DNA of ciliated protozoa

DNA was isolated from macronuclei and micronuclei of the ciliated protozoan, Stylonychia mytilus under conditions that minimize the possibility of DNA degradation. Macronuclear DNA has an S value of 10 to 11 in sucrose gradients. Macronuclear DNA has an average molecular weight of 1.15×10⁶ daltons and a range of molecular weights of 1.0×10⁶ to 1.95×10⁶ daltons. The average length of macronuclear DNA, measured by electron microscopy, is 0.80 microns and the range is 0.2 to 2.2 microns. Almost all micronuclear DNA pieces are too long to be measured by electron microscopy. The shortest piece of micronuclear DNA found was 15.0 microns in length.     

The molecular complexity of mu and pi symbiont DNA of Paramecium aurelia

The molecular size of mu and pi symbionts of Parameciumaurelia has been calculated from renaturation kinetic data. Observed values were 0.78 × 10⁹ daltons for mu particle DNA and 0.81 × 10⁹ daltons for pi particle DNA. Estimates of analytical complexity were 4.45 × 10⁹ and 5.05 × 10⁹ daltons respectively. Based on these data, mu and pi symbionts appear to possess multiple genomes and contain a minimum of 5 or 6 copies of each DNA sequence.     

Isolation and some properties of a mammalian ribosomal DNA

The DNA coding for 28 S and 18 S ribosomal RNA, including the spacer regions, has been isolated from calf (Bos taurus) thymus gland. The method used included shearing of the total DNA to a highly homogeneous size population, selective heat denaturation and S 1 nuclease treatment to remove single stranded DNA. Repeated centrifugation on density gradients yields a 140-fold purified rDNA fraction with a GC content of 61.2%. Eco RI nuclease cleaves this DNA into two fragments of 16.4 and 4.9×10⁶ daltons. Hybridization of these fragments with 28 S and 18 S rRNA shows that the 28 S coding sequence is located mostly on the 4.9×10⁶ dalton fragment, while both the 16.4 and 4.9×10⁶ dalton fragments contain the 18 S sequence. The data indicate that the ribosomal RNA gene has a repeat unit of 21.3×10⁶ daltons which includes a nontranscribed spacer of about 12.5×10⁶ daltons.     

Characterization of the plasmid DNAs of Rhodopseudomonas capsulata

Presence of extrachromosomal DNa in Rhodopseudomonas capsulata strain BH9 was shown by the appearance of a satellite band in a dye-buoyant density gradient. Radioactively labelled DNA was prepared from this satellite band and examined on a 5–20% sucrose gradient. Three radioactive peaks with sedimentation coefficients of 100 S, 94 S, and 58–64 S, respectively, were consistently observed. Analysis of these sedimentation coefficients suggested that there are two species of plasmid DNA with molecular sizes of 94×10⁶ daltons (named pBH91) and 74×10⁶ daltons (named pBH92). The 58–64 S peak is attributed to open circular molecules. DNAs from each peak of the sucrose gradient were examined by electronmicroscopy, and the results agree closely with those of the sucrose gradient analysis. Reassociation kinetics of the plasmid DNA was also followed. Addition of total DNA of strain BH9 increased the renaturation rate of the plasmid DNA. It was calculated from the magnitude of the increase that approximately 10% of the BH9 total DNA may hybridize with the plasmid sequences. DNA prepared from the gene transfer agent (GTA) produced by R. capsulata increases the renaturation rate of the plasmid to the same extent as total DNA isolated from the GTA producing strain, Y262.     

Ribosomal genes not integrated into chromosomal DNA in Drosophila melanogaster

DNA obtained by a gentle lysis procedure from adult Drosophila melanogaster was analyzed by sucrose gradient sedimentation. The major portion of the DNA has an estimated weight of at least 5–10×10⁹ daltons. All of the ribosomal genes are present in this high molecular weight DNA in adult males with one nucleolus organizer or in adult females with two nucleolus organizers as shown by hybridizing fractions of the gradient with ribosomal RNA. In female adults with one nucleolus organizer instead of the usual two, 68% of the ribosomal genes are found in high molecular weight DNA and 32% are found in DNA of smaller size (3×10⁸ daltons). We propose that these latter genes are not integrated into the DNA of the chromosome.     

