Related base sequences in the DNA of simple and complex organisms. I. DNA-DNA duplex formation and the incidence of partially related base sequences in DNA

My Secret Life

In my early childhood, my parents gave me to my maternal grandparents for a “visit” that extended over a period of nine years. I seemed to be a fairly ordinary student in primary grades, and had to take a remedial general science class upon entering high school, my first exposure to science. It was the teacher of that class, Mr. Auer, who told me that I had scored amazingly high on a science aptitude test given to all freshmen. The people who administered the testing were convinced that I must have cheated somehow. Mr. Auer suggested that I might want to consider a career in science if I liked it. I loved it, and I did. This autobiographical article recounts my changing interests as I became aware of new fields of science during my education and the start of my career. Out of basic studies of a microbe that causes plant cancer, we developed a method to engineer new and useful genes into crop plants.

Transport of viral RNA in kb cells infected with adenovirus type 2

Messenger RNA transport was studied in KB cells infected with the nuclear DNA virus adenovirus type 2. Addition of 0.04 µg/ml of actinomycin completes the inhibition of ribosome synthesis normally observed late after infection and apparently does not alter the pattern of viral RNA synthesis: Hybridization-inhibition experiments indicate that similar viral RNA sequences are transcribed in cells treated or untreated with actinomycin. The polysomal RNA synthesized during a 2 hr labeling period in the presence of actinomycin is at least 60% viral specific. Viral messenger RNA transport can occur in the absence of ribosome synthesis. When uridine-³H is added to a late-infected culture pretreated with actinomycin, viral RNA appears in the cytoplasm at 10 min, but the polysomes do not receive viral RNA-³H until 30 min have elapsed. Only 25% of the cytoplasmic viral RNA is in polyribosomes even when infected cells have been labeled for 150 min. The nonpolysomal viral RNA in cytoplasmic extracts sediments as a broad distribution from 10S to 80S and does not include a peak cosedimenting with 45S ribosome subunits. The newly formed messenger RNA that is ribosome associated is not equally distributed among the ribosomes; by comparison to polyribosomes, 74S ribosomes are deficient at least fivefold in receipt of new messenger RNA molecules.

Reduced-stringency DNA reassociation: sequence specific duplex formation

Reduced-stringency DNA reassociation conditions allow low stability duplexes to be detected in prokaryotic, plant, fish, avian, mammalian, and primate genomes. Highly diverged families of sequences can be detected in avian, mouse, and human unique sequence dNAs. Such a family has been described among twelve species of birds; based on species specific melting profiles and fractionation of sequences belonging to this family, it was concluded that permissive reassociation conditions did not artifactually produce low stability structures (1). We report S1 nuclease and optical melting experiments, and further fractionation of the diverged family to confirm sequence specific DNA reassociation at 50 degrees in 0.5 M phosphate buffer.

Intragenomic DNA sequence homologies in the chicken and other members of the class Aves: DNA re-association under reduced stringency conditions

We have investigated the intragenomic DNA sequence homologies of twelve species of birds representing five orders, and emphasizing Galliformes. This study differs in two important ways from the classical approaches taken in constructing and evaluating phylogenies based on DNA sequence similarities. Comparisons are made on the basis of sequence homologies within genomes of related birds, rather than between genomes. DNA is reassociated at 50 degrees C in 0.5M phosphate buffer; these conditions allow formation and detection of duplexes containing more mismatch than would normally be permitted using more stringent conditions, affording an opportunity to observe more ancient sequence homologies. Thermal stability profiles of DNA duplexes formed under these conditions are the basis of comparison; three general patterns were observed. This approach emphasizes differences in sequence composition between genomes while the more traditional method of intergenomic tracer DNA hybridization at higher stringency emphasizes sequence similarities. No correlation was found between taxonomic position and intragenomic sequence composition, either within or between lineages. The thermal stability profiles of DNA duplexes formed within avian genomes did not reflect the biological similarities inferred from morphology, karyotype, and studies of interspecific hybridization. While all of the differences observed could have occurred over geological time, it was surprising that the genomes of the domestic chicken and the Red Jungle Fowl (Gallus gallus) differ in their sequence compositions. It appears that amolification/reduction events and/or positional changes occur rather often during evolution of a lineage.

