatic histones primarily. Essentially pure samples of late spermatid nuclei were obtained. They lacked somatic histones. In one fraction of late nuclei, the spermatid-specific histones TH1 and TH2 were the major proteins present. In another, two additional histone-like components, not detected in previous studies, were also prominent.     

Chromosome of the mature virion of simian virus 40 contains H1 histone.

In addition to free SV40 minichromosomes in the compact form, complete virions were obtained from the nuclear extract of productively infected cells. Capsid proteins VP1, VP2, and VP3, as well as histones, were observed on electrophoregrams of proteins prepared from virions. In contrast to the widely accepted view, histone H1 was found in virions in stoichiometric amounts with respect to other histones. The same is true for virions isolated by a conventional method. Free minichromosomes present in infected cells contain all histones and practically no viral proteins.     

Some Researches on Histones

The histone extracted from calf thymus glands is a complex system of proteins, which can be fractionated by chromatography on carboxymethyl cellulose columns into three principal fractions (1) very lysine-rich, (2) moderately lysine-rich, (3) arginine-rich. When examined by starch gel chromatography each of these gives more than one band. Methods have been devised for further separation of the components in some cases. The components show characteristic differences in end groups and certain amino acids as well as in their basic character. Histones extracted from various rat tissues can be separated into similar fractions, of which the amino acid analyses are similar to those derived from calf thymus, within the experimental error. To this extent, no species or tissue specificity of the fractionated histones was observed. Although all the histone fractions contain approximately one basic amino acid to three non-basic amino acids their structure is not regular, as Phillips has shown that in certain fractions the number of non-basic groups between two basic groups may vary from 0 to seven or more. The possible functions of histones are discussed.     

Reconstitution of nucleosomes with histone macroH2A1.2.

MacroH2A histones have an unusual hybrid structure, consisting of an N-terminal domain that is approximately 65% identical to a full-length histone H2A and a large C-terminal nonhistone domain. To develop an in vitro approach for investigating the effects of macroH2A proteins on chromatin structure and function, we reconstituted nucleosomes with recombinant macroH2A1.2, substituting for conventional H2A. Recombinant macroH2A1.2 was able to efficiently replace both of the conventional H2As in reconstituted nucleosomes. The substitution of macroH2A1.2 for H2A did not appear to grossly perturb the basic structure of the nucleosome core, as assessed by sedimentation and by digestion with micrococcal nuclease or DNase I. However, two differences were observed. First, the region around the midpoint of the nucleosomal core DNA was more resistant to digestion by DNase I in nucleosome core particles reconstituted with macroH2A1.2. Second, preparations of core particles reconstituted with macroH2A1.2 had a greater amount of material that sedimented more rapidly than mononucleosomes, suggesting that macroH2A1.2 may promote interactions between nucleosomes. Recombinant macroH2A proteins should be valuable tools for examining the effects of macroH2A on nucleosome and chromatin structure.     

Basic nuclear proteins of the histone-less eukaryote Crypthecodinium cohnii (Pyrrhophyta): two-dimensional electrophoresis and DNA-binding properties

Unlike typical eukaryotes, the Dinoflagellate Crypthecodinium cohnii does not contain histones but six major basic, low molecular weight nuclear proteins which represent only 10% of the DNA mass and differ from histones in their electrophoretic and DNA-binding properties. These proteins are resolved in two-dimensional electrophoresis (AUT-PAGE x SDS-PAGE). Three proteins with an apparent molecular mass of 16, 16.5 and 17 kDa (p16, p16.5 and p17) are present in addition to the major 14 kDa basic nuclear component (HCc). HCc itself is resolved in three proteins (alpha, beta and gamma). When the proteins are not reduced with 2-mercaptoethanol before 2D-PAGE, the migration of HCc alpha, beta and gamma is modified in a way which suggests the formation of both inter- and intramolecular disulfide bridges and thus, the presence of at least two cysteines. The amino-acid analysis of HCc proteins resolved in 2D gels confirms that they are lysine-rich. HCc alpha, beta and gamma as well as p16, p16.5 and p17 are removed from isolated chromatin with 0.6 M NaCl, indicating that their affinity for DNA in vivo is lower than that of core histones. Furthermore, in vitro, they bind more tightly to single-stranded than to double-stranded DNA.     

Histones of Neurospora crassa.