Deoxyribonucleic acid base composition and genome size of Prochloron

The DNA base composition of the photosynthetic prokaryote Prochloron was determined (on samples collected from the natural environment) to be 40.8 mol% GC. The sharp differential melting curve indicated the absence of significant quantities of contaminating DNA from other organisms. The genome size, estimated from the renaturation kinetics of thermally denatured DNA, was 3.59×10⁹ daltons mol. wt, similar to that of many other prokaryotes. The fact that Prochloron has not yet been cultured in the laboratory cannot, therefore, be attributed to a reduced genetic information content.     

NUCLEAR GENE DOSAGE EFFECTS ON MITOCHONDRIAL MASS AND DNA

In order to assess the effect of nuclear gene dosage on the regulation of mitochondria we have studied serial sections of a set of isogenic haploid and diploid cells of Saccharomyces cerevisiae, growing exponentially in the absence of catabolite repression, and determined the amount of mitochondrial DNA per cell. Mitochondria accounted for 14% of the cytoplasmic and 12% of the total cellular volume in all cells examined regardless of their ploidy or their apparent stage in the cell cycle. The mean number of mitochondria per cell was 22 in the diploid and 10 in the haploids. The volume distribution appeared unimodal and identical in haploids and diploids. The mitochondrial DNA accounted for 12.6 ± 1.2% and 13.5 ± 1.3% of the total cellular DNA in the diploid and haploid populations, respectively. These values correspond to 3.6 x 10^-15 g, 2.2 x 10⁹ daltons, or 44 genomes (50 x 10⁶ daltons each) per haploid and twice that per diploid cell. On this basis, the average mitochondrion in these cells contains four mitochondrial genomes in both the haploid and the diploid.     

Evidence for dosage compensation in parthenogenetic Hymenoptera

Amount of DNA-Feulgen staining in individual somatic nuclei and mature sperm of the parthenogenetic wasps, Habrobracon juglandis, H. serinopae, and Mormoniella vitripennis, were determined with a scanning microdensitometer. The haploid genome for both species of Habrobracon was estimated to be 0.15–0.16×10^–12 g DNA, corresponding to a molecular weight of roughly 10×10¹⁰ daltons. The haploid genome of M. vitripennis is approximately twice this value, 0.33–0.34×10^–12 g, or about 20×10¹⁰ daltons. Measurements made on dividing nuclei from syncytial preblastoderm embryos of H. juglandis and M. vitripennis showed that the chromosomes of impaternate males were present in the haploid number and contained the C amount of DNA; whereas nuclei from female preblastoderm embryos contained the diploid number of chromosomes and the 2C amount of DNA. However, hemocyte and brain cell nuclei from either male or female adult wasps contained 2C and 4C amounts of DNA. Both sexes also showed equivalent levels of polyploidy (8C, 16C, or 32C) in Malpighian tubule nuclei. Therefore, in these parthenogenetic species, a mechanism must exist that compensates during later development for the initial two-fold difference in the chromatin content of somatic nuclei in haploid male and diploid female embryos. Hemocytes from impaternate Mormoniella diploid males and triploid females contain the 2C and 3C amounts of DNA, respectively. Therefore dosage compensation involves an additional cycle of DNA replication only in haploid cells, and it insures that a certain minimum quantity of DNA is received by each somatic cell.     

Organization of the 5S RNA genes in macro- and micronuclei of Tetrahymena pyriformis

The organization of the 5S genes in macro- and micronuclei of Tetrahymena pyriformis was studied using restriction endonucleases. After complete digestion of macronuclear DNA with BamH-I or Hpa I, 5S RNA hybridized to a DNA fragment of approximately 280 base pairs (bp). When macronuclear DNA was only partially digested with these enzymes, hybridization with ³²P-5S RNA demonstrated an oligomeric series with a spacing of 280 bp. These results indicate that the 5S genes are tandemly repeated in macronuclei and that the repeating unit is 280 bp (or 180,000 daltons). Since 5S RNA is 120 nucleotides, we conclude that the 5S repeat units contain a 120 bp transcribed region and a 160 bp spacer region. When macronuclear DNA was digested with Eco RI, Bgl I, or Eco RI + Bgl I, 5S RNA hybridized to DNA of molecular weight 3–4×10⁶, suggesting that these enzymes do not cleave within a 5S repeat. These 3–4×10⁶ dalton fragments define the maximum size of an average cluster of 5S repeated units. Assuming the size of the 5S repeat to be 0.18×10⁶ daltons, there are about 15–20 5S repeats per average tandem cluster, and since there are 350 5S-genes per haploid genome, there must be approximately 15–20 tandem arrays. Results obtained using micronuclear DNA suggest that organization of the 5S-genes is very similar in macro- and micronuclei. Macronuclear rRNA genes are extracnromosomal palindromic dimers. In contrast, 5S genes in Tetrahymena were found to be integrated within the genomes of both macro- and micronuclei and not linked to the rRNA genes. Moreover, it is unlikely that they are palindromes; rather they appear to be tandemly repeated in head-to-tail linkages. Thus, the organization of the 5S genes in Tetrahymena is similar to that of higher eukaryotes.     

