Transcriptional regulation in eukaryotic cells

Proteomics of nucleocytoplasmic partitioning

The partitioning of the proteome between nucleus and cytoplasm affects nearly every aspect of eukaryotic biology. Despite this central role, we still have a poor understanding of which proteins localize in the nucleus and how this varies in different cell types and conditions. Recent advances in quantitative proteomics and high-throughput imaging are starting to close this knowledge gap. Studies on protein interaction are beginning to reveal the spectrum of cargos of nuclear import and export receptors. We anticipate that it will soon be possible to predict each protein's nucleocytoplasmic localization based on its importin/exportin interactions and its estimated diffusion rate through the nuclear pore. This insight is likely to provide us with a fundamental understanding of how cells use nucleocytoplasmic partitioning to encode and relay information.

Osteogenic gene transcription is regulated via gap junction-mediated cell-cell communication

An analytical study of cell-cell communications between murine osteoblast-like MLO-A5 cells and bone marrow mesenchymal stem cell (BMSC)-like C3H10T1/2 cells was performed. C3H10T1/2 cells expressing green fluorescent protein (10T-GFP cells) were generated to enable the isolation of the BMSC-like cells from co-cultures with MLO-A5 cells. The mRNA expression levels of several osteogenic transcription factors (Runx2, Osterix, Dlx5, and Msx2) did not differ between the co-cultured and mono-cultured 10T-GFP cells, but those of alkaline phosphatase (ALP) and bone sialoprotein (BSP) were 300- to 400-fold higher in the co-cultured cells. Patch clamp and biocytin transfer assays revealed gap junction-mediated communication between co-cultured 10T-GFP and MLO-A5 cells. The addition of a gap junction inhibitor suppressed the increases in the expression levels of the ALP and BSP mRNAs in co-cultured 10T-GFP cells. Furthermore, the histone acetylation levels were higher in co-cultured 10T-GFP cells than in mono-cultured 10T-GFP cells. These results suggest that osteoblasts and BMSCs associate via gap junctions, and that gap junction-mediated signaling induces histone acetylation that leads to elevated transcription of the genes encoding ALP and BSP in BMSCs.

Transcriptional inhibition by a non-histone protein from low mobility group in homologous and heterologous in vitro systems

An acidic non-histone chromosomal protein of low mobility group (LMG) with pI of 5-5.5 and molecular weight of 160 kDa (named LMG160), has been isolated from rat liver nuclei and its inhibitory effect on transcription of DNA in vitro has been detected in a heterologous prokaryotic in vitro transcription system (T7 RNA polymerase) and also confirmed in the homologous cell-free system of rat liver nuclear extract. The results indicate that in the presence of non-histone protein LMG160, in vitro RNA synthesis represses in the both systems, which can suggest a functional role for this non-histone chromosomal protein.

Purification of nuclear cAMP-independent protein kinases from rat ventral prostate

Two nuclear cAMP-independent protein kinases (designated PK-N1 and PK-N2) were purified from rat ventral-prostate and liver. The yield of enzyme units was 4-5% and 7-9% for each enzyme from the prostatic nuclei and liver nuclei, respectively. The average fold purification for prostatic nuclear protein kinase N1 and N2 was 1360 and 1833, respectively. The respective average specific activity of the two enzymes towards casein was 81,585 and 110,000 nmol 32P incorporated/hr/mg of enzyme. Protein kinase N1 comprised one polypeptide of Mr 35,000 which underwent phosphorylation in the presence of Mg2+ + ATP. Protein kinase N2 comprised two polypeptides Mr 40,000 and 30,000 of which only the Mr 30,000 polypeptide was autophosphorylated. Both enzymes were active towards casein, phosvitin, dephosphophosvitin, spermine-binding protein, and non-histone proteins in vitro. Little activity was detected towards histones. Both enzymes were stimulated by 150-200 mM NaCl. MgCl2 requirement varied with the protein substrate but was between 2-4 mM for both enzymes. With dephosphophosvitin as substrate, the apparent Km for ATP for N1 protein kinase was 0.01 mM. GTP did not replace ATP in this reaction. Protein kinase N2 was active in the presence of ATP or GTP. The apparent Km was 0.01 mM for ATP, but 0.1 mM for GTP.

