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J H Waterborg

Publications and source records attributed to J H Waterborg.

At least 37 records · Page 2Linked to original sources
PubMed1991

Multiplicity of histone h3 variants in wheat, barley, rice, and maize.

Histone H3 proteins were purified to near homogeneity from etiolated seedlings of wheat (Triticum aestivum), barley (Hordeum vulgare), rice (Oryza sativa), maize (Zea mays), and alfalfa (Medicago sativa) to determine the number of histone H3 variants. Five distinct histone H3 variants were identified by gradient gel electrophoresis and reversed phase chromatography. These variants occur in various combinations of two to four forms in each plant species. One minor histone variant form (variant III, named H3.2 in alfalfa) appeared present and identical in all mono- and dicotyledonous plant species tested to date. All H3 proteins were acetylated to multiple levels and in every species the variant III form was acetylated most extensively. The level of histone H3 acetylation showed an inverse correlation with plant genome size. These observations support the idea that acetylated histones and especially variant III proteins are an element of transcriptionally active chromatin.

Journal Article↗
PubMed1990

Sequence analysis of acetylation and methylation in two histone H3 variants of alfalfa.

Analysis of acetylation in the two histone H3 variants of alfalfa by acid/urea/Triton-polyacrylamide gel electrophoresis has established that the minor variant H3.2 has a 2-fold higher level of acetylation than the major variant H3.1. Purification and sequence analysis of both variants showed sequence identity across the complete amino-terminal domain, which contains the 6 modified lysines 4, 8, 14, 18, 23, and 27. The two proteins have different distributions for acetylation: mono-, di-, and tri-methylation. The higher level of acetylation of H3.2 was confirmed in a wider pattern across all 6 lysines. Lysine modification levels varied for all sites in both proteins between 5 and 95%, with combinations of one to four types of modification co-existing at each residue. Additional sequence analysis of the H3.1 and H3.2 proteins and of tryptic core peptides established that the two histones differ only in residues 31, 41, 87, and 90. This indicates that major histone H3.1 is the product of the major alfalfa histone H3 gene and makes it likely that H3.2 is the product of the minor H3 gene, known from a partial cDNA clone. The variant-specific differences in lysine modifications in protein domains with identical primary structures suggest that the pattern and level of lysine modifications may be directed by the distinct chromatin environments of the two histone H3 variants.

Acetylation↗
PubMed1990

Dynamic histone acetylation in alfalfa cells. Butyrate interference with acetate labeling.

Dynamic histone acetylation of alfalfa (Medicago sativa) was studied in suspension cultures by short-term labeling with radioactive acetate. The relative labeling rates for the acetylated histones were in order of decreasing incorporation; H3.2 greater than H3.1 greater than H4 greater than H2B.1 greater than H2A.3. Histone H3 showed at least seven sites of acetylation, histone H2B.1 had six sites and histone H4 had five sites. Low numbers of acetylation sites were observed for histone H2B.2 and all histone H2A variants. The mass ratio, steady state acetylation and dynamic acetylation between major variant H3.1 and minor variant H3.2 were approx. 2:1, 1:2 and 2:5, respectively. Treatment of alfalfa cells with 50 mM n-butyrate did not lead to histone hyperacetylation, but instead interfered with histone acetylation labeling by acetate. The extent of apparent inhibition increased with time and concentration of butyrate. It is likely that the conversion of butyrate to acetylCoA results in dilution of the specific radioactivity of [3H]acetate in the acetylCoA pool thereby inhibiting the labeling reaction. This interpretation is supported by 14C-labeling of alfalfa acetylated histones by [1-14C]butyrate.

Acetates↗
PubMed1990

Involvement of cysteine residues in the electrophoretic mobility of histone H3 in acid-urea-Triton gels.

Carbamylation of cysteines 96 and 110 in histone H3 increases the electrophoretic mobility of this histone in acetic acid-urea-Triton X-100 polyacrylamide gels but has no effect in gels lacking Triton. Residue 96 appears to be a major determinant in the affinity of histone H3 for the nonionic detergent Triton. Carbamylation and carboxymethylation of cysteine 96 caused a major loss of the gel retardation caused by Triton. Carbamylation of cysteine 110 did not affect Triton binding but prevented ionization of the thiol side-chain moiety in the acetic acid-urea-Triton X-100 gel.