Neurospora crassa chromatin isolated by a rapid method minimizing proteolytic degradation contains approximately one weight of acid-extractable basic protein per weight of DNA. This basic protein consists of five major polypeptide species which are similar in size to the histone proteins of higher eukaryotes and are present in approximately the same molar ratios. These five polypeptides have been purified by polyacrylamide gel electrophoresis in the presence of sodium dodecyl sulfate. Their electrophoretic mobilities in polyacrylamide gels and their amino acid compositions indicate that they are histones homologous, although not identical, to the H1, H2A, H2B, H3, and H4 histones of mammals. The first 3 residues in the amino acid sequence of Neurospora H3 histone are identical to the first 3 residues in calf and pea H3; Neurospora H1, H2A, and H4 histones have blocked NH2 termini, like their mammalian counterparts. The finding of recognizable H1, H2A, H2B, H3, and H4 histones in Neurospora extends the range of eukaryotes now shown to contain a full complement of these strongly conserved chromosomal proteins, and supports the view that histones became involved in chromosome structure at a very early point in the evolution of eukaryotes.     

Resistance of ADP-ribosylated histones and HMG proteins to proteases.

Calf thymus histones (individually isolated or mixtures) and high mobility group proteins were ADP-ribosylated in vitro using [32P]NAD+ and immobilized purified poly(ADP-ribose) polymerase. The modified histones were then subjected to V8 protease or alpha-chymotrypsin digestion and the resulting peptides were separated by electrophoresis on acetic acid-urea-Triton gels. It was found that in vitro ADP-ribosylated histones were much more resistant to proteases than unmodified histones. A similar approach was applied to histones modified by the endogenous poly(ADP-ribose) polymerase in permeabilized NS-1 mouse myeloma cells in culture. In this case, the proteases could not discriminate between modified and unmodified histones and putative mono(ADP-ribosyl)ated peptides appeared in a digestion frame corresponding to that of bulk peptides. These differences are most probably due to the specificity or number of ADP-ribose groups added to the histones by the endogenous or exogenous poly(ADP-ribose) polymerase. Thus, depending on the size of poly(ADP-ribose) attached to nuclear proteins, these modified proteins might display different degrees of resistance to proteolysis.     

Analyse de la structure chromatinienne du sperme par la cytométrie en flux à l’acridine orange. — intérêt clinique

During spermatozogenesis, sperm nucleosomal DNA type, linked to histones, is transformed into a special form bound to small basic proteins, the protamines. This process allows sperm nucleus to condense and mature. This maturation process is achieved in the epididymis. When a spermatozoon enters an oocyte, protamines are released and replaced by histones, enabling the sperm nucleus to expand into a male pronucleus. Flow cytometry using acridine orange staining is an objective and quantitative technique well-adapted for the investigation of the chromatin structure at the level of each spermatozoon, as well as the whole ejaculate. This technique allows tracing the young sperm cell nuclei from the diploid stage, through tetraploid until the final haploid stage in mature spermatozoa. It allows also following the sperm maturation process during the epididymal transit. It detects various sperm chromatin condensation defects, hypocondensation, hypercondensation or other aberrations, as well as decondensation defects by using an in vitro assay. These defects may impair sperm fertilizing ability, even after sperm microinjection into the oocyte. Better understanding of sperm chromatin integrity and stability prerequisites might help us improving the quality of various technologies used in assisted medical procreation.     

Application of a new vector system for efficient protein purification in the crystallization of PA5104/ORF from Pseudomonas aeruginosa

We have developed a new T7-based vector system for rapid purification and high-throughput capability applicable for structural studies. The system allows purification of target proteins to homogeneity in two steps with a single Ni-affinity column. The first step relies on affinity purification of the N-terminal His-tagged protein in the conventional way, eluting the protein with imidazole. Addition of a His-tagged 3C protease to cleave the His-tag permits a second pass through the nickel column, this time all impurities bind to the column while the pure protein does not. This has the major advantage of quickly removing the residual contaminating proteins that are associated with nickel affinity purification as well as the protease and His-tag. Here, we describe the application of this system to over-express and purify ORF PA5104 from Pseudomonas aeruginosa. The protein was successfully crystallized and crystals were shown to diffract to atomic resolution. Additionally preliminary X-ray diffraction analysis of two crystals forms is presented, one diffracting to 1.9 A and the other to 0.96 A resolution.     

Histone mediated changes in morphology and confluent density of cultured cells

Calf thymus histones and histone subfractions were added to media overlying subconfluent mouse fibroblast cells in culture. The histones caused significantly higher cell densities at confluence than control cultures and disruption of the normal ordered arrangement of cells. These changes were seen on application of histones to growing cells but not confluent cells and were reversed when the histones were removed and the cells replated with more growth area. The slightly lysine rich histone fraction had the greatest effect and the lysine rich fraction had the least effect on cell morphology and cell number at confluence. These effects could not be duplicated with other highly charged basic proteins.