Purification of cytosolic cAMP-independent protein kinases from rat ventral prostate

Two cAMP-independent protein kinases were purified from rat ventral-prostate and liver cytosol, and were designated PK-C1 and PK-C2 to distinguish them from the nuclear protein kinases described in the preceding paper. The yield of the prostate enzymes was about 5% each, and about 10% each for the liver enzymes. The average fold purification of the prostatic enzymes was 1892 and 3176 for protein kinase C1 and C2, respectively. Their average respective specific activity towards casein was 40,111 and 67,340 nmol 32P incorporated/hr per mg of enzyme protein. protein kinase C1 comprised one polypeptide of Mr 39,000 which underwent phosphorylation in the presence of Mg2+ + ATP. Protein kinase C2 comprised three polypeptides of Mr 41,000; 38,000; 26,000. Of these only the Mr 26,000 polypeptide was autophosphorylated. The Mg2+ requirement for protein kinase C1 and C2 was between 1 and 4 mM depending on the nature of the protein substrate. Both enzymes were stimulated by 100-200 mM NaCl. Km for ATP for C1 and C2 kinases was 0.01 mM; GTP could be used only by protein kinase C2 but with a markedly lower affinity. The enzymes were active towards casein, phosvitin, dephosphophosvitin, and spermine-binding protein in vitro, but demonstrated little activity towards histones. Despite several similarities in these general properties of cytosolic protein kinases C1 and C2 with those of nuclear protein kinases N1 and N2, a number of differences are also noted.

Differential effects of polyamines on the phosphorylation of chromatin-associated proteins

Studies are presented on the nature of chromatin-associated phosphoproteins whose phosphorylation is influenced by polyamines. After labelling with 32P, chromatin-associated proteins were separated into four fractions. Fraction I comprised neutral and basic non-histone phosphoproteins, including high-mobility-group non-histones; fraction II consisted mostly of histones; fraction III consisted of a class of (salt-soluble) acidic non-histone phosphoproteins; and fraction IV consisted of residual (salt-insoluble) acidic non-histone phosphoproteins. The average relative distribution of protein in the four fractions (I-IV) was about 1:4:2:1 for both liver and prostate. However, tissue-dependent differences were observed in the incorporation of 32P in various protein fractions. In the presence of polyamines (e.g. 1 mM-spermine or 2 mM-spermidine) maximal stimulation of phosphorylation was observed in non-histone proteins of fraction I (160-180%), followed by that in non-histone proteins of fraction III (80-110%). The phosphorylation of residual non-histone proteins in fraction IV, and the small extent of phosphorylation of histones in fraction II, remained unaltered in the presence of polyamines. Thus polyamines do not stimulate the phosphorylation of all non-histone proteins; their stimulative effect is most prominent in the phosphorylation of neutral and basic non-histone proteins and a class of salt-soluble acidic non-histone proteins. In accord with our hypothesis, these differential effects of polyamines on phosphorylation of endogenous non-histone proteins may relate to the conformation of these substrates rather than to endogenous kinases.

A genetic aspect of chromatin proteins of human brain tumors

Electrophoretic analysis of chromatin proteins was performed on rat and human tissues. Species and organ specific patterns were demonstrated in them. Twenty cases of human brain tumours were also analyzed and each tumor had typical phoretic patterns of chromatin. Proteins obtained from histologically similar tumors display similar electrophoretic patterns. As to the ratio of chromatin protein to DNA, no apparent differences between benign and malignant human brain tumors were observed.

[Regulatory proteins in chromatin of eucaryotes]

Experimental evidence for a role of histones and chromosomal nonhistone proteins in the regulation of transcription in eucaryots is described. A speculative model on the regulation of gene activity in higher organisms is presented.

Effects of polyamines on prostatic chromatin- and non-histone-protein-associated protein kinase reactions

Studies are presented on the influence of polyamines on prostatic chromatin- and non-histone-protein-associated protein kinase reactions involving both exogenous and endogenous substrates. The activities toward the model acidic protein substrate, dephosphophosvitin, were maximal at 160--200mM-NaCl (or -KCl or -NH4Cl). Under these conditions, spermidine and spermine added in concentrations up to 2mM were essentially without effect. However, without addition of NaCl to the medium, marked stimulation of these reactions was elicited by these polyamines at 1--2mM concentrations. The stimulatory effects were not due to non-specific changes in the ionic strength or to substitution of spermine for Mg2+, as maximal stimulation by 1 mM-spermine was observed only at optimal (2--4mM) Mg2+ concentrations. Qualitatively similar effects of polyamines were observed with enzyme preparations from the prostates of castrated rats, and with chromatin and non-histone-protein preparations from other tissues besides ventral prostate. When phosphorylation of endogenous non-histone proteins of the chromatin was measured, spermine stimulated both the initial rates and the final extent of transphosphorylation, even in the presence of optimal concentration of NaCl. By contrast, spermine or spermidine had no effect on the chromatin- and non-histone-protein-associated protein kinase reactions determined with lysine-rich histones as substrates. Chemically NN-dimethylated dephosphophosvitin was a less active substrate for the chromatin-associated protein kinase, but its phosphorylation was more markedly stimulated by spermine in comparison with unmodified dephosphophosvitin. These observations hint that the polyamine stimulations of the various protein kinase reactions may be due to effects on the conformations of the non-histone protein substrates rather than on the kinases themselves.