Analysis of DNA of male and femaleSphaerocarpos donnellii Aust. (Liverwort)

Summary The karyotypes of females and males ofSphaerocarpos donnellii differ in that there is a large essentially heterochromatic X chromosome in the female (approx. 25 volume-% of the autosomes) and a small Y chromosome in the male (0.1–3 volume-% of the autosomes). DNA from females and males differ in buoyant densities in cesium chloride equilibrium gradients (1.702₅ and 1.703₅g cm^-3, respectively) and in melting points (87.5 and 88.5°C in SSC). The differences are statistically significant. Base analyses revealed 2.5 Mol-% of the rare base 5-methyl cytosine. Upon reassociationSphaerocarpos DNA behaves kinetically in a heterogeneous manner. About 22% of the DNA is repetitive with an average kinetic complexity of 1.6×10⁸ daltons. The kinetic complexity of the slow reassociating DNA fraction, considered to be of the single copy type, is 3.2×10¹⁰ daltons. No difference in the renaturation behavior between DNA of males and females could be detected with the techniques used. Our data thus indicate that X chromosomal DNA cannot contain large amounts of highly repeated nucleotide sequences and that it is slightly enriched in AT content compared to the autosomes.     

DNA amounts in the nuclei of Paramecium bursaria

DNA amounts in the macronuclei and micronuclei of syngen 4 of Paramecium bursaria were determined. There was a wide distribution of values for the amount of DNA in the macronucleus. This distribution remained wide, but moved to lower values as the animals were starved. The micro-nuclear DNA values were constant under all culture conditions, at a value of 7.5 × 10^–12 g per nucleus. This gave an estimate of the haploid genome size, 2.25 × 10¹² daltons, which is approximately ten times that obtained by DNA renaturation studies.This work was supported by a Commonwealth Scholarship to the author. Thanks are due to the Medical Research Council for funds to purchase the Vickers densitometer.     

Isolation and characterization of plasmid from the Bacillus brevis var. G.-B. cells

Summary The plasmid designated pAD1 was isolated from the cells of four variants of Bacillus brevis var. G.-B. The plasmid DNA has a molecular weight of about 47.1×10⁶ daltons and contains 43.4 mole % G+C. The bulk of pAD1 DNA (96–98%) is associated with the fraction of chromosome DNA and membranes.Restriction endonucleases SmaI, SalI and BamHI cleaved the plasmid DNA into two, two and six fragments, respectively. The cleavage map of the pAD1 genome has been constructed for these three endonucleases. Restriction enzymes EcoRI, HindIII, KpnI and PstI hydrolized the plasmid DNA into 16, 21, 10 and 9 fragments, respectively. The presence of repeated sequences in the plasmid genome was shown based on pAD1 DNA cleavage by these endonucleases.     

The pattern of protein and nucleic acid synthesis in germinating spores of Phycomyces blakesleeanus

Summary Synthesis of proteins, RNA and DNA is measured by incorporation of labelled precursors at different times during germination of Phycomyces spores.RNA and protein synthesis increases immediately after activation. DNa synthesis begins at a later stage (± 8 h) of germination when germ tubes are already present. Nuclear division occurs earlier in germination (±4–5 h) and is accompanied by a decrease in RNA synthesis. It can be concluded that at least most of the dormant spores are in the G2 phase of the cell cycle.Analysis of ribosomal RNA after pulse-chase labelling shows only three labelled compounds: a precursor molecule (2.25×10⁶ daltons) and the two mature ribosomal RNA compounds (1.4×10⁶ and 0.7×10⁶ daltons). This suggests that the two rRNAs are formed directly from the precursor molecule. Cycloheximide totally blocks the transformation of the ribosomal precursor molecule into mature rRNA.     

