Studies on protein-phosphorylation reactions in isolated chromatin

Lectin-induced changes among polyadenylated and non-polyadenylated mRNA in lymphocytes. mRNAs for actin, tubulin and calmodulin respond differently

The differentiation of T-cell-enriched concanavalin-A-stimulated bovine lymphocytes was studied in vitro. mRNA was isolated from resting and stimulated cells. The amount of polyadenylated RNA increases from 3.6 X 10(-9) to 12 X 10(-9) micrograms/cell during 40 h concanavalin A stimulation. The estimated maximum length of the 3'-poly(A) tract in this RNA is reduced from 240 to 220 residues in stimulated cells. During translation in the rabbit reticulocyte lysate in vitro mRNA from stimulated cells consistently incorporates about 1.6-3 times more radioactivity/micrograms RNA into proteins than mRNA from resting cells. Three translation products have been identified on two-dimensional gels as actin, tubulin and calmodulin. Large quantitative shifts are seen between proteins translated from mRNAs isolated from resting cells and stimulated cells respectively. Actin and calmodulin are already major products from resting cell mRNA. Actin, however, increases about fivefold after stimulation while calmodulin does not change. Tubulin appears in substantial amounts only among stimulated cell mRNA products. Tubulin and calmodulin, on the other hand, remain mainly in the polyadenylated RNA fraction after stimulation while 50% of the actin together with a group of about six other major products is found among proteins translated from non-polyadenylated RNA. We conclude that in lectin-stimulated lymphocytes, besides a general increase in the amount of mRNA, alterations in post-transcriptional processing reactions are active in determining the fate of individual mRNAs.

Theoretical mechanism for synthesis of carcinogen induced embryonic proteins: VIII. Transcriptional theory

In this paper an extension of prior writings on the mechanism by which changes in genic expression is presented. The previous development of these ideas led to a unifying concept of alterations in heterochromatin due to a variety of carcinogenic agents as a pivital process leading to potential re-expressions of genes (1). The following deals just with structural features of chromatin before continuing to finer control levels of gene expression, especially in reference to cancer cells. The DNA methylation status is presented as being an important step in an intermediate stage of chromatin expression along with protein acetylation, phosphorylation and methylation as other means of modifying chromatin status.

Histone-dependent reconstitution and nucleosomal localization of a nonhistone chromosomal protein: the H2A-specific protease

We have described earlier a chromatin-bound protease with unique specificity for histone H2A [Eickbush, T. H., Watson, D. K., & Moudrianakis, E. N. (1976) Cell (Cambridge, Mass.) 9, 785--792]. In the present study, we explore the nature of interactions that form and stabilize the enzyme-chromatin system by using the activity of the protease to monitor its binding to DNA and DNA-histone complexes. During salt extraction of chromatin, the protease is released at an ionic strength between that required for the extraction of the slightly lysine-rich histones (H2A and H2B) and the arginine-rich histones (H3 and H4). The reassociation of this nonhistone protein to DNA has an absolute requirement for the H3--H4 tetramer and is only enhanced by the H2A--H2B dimer in the presence of the tetramer. We believe that the binding of the enzyme onto DNA requires some histone-elicited compaction of the helix. We have also examined the distribution of this enzyme within the chromatin fiber by isolating pools of monomer nucleosomes from micrococcal nuclease digests of 0.6 M NaCl extracted chromatin and from reconstituted DNA-protein complexes. The H2A-protease is found with these monomer nucleosome pools, and no activity can be detected in the low molecular weight products released during the digestion. Thus, by virtue of its extraction characteristics from chromatin and its association with isolated nucleosomes, this nonhistone protein exhibits properties hitherto assigned only to the inner histones.