Studies on the tissue specificity of the high-mobility-group non-histone chromosomal proteins from calf

The high-mobility-group (HMG) non-histone chromosomal proteins from calf thymus, liver, spleen and kidney were extracted, and fractionated by CM-Sephadex chromatography and trichloroacetic acid precipitation. The isolated proteins HMG 1, HMG 2 and HMG 17 from the tissues were compared by polyacrylamide-gel electrophoresis, isoelectric focusing and amino acid analysis. The results show that the three proteins are very similar in the tissues studied, implying a lack of tissue specificity.

Changes in liver nuclear protein metabolism after a single dose of urethane to suckling mice

Treatment of 8-9-day-old C57BL/A mice with a single carcinogenic dose of urethane, at 1.2 mg/g body wt., resulted in an immediate decrease in liver DNA synthesis reaching a maximum at about 16-18 h after injection, the rate of synthesis returning to normal after 48 h. When the nuclear proteins were radiolabelled, the non-histone protein (NHP) fraction showed a significant decrease in specific activity 8-18 h after injection of urethane and slight increase in specific activity after 24 h. Histone and residual proteins did not show any significant change. The liver NHP were analysed by isoelectric focusing (IEF) and sodium dodecyl sulphate (SDS) electrophoresis in polyacrylamide gels. The latter technique failed to show any distinctive differences but IEF results indicated some quantitative and qualitative changes in protein content and synthesis were induced by the urethane treatment. The most noticeable change in the stained gels was an increase in a protein component having a pI of 7.35 and the appearance of new bands at pI's of 7.85 and 5.55 in the 18 h treated livers. However, the [3H]tryptophan labelling pattern indicated that this was not due to an increased synthesis of these components. 24 h after urethane there appeared to be an increased rate of synthesis of some of the major components of the mixture, particularly at the pI 5.65 region. Histone and residual protein fractions were also analysed by electrophoresis and showed no difference between treated and control livers.

The effect of gamma-radiation on the interaction of DNA with nuclear non-histone proteins

The interaction of nuclear sap proteins and chromatin non-histone proteins with DNA was studied by two methods: membrane filter technique and chromatography of 32P-labelled proteins on DNA-containing columns. Irradiated DNA binds a slightly greater amount of these proteins and much more firmly than the native DNA. The effect is caused by the appearance of the locally denatured sites in irradiated DNA. Irradiation of non-histone proteins disturbs their specific interaction with DNA more easily than the non-specific binding.

Diurnal variations in endogenous RNA polymerase activity and amounts of nuclear non-histone protein, DNA and cytoplasmic protein in rat liver

From rats fed ad libitum and kept under a 12 + 12 h light/dark regimen, the DNA dependent RNA polymerase activity of liver cell nuclei was determined avery four hours. From identical rats, nuclear non-histone protein and DNA, and cytoplasmic protein was determined by Feulgen-Naphthol Yellow S cytophotometry of isolated liver cells. The minimum: maximum ratio of the RNA polymerase activity is 0.77; the min:max ratio of nuclear non-histone protein is 0.84. These two parameters have identical time courses with a gradual decline during the light period and a sharp rise after the onset of the dark period. The variations in nuclear DNA content, estimated as the amount of Feulgen stain bound, closely parallel those of the RNA polymerase activity and nuclear non-histone protein content (min:max = 0.96). The amount of cytoplasmic protein per cell also varies throughout the day, but its time curve lags behind those of nuclear non-histone content and RNA polymerase activity. These results are consistent with the concept of nuclear non-histone proteins as de-repressors of the DNA template in differentiated, non-proliferating cells, and support the validity of using Feulgen-Naphthol Yellow S cytophotometry of nuclear non-histone proteins as an estimate of gene expression in such cells.