Determination of the nuclear DNA content of Saccharomyces cerevisiae and implications for the organization of DNA in yeast chromosomes.

The DNA content of the nucleus of the yeast Saccharomyces cerevisiae has been determined by both renaturation kinetics and DNA per cell measurements. Renaturation kinetics experiments were performed by following the decrease of optical hyperchromicity at 260 nm and by hydroxyapatite chromatography. DNA per cell measurements were made by the diaminobenzoic acid method and by the ethidium bromide method of Klotz &; Zimm (1972b). The conclusion from the above experiments is that the S. cerevisiae nucleus contains 9 × 10⁹ ± 2 × 10⁹ daltons of DNA. Previously we (Lauer &; Klotz, 1975) had measured the molecular weight of the largest piece of DNA in the yeast nucleus to be 2 × 10⁹ ± 0.2 × 10⁹. Here we extend this work by using a more highly protein-denaturing buffer system and conclude that the largest piece of DNA in the S. cerevisiae nucleus contains 1.5 × 10⁹ to 2.2 × 10⁹ daltons of DNA in both haploid and diploid cell lysates. From genetics, the largest yeast chromosome should contain 13% of the genome, or 0.9 × 10⁹ to 1.5 × 10⁹ daltons of DNA (using our DNA per cell range). Thus, the large DNA we measure contains from one to two times the amount of the DNA predicted from genetics to be in the largest chromosome. In light of these new data, viscoelastic measurements on yeast DNA are now consistent with the idea that each chromosome contains one piece of DNA.     

Evidence that in higher plants the 25S and 18S rRNA genes are not interspersed with genes for 5S rRNA

DNA samples from various higher plants (Phaseolus aureus, Glycine max, Matthiola incana, Brassica pekinensis, Cucumis melo) were centrifuged in actinomycin-caesium chloride gradients and the genes coding for the ribosomal RNAs were detected by hybridisation with tritium labelled 5S and 25S+18S rRNA, respectively. With DNA of low molecular weight (< 5×10⁶ daltons) the 5S and 25S+18S rRNA genes are often fractionated together. A good separation of the genes for 25S+18S rRNA from the 5S rRNA genes occurred only with high molecular weight DNA (> 10×10⁶ daltons) indicating that at least most of the 5S rRNA genes are not linked to, or interspersed with, the genes coding for 25S and 18S rRNA. This result is in agreement with the situation in animal cells and in contrast to that reported for bacteria, lower eukaryotes and chloroplasts.     

Chromosome-sized DNA molecules from Drosophila

Measurements of viscoelastic retardation times of detergent-Pronase lysates of Drosophila cells demonstrated the presence of large numbers of DNA molecules of a size commensurate with that of the chromosomes. The values estimated from the retardation times for the molecular weights of the largest molecules ranged from about 20×10⁹ to 80×10⁹ daltons depending on the species of Drosophila. The molecular weights of the DNA molecules were independent of the metaphase shapes (i.e., metacentric or submetacentric), but were proportional to the DNA contents of the chromosomes in the case of translocations or deletions. It was concluded, therefore, that the DNA molecules must run the length of the chromosome and cannot be discontinuous at the centromere. When compared with the values of the DNA contents of Drosophila chromosomes determined by other methods, the results were consistent with the model of one, or possibly two, DNA molecules per chromosome; the simplest conclusion, that there is only one DNA molecule per chromosome (for simple chromosomes), rests on a long extrapolation of an empirical relation between retardation time and molecular weight, but is also favored by indirect evidence. Further possibilities which could not be excluded were that the large DNA molecules contained Pronase-resistant, non-DNA links, or that a fraction of smaller DNA molecules might also have been present in the chromosomes. Chromosome-sized DNA molecules were obtained almost quantitatively from unsynchronized cultured cells, suggesting that the size of the chromosomal DNA is conserved throughout much of the cell cycle. The molecules were stable for periods of up to several days at 50° C in solutions containing detergent, Pronase, and EDTA.     