[Structural arrangement of chromatin (author's transl)]

Recent observations and hypotheses on the structure of chromatin are reviewed. Elementary "subunit" for higher structural orders is the nucleosome, consisting of a histone octamer and doublehelical DNA wrapped around it. During the last years details of the nucleosomal structure could be deduced down to a resolution of 2 nm. In the chromatin fiber, built up by (mono-)nucleosomes, the superhelical DNA has a tertiary structure, from which structures of still higher order (quaternary structure of DNA) can be formed. The correlation of these structures to the terms euchromatin and heterochromatin are discussed. Finally, some functional aspects, especially transcription and replication, are discussed in view of the new knowledge of chromatin structure.

A histone H4-specific methyltransferase. Properties, specificity and effects on nucleosomal histones

A histone H4-specific methyltransferase was purified 80-100-fold from nuclei of calf lymphocytes and from calf thymus. Some biochemical properties of the enzyme are described. The enzyme transfers in vitro methyl groups from S-adenosylmethionine preferentially to the lysine residue 20 of histone H4. This is the major in vivo methylation site of H4. DNA-bound or nucleosomal H4 is not methylated in vitro. We have used methylated and unmodified H4 (in the presence of sufficient quantities of the other core histones) for nucleosome reconstitution in vitro and have not found significant differences in the efficiencies of assembly.

On the activity and fidelity of chromatin-associated hepatic DNA polymerase-beta in aging murine species of different life spans

Activity and accuracy of chromatin-directed DNA replication have been compared in young and aged Mus musculus and Peromyscus leucopus, two murine species with contrasting maximum lifespans. Chromatin isolated from livers of mature adults of both species copied efficiently exogenous DNA templates using predominantly DNA polymerase-beta. The DNA synthetic activity of liver chromatin remained constant in both species throughout their lifetimes. The fidelity of chromatin-directed poly [d(A-T)] synthesis was similar for the comparatively short-lived M. musculus and the relatively long-lived P. leucopus and remained unaltered in old animals. The fidelity of poly [d(A-T)] copying catalyzed by DNA polymerase-beta-dissociated from liver chromatin was comparable to that of the chromatin-directed synthesis. The dissociation enzymes did not exhibit diminished fidelity of poly [d(A-T)] synthesis with age. In all ages of both species examined, the murine liver DNA polymerase-beta, both chromatin-associated and solubilized, exhibited high error frequencies; approximately one dGMP was incorporated for every 500-1,000 complementary nucleotides polymerized. The relationship of these results to the accuracy of DNA replication and repair as a determinant of aging is considered.

Chromatin-associated protein kinases specific for acidic proteins

Protein kinases (EC 2.7.1.37) were eluted by 0.4 NaCl from chromatin of several mammalian cell typs. The enzymes were partially purified by ion-exchange chromatography, DNA-cellulose columns and sucrose gradient centrifugation. At least five different enzymes could be distinguished by their biochemical properties and their substrate specificities. Three of the enzyme activities tested phosphorylate different sets of histones, while two enzymes phosphorylate acidic nonhistone chromatin proteins or artificial substrates like casein and phosvitin. The two nonhistone protein kinases have slightly different pH and salt optima. They sediment through sucrose gradients with approx. 4 S and approx. 8 S, respectively. These enzymes are further characterized by their different substrate specificity, since they phosphorylate different, though partially overlapping sets of nonhistone chromatin proteins. Enzymes with these properties were deteced in chromatin from mouse ascites cells, bovine lymphocytes, African green monkey kidney cells and a human SV40 transformed cell line.

Replicative activity of isolated chromatin from proliferating and quiescent early passage and aging cultured mouse cells

Replicative activity of isolated chromatin from late passage cultured mouse cells has been compared to the activities of chromatin preparaions from dividing and quiescent early passage cells. Rates of endogenous DNA synthesis are similar for chromatin from growing or resting cells but this activity is stimulated 2.5-fold in senescent cell chromatin. Chromatin from growing young cells copies exogenously added single stranded DNA at the highest efficiency. Chromatin of senescent cells copies this template at a lower rate and resting young cell chromatin replicates single stranded DNA at the lowest efficiency. Similar relative rates are obtained when activated DNA is copied by the various chromatin preparations. Total activity of DNA polymerase extracted by salt from chromatin is similar for dividing and quiescent young cells but the proportion of DNA polymerase beta is higher in the latter. Elevated activities of DNA polymerases are extracted from chromatin of old cells. It is concluded, therefore, that chromatin-directed replication is differently arrested in non-dividing senescent cells and in quiescent early passage cells. The possible regulatory mechanisms of DNA replication in quiescence and aging are discussed.