On the question of integration of Agrobacterium tumefaciens deoxyribonucleic acid by tomato plants

Treatment of tomato plants with Agrobacterium tumefaciens causes subsequently administered [3H]thymidine to be preferentially incorporated into a satellite deoxyribonucleic acid (DNA) whose buoyant density is between that of bacterial DNA (rho = 1.718 g/cm3) and plant main band DNA (rho = 1.692 g/cm3). Satellite DNA upon shearing or sonic treatment releases fragments of higher and lower buoyant density, as reported by earlier investigators. The satellite has no significant base sequence homology with A. tumefaciens DNA, for its rate of reassociation is not accelerated by the addition of high concentrations of the latter. Tomato DNA isolated from shoots or from leaf nuclei accelerates renaturation of labeled satellite DNA. We conclude that the intermediate density labeled DNA is a plant satellite and not the product of covalent joining of bacterial and plant DNA as suggested by earlier investigators.

On the question of the integration of exogenous bacterial DNA into plant DNA

Extensive studies with pea, tomato, and barley failed to confirm the evidence presented by previous investigators for integration or replication of exogenously applied bacterial DNA in these plants. Labeled DNA of buoyant density in CsCl intermediate between that of high density donor bacterial DNA and of plant DNA was never observed with axenic plants. Intermediate peaks, similar to those used as evidence for recombination by earlier investigators, were observed only when the plants were contaminated with bacteria. Plant DNA prepared by a published procedure [Ledoux, L. & Huart, R. (1969) J. Mol. Biol. 43, 243-262] was found to be contaminated with unidentified impurities. Such DNA was partially protected from the action of DNase and produced aberrant banding patterns in CsCl after shearing. Much of the published evidence for integration of foreign DNA in plants is based upon experiments with plant DNA prepared by this procedure. We conclude that contamination is the likely explanation for what has been interpreted as evidence for integration.

Application of the deoxyribonucleic acid/ribonucleic acid hybridization technique in Bdellovibrio as a model for studying ribonucleic acid turnover in host-parasite systems

The kinetics of host ribonucleic acid (RNA) degradation and its resynthesis into Bdellovibrio-specific polyribonucleotides has been studied. The kinetics of RNA turnover was followed during a one-step synchronous growth cycle of Bdellovibrio growing within 32-po4-Labeled Escherichia coli host cells. The species of labeled RNA present at any given time was ascertained through the specificity of the deoxyribonuclei acid (DNA)/RNA hybridization technique. At nearsaturating levels of RNA and at zero time, 7% of the host DNA sequences and only 0.04% of the Bdellovibrio DNA became hybridized with 32-P-labeled host cell RNA (greater than 99% host specific). At the end of the burst, 98% of the labeled RNA sequences were specific for Bdellovibrio DNA. About 74% of the initial labeled host cell RNA became turned over into Bdellovibrio-specific sequences. We provide data indicating that host cell ribosomal RNA is assimilated by Bdellovibri. Degradation of host cell RNA occurs in a gradual fashion over most of the Bdellovibrio developmental growth cycle. This application of the DNA/RNA hybridization technique and its general concept should be of value in elucidating the kinetics of nucleic acid turnover in other types of host-parasite systems.

Attempts to detect Agrobacterium tumefaciens and bacteriophage PS8 DNA in crown gall tumors by DNA-DNA-filter hybridization