Regulation of mammalian protein synthesis in vivo. Protein synthesis in rat liver and kidney after the administration of sublethal doses of cyclohyximide

Protein synthesis in vivo was studied at various times after the administration of sublethal doses of cycloheximide to rats. Cycloheximide caused an inhibition, followed by a dose-and time-dependent stimulation, of incorportation of labelled precursor into proteins of the liver and kidney. The stimulation of protein synthesis at 24h was not due to a change of precursor pool or the specific radioactivity of the precursor used. During the stimulatory period, leucine incorporation into various cellular protein fractions varied; incorporation into total nuclear protein was the most affected.

Chromosomal proteins of rat brain: increased synthesis and affinity for DNA following a pulse of the carcinogen ethyinitrosourea in vivo

A single pulse of ethlnitrosourea (EtNU), administered to 10-day-old BD IX-rats, specifically results in a high incidence of neuroectodermal tumors in the central and peripheral nervous system. At five days after an EtNU-pulse, analyses of protein-DNA interactions were performed using chromatin dissociation and re-association experiments, following incorporation of radioactive leucine into brain chromosomal proteins (CP) during short-term suspension culture. In comparison with 15-day-old control animals, the brain cells of EtNU-treated rats exhibited (i) an increased rate of CP synthesis, and (ii) an increased affinity of the newly-synthesized CP for brain DNA of both control and EtNU-treated animals.

Chicken antichromatin antibodies: specificity to different chromatin fractions

Specific complement-fixing and precipitin antibodies were induced in chicken to chromatin from WI-38 human diploid fibroblast. Chicken antibodies were chosen because they present two major advantages with respect to rabbit antibodies: (a) the optimal NaCl concentration for chicken precipitin is 1.5 M, which is also an optimal solvent for chromatin proteins that are insoluble at the lower salt concentration required by rabbit precipitin; (b) chicken antichromatin antibodies require an antigen concentration much lower with respect to rabbit antibodies for saturation at the complement-fixation reaction. These antibodies are species specific and they react at the complement-fixation and precipitin assay not only with the whole chromatin but also with dissociated proteins, albeit at a higher concentration of both antigen and antibodies. The specificity of these antibodies to different fractions of chromosomal proteins and of the chromatin after washing with a solution at a different sodium chloride concentration has been investigated.

Effect of chromosomal proteins extractable with low concentrations of NaCl on chromatin structure of resting and proliferating cells

When quiescent WI-38 cells are stimulated to proliferate by nutritional changes, the chromatin of stimulated cells shows an increased ellipticity in circular dichroism spectra and an increased ability to bind ethidium bromide. The differences between the chromatins of quiescent and stimulated cells are abolished if both chromatins are treated with 0.25 M NaCl. However, when salt-treated chromatins are reconstituted by dialysis agains 10 mM Tris-HCl, the difference in circular dichroism spectra and ethidium bromide binding re-appear. Furthermore, addition of the 0.25 M NaCl extract from chromatin of stimulated cells to chromatin of quiescent cells causes an increased ellipticity in circular dichroism spectra similar to that of stimulated chromatin. Since only proteins (mostly nonhistones) are detectable in the 0.25 M NaCl extract, these results strongly suggest that the chromosomal proteins extractable with low concentrations of salt are responsible for the functional and structural changes occurring in chromatin of WI-38 cells stimulated to proliferate.

Proteins from different classes of liver nuclei in normal and thioacetamide-treated rats

1. In normal rats the amounts of each of the main types of nuclear protein, i.e. soluble proteins, histones, non-histone chromosomal proteins and residual proteins, vary within the different classes of rat liver nuclei fractionated by zonal centrifugation. 2. Heterogeneity is observed in the non-histone chromosomal proteins prepared from different classes of liver nuclei. These differences were observed by analysis of the proteins both by sodium dodecyl sulphate-polyacrylamide-gel electrophoresis and electrofocusing electrophoresis. They are most evident between the non-histone chromosomal proteins obtained from stromal and parenchymal nuclei. However, some differences are also found for the parenchymal nuclei, between the diploid parenchymal and the tetraploid parenchymal, and between them and the nuclei involved in the synthesis of DNA respectively. 3. Drastic alterations in the nuclear proteins are found after the administration of thioacetamide. The changes observed are complex and not uniform. They vary with the age of the animal and the type of nucleus. In general an increase in the soluble proteins and non-histone chromosomal proteins and a decrease in the residual proteins is observed. There is a decrease in the specific radioactivity of soluble and residual proteins. 4. Electrophoretic analysis of the non-histone chromosomal proteins showed that specific changes occurred after administration of thioacetamide, which are different in adolescent and young adult rats.