Simple isolation of DNA hydrophobically complexed with presumed gene regulatory proteins (M3)

Chromatin from chicken reticulocytes and mouse Ehrlich ascites tumor cells has been extracted with 2 M NaCl, leaving a portion of the DNA still complexed with a fraction of nonhistones (designated M3, since it can be dissociated from DNA in solutions of 3 M NaCl containing 5 M urea). The DNA complexed with M3, separated from the bulk DNA by centrifugation, was found to contain sequences poorly represented in bulk DNA. Specifically we found that DNA--M3 complexes isolated from chicken reticulocyte chromatin were enriched in globin gene sequences by 20-fold relative to unfractionated DNA and by over 1000-fold relative to DNA rendered free of protein following the extraction of chromatin with 2 M NaCl. We have therefore isolated DNA fractions complexed with M3 which are enriched in specific sequences as may be determined by M3.

Protein kinases and their protein substrates associated with chromatin and ribosomes in SV40-transformed rat cells

The level of endogenous protein phosphorylation in non-histone chromosomal and ribosomal wash proteins is 7--10 times greater in SV40-transformed rat cells than in untransformed parental cells. Protein kinase activity in these proteins was fractionated by either phosphocellulose or DEAE-cellulose chromatography. One major and one minor component were detected in non-histone proteins and only one component in ribosomal wash proteins when the activity in each fraction was measured with an exogenous substrate, casein. These enzymes prefer casein to whole histone as substrate and are cyclic AMP-independent. The enzyme activity in a major peak of non-histone proteins and in ribosomal wash proteins measured with casein as substrate is 3 times greater in transformed cells than in untransformed cells, whereas pH optimum, cation requirements and apparent Km values for casein and ATP are identical or very similar in the two cell types. No significant phosphatase was detected in non-histone and ribosomal wash proteins from the two types of cell. The patterns of endogenous protein phosphorylation in these protein fractions analysed by gel electrophoresis are significantly different between these cells. These results suggest that the high level of endogenous protein phosphorylation in non-histone and ribosomal wash proteins from SV40-transformed cells is caused mainly by the increased activity of protein kinase and the nature of protein substrates.

Nucleosome-associated proteins and phosphoproteins of differentiating Friend erythroleukemia cells

Mononucleosomes derived from brief digestion of uninduced Friend cell nuclei with micrococcal nuclease contain a set of non-histone chromosomal proteins which are partly or altogether missing in the oligomeric nucleosomes. On the other hand, the latter contain a protein of Mr 190,000 not seen in the mononucleosomes. Longer digestion removes most of these non-histone proteins, excepting the Mr 190,000 protein. Brief digestion of nuclei from Friend cells induced by DMSO or by n-butyrate removes most of the non-histone proteins from the nucleosomes, as did the prolonged digestion of uninduced nuclei. The Mr 190,000 protein remains, while a protein of Mr 27,000 is increased. The rate of phosphorylation of histone H1 associated with mononucleosomes was 3 to 4-fold greater in cells induced with DMSO. The major phosphoprotein and most of the other phosphorylated non-histones were modified at the same rate in control and induced cells. However, a Mr 95,000 protein was less phosphorylated in the induced cells.

Association of DNA polymerase with nucleosomes from mammalian cell chromatin

More than half of the DNA polymerase beta in mouse ascites cell chromatin was found to be associated with monomeric nucleosomal particles (produced by micrococcal nuclease treatment of chromatin). Almost all nuclear DNA polymerase activity in lymphocytes was found to be associated with nucleosomes. The nucleosome-associated enzyme was mainly DNA polymerase beta in chromatin from resting and mainly DNA polymerase alpha in chromatin from concanavalin-A-stimulated lymphocytes.