A systematic study of the DNA-DNA-filter reaction is presented which measures its ability to detect small amounts of simple DNA (bacterial or bacteriophage) in model mixtures of DNA immobilized on filters. Saturation curves show qualitatively that significant binding occurs when there is 10% Agrobacterium tumefaciens DNA on the filter but not 1%. PS8 bacteriophage DNA is detectable at a level of 0.1%. True saturation is not attained in the bacterial DNA reaction : radioactivity bound represents only 3% of the theoretical saturation value. The bacteriophage DNA reactions attain 15-30% of the expected saturation value. When crown gall tumor DNA filters were tested for the presence of A. tumefaciens or PS8 bacteriophage DNA by saturation reactions, an apparently significant amount of binding was observed compared with usual background levels for heterologous DNA filters. However thermal dissociation profiles revealed that no well-matched duplexes were formed. Normal tobacco callus DNA filters exhibited the same type of binding of labeled DNA to a similar extent (50-100% as much as tumor DNA filters). Both types of DNA-filters bound Bacillus subtilis and bacteriophage T4 DNA as efficiently as A. tumefaciens and PS8 DNA. The high non-specific background binding of labeled DNA by filters containing DNA isolated from plant tissue culture materials is ascribed to low single strand molecular weight of the filterbound DNA. This study provides no evidence for foreign DNA in crown gall tumors, and raises objections to the interpretation of the data of earlier investigators (Quetier, F., Huguet, T. and Guille, E. (1969) Biochem, Biophys. Res, Commun. 34, 128-133 and Srivastava, B.I.S. (1970) Life Sci. 9, 889-892) who claimed to detect A. tumefaciens DNA in crown gall tumors by DNA-DNA-filter hybridization.

Quantitative estimation of Agrobacterium tumefaciens DNA in crown gall tumor cells

Several reports suggest that Agrobacterium tumefaciens nucleic acids can induce transformation of the cells of susceptible host plants and that bacteria-free tissue cultures of transformed cells contain A. tumefaciens DNA, RNA, antigens, or bacteriophages. We assayed Vinca rosea tumor DNA for base sequence homologies with A. tumefaciens DNA by DNA.DNA solution enrichment and DNA.DNA filter saturation hybridization techniques. No homologies were found by either method. The filter saturation hybridization technique included model filters containing known percentages of bacterial DNA mixed with V. rosea leaf DNA. Using this sensitive technique, we found that no more than 0.02% of the crown gall tumor genome could be homologous to A. tumefaciens DNA. This upper estimate of homology corresponds to 0.2 bacterial genome equivalent per diploid tumor cell.

Attempts to detect deoxyribonucleic acid from Agrobacterium tumefaciens and bacteriophage PS8 in crown gall tumors by complementary ribonucleic acid-deoxyribonucleic acid-filter hybridization

Labeled ribonucleic acid (RNA) complementary to Agrobacterium tumefaciens DNA and PS8 bacteriophage DNA (cRNA) were used in a systematic study of the sensitivity of cRNA/deoxyribonucleic acid (DNA)-filter hybridization for detection of small amounts of phage or bacterial DNA immobilized on filters. A. tumefaciens cRNA of specific activity 10(6) to 2 x 10(6) counts per min per mug reacted to a significant extent when the DNA-filter contained 1% A. tumefaciens DNA in a salmon DNA background, but 0.1% A. tumefaciens DNA was not detectable. PS8 phage cRNA of the same specific activity reacted to a significant extent when the DNA-filter contained as little as 0.01% PS8 DNA in a salmon DNA background. Both kinds of cRNA were found to bind to tobacco crown gall tumor DNA-filters. Similar reaction was found with control normal callus DNA-filters but not with tobacco seedling DNA-filters. The "hybrids" formed by cRNA with normal callus and tumor DNA-filters had low thermal stability. Attempts to purify the tumor and normal callus DNA prior to immobilization on the filter resulted in elimination of this spurious binding. No evidence was found for bacterial or phage DNA in crown gall tumor DNA.

Molecular heterogeneity of the Bdellovibrios: evidence of two new species

A systematic examination of a variety of isolates of the bacterial endoparasite Bdellovibrio has revealed extensive molecular diversity. The quantity of deoxyribonucleic acid (DNA) polynucleotide homology ranges from more than 90% among the isolates with DNA containing 50 to 51% guanine plus cytosine (GC) to undetectable levels between the 43% GC and 51% GC isolates. The two isolates with low GC-containing DNA (H-I Bdellovibrio A3.12 and UKi2) have only 16% DNA homology. H-I Bdellovibrio A3.12 and 109 have barely detectable ribosomal ribonucleic acid (rRNA) homology, whereas the homology approaches 100% among all the high GC isolates tested. Cases of high DNA/DNA and DNA/rRNA homologies are reflected in low dissimilarities of enzyme migration patterns in starch gel electrophoresis. The dissimilarities exhibited among the high GC Bdellovibrio isolates are as low as those previously reported for different Escherichia coli strains. The zymograms of H-I Bdellovibrio A3.12 and UKi2 are completely different from each other as well as from all other bdellovibrios (100% dissimilarity). Genome sizes determined for the representative isolates demonstrate three size ranges which coincide with group differences based on the above measurements. Enzyme assays reveal that all isolates possess a tricarboxylic acid cycle and most contain an alanine and glutamic dehydrogenase. We conclude that the use of bacterial endoparasitism as a defining trait has resulted in a molecularly diverse collection of isolates. It is recommended that the specific epitaph bacteriovorus be used only for the type specimen (Bdellovibrio 100 of Stolp and Starr, 1963) and for other related 50 to 51% GC isolates. The heterogeneity of the group warrants two new species. We designate Bdellovibrio A3.12 as the nomenclatural type of B. starrii sp. n. and Bdellovibrio UKi2 as the nomenclatural type of B. stolpii sp. n.