Acetylation↗
PubMed1989

Differential Histone Acetylation in Alfalfa (Medicago sativa) Due to Growth in NaCl : Responses in Salt Stressed and Salt Tolerant Callus Cultures.

The steady state distribution of histone variant proteins and their modifications by acetylation were characterized in wild type and salinity stress adapted alfalfa (Medicago sativa). Isotopic labeling detected dynamic acetylation at four sites in the histone H3 variants and five sites in histones H4 and H2B. Histone variant H3.2 was the most highly acetylated histone with 25% higher steady state acetylation and a two- to threefold higher acetylation labeling than histone H3.1. Histone phosphorylation was limited to histone variants H1.A, H1.B, and H1.C and to histone H2A.3, which was also acetylated. Histone variant composition was unaffected by cellular exposure to NaCl. Histone acetylation was qualitatively similar in salt-tolerant and salt-sensitive cells under normal growth conditions. However, short term salt stress in salt sensitive cells or continued growth at 1% NaCl in salt tolerant cells led to major increases in the multiacetylated forms of histone H4 and the two variants of histone H3. These changes were more pronounced in the diploid than in the tetraploid alfalfa strains. The increase in multiacetylation of core histones serves as an in vivo reporter suggesting an altered intranuclear ionic environment in the presence of salt. It may also represent an adaptive response in chromatin structure to permit chromatin function in a more saline intranuclear environment.

Journal Article↗
PubMed1987

Western blotting of histones from acid-urea-Triton- and sodium dodecyl sulfate-polyacrylamide gels.

We have developed a method for histone transfer from acid-urea-Triton (AUT)-polyacrylamide gels to nitrocellulose filters which prevents the interference of Triton X-100 with the binding of histones to nitrocellulose. Equilibration of AUT gels in 50 mM acetic acid and 0.5% sodium dodecyl sulfate (SDS) allowed displacement of Triton by SDS without loss of band resolution. Electrotransfer of all histone species from treated AUT gels or from equilibrated SDS gels was complete within 1 h in a transfer buffer of Tris-glycine with SDS for increased transfer efficiency and methanol for histone binding. Nitrocellulose with a pore size of 0.2 micron was optimal for histone detection.

Animals↗
PubMed1987

Histone variants and acetylated species from the alfalfa plant Medicago sativa.

The histones from the alfalfa plant Medicago sativa have been characterized in terms of type variants and levels of acetylation. Histones were isolated directly from total plant tissue (callus), eliminating the need to develop methods for nuclear isolation. An acid-urea-polyacrylamide gel with a transverse Triton X-100 gradient resolved and identified in a single gel at least one type of histone H4, two variant forms of histone H2B, two variant forms of histone H3, and four variant forms of histone H2A from a crude histone preparation. Histone H4 was present 25% in an unmodified state and 75% as monomodified, presumably as monoacetylated histone. Both histone H3 variants displayed five bands, consistent with up to four internal sites of acetylation. The two H3 variants differed in their steady-state level of acetylation, suggesting that they may reside in different chromatin environments. Several histone H1 species were identified by solubility and cross-reactivity with antiserum raised against the globular part of bovine H1(0), indicating conservation of epitopes between histone H1 of mammals and higher plants.

Acetylation↗
PubMed1986

A standard multidimensional, easy-access data file structure for Apple II computers.

A random access file structure was designed for Apple II microcomputers that allows data storage of more than 65,500 data values at 170 per Kbyte with a dynamic range of nearly 5 orders of magnitude. All or part of the data are easily accessible from BASIC under ProDOS operating conditions. The file structure accommodates single or multiple data sets in a single data file. Data values within a file with one set of data may interrelate by equal spacing along a second coordinate, such as time or space. Multiple data sets in a file can be independent, parallel or interdependent. Each interdependent data set defines the position of a data point along its coordinate in a two- or multidimensional registration system. The lowest and highest values of each data set are separately recorded to allow easy manipulation of even part of the data, e.g. for graphical presentation. The possibility of storing large numbers of data values in a single file facilitates high-resolution recording of events and simple mathematical manipulation.

Computers↗
PubMed1984

Patterns of histone acetylation in Physarum polycephalum. H2A and H2B acetylation is functionally distinct from H3 and H4 acetylation.

