Biomedical subjects

J H Waterborg

Publications and source records attributed to J H Waterborg.

14 recordsLinked to original sources

PubMed1992

Identification of five sites of acetylation in alfalfa histone H4.

Radioactive acetylation in vivo of plant histone H4 of alfalfa, Arabidopsis, tobacco, and carrot revealed five distinct forms of radioactive, acetylated histone. In histone H4 of eukaryotes ranging from fungi to man, acetylation is restricted to four lysines (residues 5, 8, 12, and 16) possibly caused by a quantitative methylation of lysine-20. Chemical and proteolytic fragmentation of the amino terminally blocked alfalfa H4 protein, dynamically acetylated by radioactive acetate in vivo, allowed protein sequencing and identification of selected peptides. Peptide identification was facilitated by analyzing fully characterized calf histone H4 in parallel. Acetylation in vivo of alfalfa histone H4 was restricted to the lysines in the amino-terminal domain of the protein, residues 1-23. Lysine-20 was shown to be free of methylation, as in pea histone H4. This apparently makes lysine-20 accessible as a novel target for histone acetylation. The in vivo pattern of lysine acetylation (16 greater than 12 greater than 8 greater than or equal to 5 = 20) revealed a preference for lysines -16 and -12 without an apparent strict sequential specificity of acetylation.

Acetylation↗

PubMed1992

Existence of two histone H3 variants in dicotyledonous plants and correlation between their acetylation and plant genome size.

Histone H3 proteins were purified to near homogeneity from callus cultures of dicotyledonous plants alfalfa, soybean, Arabidopsis, carrot and tobacco to determine the number of histone H3 variants. In every species two histone H3 variants were identified by gradient gel electrophoresis and reversed-phase chromatography. They were named H3.1 and H3.2 in order of increasing mobility in acid-urea-Triton gels. Co-electrophoresis of histone H3.2 proteins of all species in this gel system and HPLC co-chromatography suggest that all histone H3.2 variants have a primary protein sequence identical to alfalfa H3.2. Two distinct H3.1 variant forms were identified, represented by alfalfa and Arabidopsis H3.1 proteins which differ only at residue 90. Soybean H3.1 resembles H3.1 of alfalfa. Carrot and tobacco H3.1 appear identical to the Arabidopsis H3.1 histone variant. All H3 proteins were acetylated to multiple levels and in each plant the histone H3.2 forms were more highly acetylated. An inverse relationship was observed between plant genome size and the relative abundance of histone variant H3.2 and also with the level of acetylation of both histone H3 variants. This correlation matches the general tendency that in plants with smaller genomes a larger fraction of the genome is transcriptionally active.

Acetylation↗

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↗

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↗

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

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↗

PubMed1979

Purification of an alkaline nuclease from Physarum polycephalum.

An alkaline nuclease was purified from microplasmodia of Physarum polycephalum. The nuclease, active on denatured DNA and RNA and free of contamination by other nucleolytic activities, appeared to be a zinc-metallo protein. The enzyme was only active under conditions, where Zn2+ were retained in the enzyme. Loss of zinc occurred by the chelating action of EDTA, EGTA or ampholines, by acid of highly alkaline pH conditions or by high ionic strength. The addition of ZnCl2 to compensate losses, restored all activity, while all other divalent cations caused inhibition. The nuclease, with a molecular weight of 32 000, was stable at neutral pH at high temperatures with a half-life of 20 min at 80 degrees C. It was inhibited by any salt of buffer concentration above the level of zero ionic strength and showed a special sensitivity towards phosphate ions. The possible similarity of this enzyme to nuclease S1 from Aspergillus oryzae is pointed out.

Deoxyribonucleases↗

PubMed1977

Endonuclease activity in nuclei of Physarum polycephalum. Partial purification and characterization.

An endonuclease, present in the microplasmodia of Physarum polycephalum, has been partially purified from isolated nuclei by DEAE-cellulose and Sephadex G-75 chromatography. 1. The endonuclease produced single-strand scissions in double-stranded DNA which resulted in the generation of 5'-phosphoryl and 3'-hydroxyl termini. No activity was observed with single-stranded DNA as substrate. 2. The pH optimum was approximately 8.5. 3. Divalent cations were essential for enzyme activity. MnCl2 and MgCl2 gave maximal activity. CaCl2, ZnCl2 or CoCl2 did not activate the enzyme. 4. The endonuclease activity was highly sensitive to monovalent cations. 5. Endonuclease activity was found in two forms after gel filtration: an activity in a homogeneous peak with a molecular weight of approx. 20 000, and an activity that had a heterogeneous molecular weight and which was isolated in a complex with DNA. A possible function of the endonuclease in DNA replication is discussed.

Cations, Divalent↗