An adenylic acid-rich sequence in messenger RNA of HeLa cells and its possible relationship to reiterated sites in DNA

Messenger RNA from HeLa cells contains, as part of the polynucleotide chain, RNase-resistant sequences that are labeled by adenosine but not by uridine. Heterogeneous nuclear RNA also contains adenylate-rich RNase-resistant regions, but in lower proportion than messenger RNA. Hybridization to DNA of (32)P-labeled messenger RNA reveals that some of the adenylate-rich region is included in the rapidly-hybridizing fraction.

Evolution of higher-organism DNA

A great deal of information about evolutionary events and processes has been inferred from careful studies of fossil records. Other forms of evidence have also contributed greatly to the understanding of evolution. Comparative biochemistry (Florkin, 1949), immunology (Boyden, 1942), protein sequencing (Dayoff, 1969; Anfinsen, 1959), and early DNA studies (McCarthy & Bolton, 1963; Schildkraut, Marmur & Doty, 1961) have for the most part corroborated earlier evolutionary findings, and at the same time provided new understanding of molecular processes in evolution. Of these approaches the comparison of DNA seems most promising since a relatively precise quantitative comparison can be made of all of the genetic material of different species.

A comparison between heterogeneous nuclear RNA and polysomal messenger RNA in HeLa cells by RNA-DNA hybridization

Heterogeneous nuclear RNA (HnRNA) and mRNA from cytoplasmic polyribosomes of HeLa cells have been compared by RNA-DNA hybridization tests. 1 microg of HeLa cell DNA binds 0.05-0.10 microg of either HnRNA or mRNA. In addition, HeLa DNA that is preexposed to unlabeled HnRNA was found to have a reduced capacity to bind either HnRNA or mRNA. The results are compatible with considerable sequence similarity in the two types of RNA but, as is discussed, firm conclusions are precluded by imperfections of the hybridization reaction as presently employed.

Ribosomal RNA homologies among distantly related organisms

The similarity in base sequences of ribosomal RNA (rRNA) in widely divergent organisms was compared. Hybrids were prepared between Escherichia coli and pea rRNA on the one hand and the DNA of several organisms on the other. The varying thermal stabilities of these hybrids were taken as evidence for a hierarchy of rRNA relatedness among some higher plants, and for phylogenetic relationships among some species of bacteria, protozoa, fungi, plants, and animals. The large rRNA molecule appears to have evolved faster than the small rRNA molecule.

Nucleic acid homologies among species of Saccharomyces

Evolutionary divergence among species of the yeast genus Saccharomyces was estimated from measurements of deoxyribonucleic acid (DNA)/DNA and ribosomal ribonucleic acid (RNA)/DNA homology. Much diversity was found in the DNA base sequences with several species showing little or no homology to the three reference species, S. cerevisiae, S. lactis, and S. fragilis. These three reference species also showed little or no homology to each other. On the other hand the diversity among ribosomal RNA base sequences was small since most species showed a high degree of homology to the reference species. The arrangement of species based on ribosomal RNA homologies agrees in most cases with current taxonomic groupings. A yeast hybrid (S. fragilis x S. lactis) was shown to contain two nonhomologous genomes. A minimum genome size of 9.2 x 10(9) daltons for S. cerevisiae was calculated from the rate of DNA renaturation.