Physical and mapping properties of distant linkages between genetic markers in transformation of Bacillus subtilis

Summary DNA purified by a procedure based on phenol extraction contained many intact linkages, i.e. between genetic markers showing less than 20% cotransfer. The molecular weight of this DNA, as revealed by zone centrifugation, varied between 4.5×10⁷ and 2.5×10⁸. Linkages with cotransfer frequencies greater than 10% were found to consist of not more than 6.0×10⁷ daltons of DNA, while one linkage showing only 2% cotransfer was provisionally estimated to be about 1.5×10⁸ daltons. With the aim of extending the transformation map of B. subtilis, 16 mutations for nutritional requirements, not suspected—on the basis of the phenotypes involved—to be linked to any other markers, were examined for linkage with each other and to markers on the existing map. Three new pairs of distantly linked markers were found, but no linkage to any location on the known map.The study of the linkage properties of markers which Oishi, Yoshikawa and Sueoka localized on their replication map suggests that some of these markers may have been misplaced.     

DNA of ciliated protozoa: DNA sequence diminution during macronuclear development of oxytricha

We have measured the reassociation kinetics of DNA from the micronucleus and from the macronucleus of the hypotrichous cillate Oxytricha. The micronuclear DNA reassociates with at least a two-component reaction, indicating the presence of both repeated and non-repeated sequences. The kinetic complexity of micronuclear non-repeated DNA is in the range of 2 to 15 × 10¹¹ daltons; the haploid DNA content of the micronucleus is 4 × 10¹¹ daltons (0.66 pg), measured microspectrophotometrically. The DNA of the macronucleus reassociates as a single second-order reaction, with a kinetic complexity of 3.6 × 10¹⁰ daltons. A comparison of the kinetic complexities of micronuclear and macronuclear DNAs suggest a 5 to 30 fold reduction in DNA sequence complexity during the formation of a macronucleus from a micronucleus. Macronuclear DNA is in pleces with an average molecular weight of 2.1 × 10⁶ daltons. Since the kinetic complexity of macronuclear DNA is 3.6 × 10¹⁰ daltons, the macronucleus must contain about 17,000 different kinds of DNA pieces.Each macronucleus contains 3.5 × 10¹³ daltons (58 pg) of DNA, indicating that each sequence must be present about 1000 times per macronucleus or 2000 times per cell.     

Deoxyribonucleic acid homologies among 96 strains of ammonia-oxidizing bacteria

DNA of 96 strains of the genera Nitrosomonas, Nitrosococcus, Nitrosospira, Nitrosolobus, and Nitrosovibrio was isolated and analysed spectrophotometrically. Percentages of guanine plus cytosine (G+C) content, genome sizes, and DNA-DNA homologies were determined. The results indicated the presence of eight Nitrosomonas species, three or four Nitrosococcus species, five Nitrosospira species, and two species of both Nitrosolobus and Nitrosovibrio. DNA homologies between strains of a separate species ranged from 56–100%. Average homologies between strains of different species were 33% in Nitrosococcus, 36% in Nitrosomonas, 37% in Nitrosolobus, 40% in Nitrosospira, and 42% in Nitrosovibrio. Average homologies between species of different genera were 33% and thus not significantly above the background value of 30% detected between DNA of ammonia-oxidizing bacteria and Escherichia coli. Genome sizes ranged from 1.90–2.74×10⁹ dalton in Nitrosomonas, 2.09–2.37×10⁹ dalton in Nitrosococcus, 1.87–2.15×10⁹ dalton in Nitrosospira, 1.92–2.10×10⁹ dalton in Nitrosolobus, and 1.91–2.15×10⁹ dalton in Nitrosovibrio. Differences in genome sizes were in accordance with DNA homologies.     

Repair of DNA double-strand breaks in Escherichia coli, which requires recA function and the presence of a duplicate genome.

A method was devised for extracting, from cells of Escherichia coli K12, DNA molecules which sedimented on neutral sucrose gradients as would be expected for free DNA molecules approaching the genome in size. Gamma ray irradiation of oxygenated cells produced 0.20 DNA double-strand breaks per kilorad per 10⁹ daltons. Incubation after irradiation of cells grown in K medium, with four to five genomes per cell, showed repair of the double-strand breaks. No repair of double-strand breaks was found in cells grown in aspartate medium, with only 1.3 genomes per cell, although DNA single-strand breaks were still efficiently repaired. Cells which were recA^? or recA^?recB^? also did not repair double-strand breaks. These results suggest that repair of DNA double-strand breaks may occur by a recombinational event involving another DNA double helix with the same base sequence.