Histone acetylation has previously been correlated with both chromosome replication and transcription. We present evidence that (a) confirms both correlations in the true slime mold, Physarum polycephalum and (b) shows that quite a different pattern of acetate turnover is associated with replication compared with transcription. The pattern associated with replication involves turnover of acetate on all four core histones on species containing one or two acetates per molecule. This pattern was resolved from the transcription-associated pattern by three different procedures: (a) detailed analysis of gels of histones pulse-labelled with acetate; (b) the pattern of acetylation of histones pulse-labelled with [3H]lysine; and (c) the pattern of acetylation of soluble histones. The pattern associated with transcription is restricted to histones H3 and H4 and occurs mostly on highly acetylated species. This pattern was resolved by (a) analysis of gels of histones pulse-labelled with acetate; (b) the pattern of histone acetylation in G2 phase of the cell cycle; and (c) the pattern of histone acetylation in the presence of cycloheximide.

Acetates↗
PubMed1983

Acetylation and methylation sites in histone H4 from Physarum polycephalum.

Histone H4 has been isolated and purified from plasmodia of Physarum polycephalum. The four major fragments produced by hydrolysis of H4 by acetic acid were separated and the complete amino acid sequence of two of them was determined. By analogy with calf H4, these peptides are at the C-terminus and give the sequence from residue 68 to the C-terminus (residue 102). In this 35 residue sequence there are two minor differences from calf H4: (i) residue 77 is arginine in Physarum H4 and lysine in calf H4; (ii) lysine-79 is partially methylated in Physarum. Arginine occurs at position 77 in pea H4 but the occurrence of methylated lysine at position 79 has not been reported for other species. In the N-terminal region, amino acid compositions of acetic acid, tryptic and chymotryptic peptides indicate that Physarum H4 and calf H4 have identical sequences from the N-terminus to residue 47. There may be minor differences in the region from residue 46 to residue 67. The sites of acetylation were determined by Edman degradation of acetate-labelled peptide 4-17 of Physarum H4. Acetylation was observed at positions 5, 8, 12, and 16. The only other labelled peptide was the N-terminal peptide, which is not susceptible to Edman degradation and is thus probably alpha-N-acetylated as in most other organisms. The results confirm the conservation of H4 sequence and place Physarum H4 in an intermediate position between lower eukaryote H4, such as yeast or Tetrahymena H4, and higher eukaryote H4, such as mammalian H4 or pea H4.

Acetylation↗
PubMed1983

Patterns of histone acetylation in the cell cycle of Physarum polycephalum.

Labeling of histones in the naturally synchronous cell cycle of Physarum polycephalum with short pulses of tritiated acetate in vivo clearly showed three distinct patterns of histone acetate turnover. In G2 phase, turnover of acetate was observed only in histones H3 and H4, predominantly on the multiple acetylated forms. No acetate turnover was found in histones H2A and H2B compared with histones H3 and H4. In S phase, intense labeling was seen in all four core histones, in histones H3 and H4 predominantly in the low acetylated forms. In addition, cotranslational acetylation of the amino-terminal serines of histones H4 and H1 was observed during S phase. During mitosis, from condensation at prophase to decondensation after telophase, acetate turnover is almost zero. This suggests that within the mitotically condensed chromosomes all potential histone acetylation sites are masked. In G2 phase, when transcription is occurring, only histones H3 and H4 are available for acetate turnover, but in S phase, when both transcription and replication occur, all four histones are available for acetate turnover.

Acetylation↗
PubMed1983

Isolation, identification, and characterization of histones from plasmodia of the true slime mold Physarum polycephalum using extraction with guanidine hydrochloride.

Histones from plasmodia of the true slime mold Physarum polycephalum have been prepared free of slime by an approach to histone isolation that uses extraction of nuclei with 40% guanidine hydrochloride and chromatography of the extract on Bio-Rex 70. This procedure followed by chromatography or electrophoresis has been used to obtain pure fractions of histones from Physarum microplasmodia. Physarum microplasmodia have five major histone fractions, and we show by amino acid analysis, apparent molecular weight on three gel systems containing sodium dodecyl sulfate, mobility on gels containing Triton X-100, and other characterizations that these fractions are analogous to mammalian histones H1, H2A, H2B, H3, and H4. Significant differences between Physarum and mammalian histones are noted, with histone H1 showing by far the greatest variation. Histones H1 and H4 from Physarum microplasmodia have similar, but not identical, products of partial chymotryptic digestion compared with those of calf thymus histones H1 and H4. Labeling experiments, in vivo, showed that histone H1 is the major phosphorylated histone and approximately 15 separate phosphopeptides are present in a tryptic digest of Physarum histone H1. The core histones from Physarum, histones H2A, H2B, H3, and H4, are rapidly acetylated; histone H4 shows five subfractions, analogous to the five subfractions of mammalian histone H4 (containing zero to four acetyllysine residues per molecule); histone H3 has a more complex pattern that we interpret as zero to four acetyllysine residues on each of two sequence variants of histone H3; histones H2A and H2B show less heterogeneity. Overall, the data show that Physarum microplasmodia have a set of histones that is closely analogous to mammalian histones.

Chemical Phenomena↗
PubMed1983

Intranuclear localization of histone acetylation in Physarum polycephalum and the structure of functionally active chromatin.

Based on studies of histone acetylation in vivo in Physarum polycephalum, we present the following hypotheses: (1) Transcription-specific histone acetylation on histones H3 and H4 is a localized process at the nuclear matrix; (2) Histone acetylation in the S phase, which is specific for newly synthesized histones, occurs in an intranuclear nonlocalized process. These hypotheses can explain: (1) the histone specificity of histone acetylation that is dependent on the functional state of the chromatin; (2) the apparent absence of turnover of histone acetylation in the bulk of the chromatin despite a definite low level of steady-state acetylation of all four core histones in bulk chromatin; (3) the pattern of butyrate-induced hyperacetylation observed for active and inactive chromatin.

Acetates↗
PubMed1982

Substrate specificity and mode of action of the zinc-metallo nuclease from Physarum polycephalum.

The alkaline zinc-metallo nuclease of Physarum polycephalum is an endonuclease with a high specificity for single-stranded nucleic acids. Single-stranded DNA was cleaved at least 6,000 times faster than double-stranded DNA under identical conditions. In the supercoil-induced single-stranded region of Form I PM2 DNA only a single nick was made. The nuclease showed nucleotide specificity. Poly(A), poly(I), and poly(dT) were preferentially hydrolyzed. Product analysis showed that it acted by an endonucleolytic mechanism: long polynucleotides were fragmented via intermediate length products to oligo- and mono-nucleotides with the phosphate group at the 5'-terminal position. Extensive similarities exist with the single-strand-specific nuclease S1 from Aspergillus. The zinc-metallo endonuclease from Physarum could be used as a similar probe for single-stranded nucleic acids at neutral or alkaline pH conditions.

DNA↗
PubMed1980

Purification and enzymatic characterization of three endoDNase isoenzymes from Physarum polycephalum.

Three alkaline DNases, A, B, and C, with preference for the digestion of double-stranded DNA (dsDNA) were partially purified from microplasmodia of Physarum polycephalum. They were very similar but differed in their isoelectric points. These were pH 5.8 for DNase A, 7.1 for DNase B, and 9.1 for DNase C. All three enzymes consisted of a single polypeptide chain with a molecular weight of 16,000 to 17,000, which readily formed high molecular weight complexes with low enzyme activity. These complexes could be reversibly dissociated by urea, and DNase activity was quantitatively reactivated. The DNases hydrolyzed the substrate DNA by an endonucleolytic mechanism which gave 5'-phosphorylated products. Divalent cations, MnCl2 or MgCl2, were essential for enzyme activity at the optimum pH of approximately 8.5 and at low ionic strength. The optimal conditions of pH, buffer, divalent cations and ionic strength and the extent of inhibition by salt, phosphate ions or urea differed slightly but significantly between the different isoenzymes.

Chromatography, DEAE-Cellulose↗
PubMed1980

Nucleic acids and related enzymes. Secretion of four alkaline DNases by plasmodia of Physarum polycephalum.

In plasmodia of Physarum polycephalum, DNase activity with a preference for native DNA was found in a pattern of three or four isoenzymes. During growth a constant specific activity of approx. 0.3 unit of DNase activity per mg protein was found in the plasmodia, with a broad maximum during the G2-phase in the naturally synchronous flat cultures. Under conditions of starvation or sclerotization, DNase activity was secreted by the plasmodia in amounts which were up to ten times higher than the internal level of enzyme activity. Purification of the secreted DNase activity to high purity by three simple chromatographic steps showed that four different DNase isoenzymes existed which were identical with the intracellular ones. The relative abundances of the various isoenzyme forms inside and outside the plasmodia seemed to be slightly different. The possible functions of the DNase activities are discussed.

Cell Cycle↗