DNA segregation in Escherichia coli cells with 5-bromodeoxyuridine-substituted nucleoids.

The pattern of segregation of DNA in Escherichia coli K-12 was analyzed by labeling replicating DNA with 5-bromodeoxyuridine followed by differential staining of nucleoids. Three types of visible arrangement were found in four-nucleoid groups derived from a native nucleoid after two replication rounds. Type A, segregation of both old strands toward cell poles, appeared with the highest frequency (0.6 to 0.8). Type B, segregation of one old strand toward the cell pole and the other toward the cell center, was twice as frequent as type C, segregation of both old strands toward the cell center. These results confirm previous data showing that DNA segregation in E. coli is nonrandom while presenting a certain degree of randomness. The proportions of the three indicated types of arrangement suggest a new probabilistic model to explain the observed segregation pattern. It is proposed that DNA strands segregate either nonrandomly, with a probability of between 0 and 1, or randomly. In nonrandom segregation, both old strands are always directed toward cell poles. Experimental data reported here or by other authors fit better with the predictions of this model than with those of other previously proposed proposed deterministic or probabilistic models.     

Cytological Studies of Deoxyribonucleic Acid Replication in Escherichia coli 15T−: Replication at Slow Growth Rates and After a Shift-Up into Rich Medium

We examined the gross nuclear morphology of Escherichia coli 15T⁻ grown in different media with doubling times ranging from 22 to 270 min. In slowly growing cells, deoxyribonucleic acid synthesis was measured by autoradiography and shown to occur with greatest probability during the first two-thirds of the division cycle. In such cells, segregation occurred later, at the end of the division cycle rather than at the end of deoxyribonucleic acid replication. Nuclear regions in L-broth cells (22-min doubling time) cannot correspond to separate chromosomes but probably represent regions of replication activity. Segregation of template nucleotide strands was measured after a shift-up from proline M9 or glucose M9 media into L broth. A model is presented to account for the pattern of segregation observed.     

Four proteins synthesized in response to deoxyribonucleic acid damage in Micrococcus radiodurans.

Four proteins, alpha beta, gamma, and delta, preferentially synthesized in ultraviolet light-treated cells of Micrococcus radiodurans, were characterized in terms of their molecular weights and isoelectric points. Within the sublethal-dose range, the differential rate of synthesis for these proteins increased linearly with the inducing UV dose. The degree of induction reached 100-fold, and the most abundant protein beta, amounted to approximately 2% of the total newly synthesized protein after irradiation. Damage caused by ionizing radiation or by treatment with mitomycin C also provoked the synthesis of the four proteins. The proportions between the individual proteins, however, varied strikingly with the damaging agent. In contrast to treatments which introduced damage in the cellular deoxyribonucleic acid, the mere arrest of deoxyribonucleic acid replication, caused by nalidixic acid or by starvation for thymine, failed to elicit the synthesis of either protein. Repair of deoxyribonucleic acid damage requires that a number of versatile and efficient processes by employed. It is proposed that the induced proteins participate in deoxyribonucleic acid repair in M. radiodurans. Mechanisms are discussed which would allow a differentiated cellular response to damages of sufficiently distinctive nature.     

Control of cell length in Bacillus subtilis.

During inhibition of deoxyribonucleic acid synthesis in Bacillus subtilis 168 Thy-minus Tryp-minus, the rate of length extension is constant. A nutritional shift-up during thymine starvation causes an acceleration in the linear rate of length extension. During a nutritional shift-up in the presence of thymine, the rate of length extension gradually increases, reaching a new steady state at about 50 min before the new steady-state rate of cell division is reached. The steady-state rates of nuclear division and length extension are reached at approximately the same time. The ratio of average cell length to numbers of nuclei per cell in exponential cultures is constant over a fourfold range of growth rates. These observations are consistent with: (i) surface growth zones which operate at a constant rate of length extension under any one growth condition, but which operate at an absolute rate proportional to the growth rate of the culture, (ii) a doubling in number of growth zones at nuclear segregation, and (iii) a requirement for deoxyribonucleic acid replication for the doubling in a number of sites.     

Incorporation and excision of 5-fluorouracil from deoxyribonucleic acid in Escherichia coli.

When Escherichia coli are grown in the presence of 5-fluorouracil, the 5-fluorouracil is incorporated almost exclusively into ribonucleic acid as fluorouridylate. In this study, small but detectable amounts were incorporated into ribonucleic acid as fluorocytidylate and into deoxyribonucleic acid as fluorodeoxyuridylate and fluorodeoxycytidylate. The amount of 5-fluorouracil found in deoxyribonucleic acid as fluorodeoxyuridylate increased 50-fold when the cells were deficient in both deoxyuridine triphosphatase and uracil-deoxyribonucleic acid glycosylase activities. Therefore, the same mechanisms which excluded uracil from deoxyribonucleic acid in vivo also excluded 5-fluorouracil. Even though purified uracil-deoxyribonucleic acid glycosylase excised 5-fluorouracil from deoxyribonucleic acid at only 5% the rate with which it excised uracil, most of the 5-fluorouracil excised from deoxyribonucleic acid in vivo was apparently excised directly by uracil-deoxyribonucleic acid glycosylase rather than by repair initiated by excision of uracil.     

Rate stimulation of deoxyribonucleic acid synthesis after inhibition.

The degree to which the rate of deoxyribonucleic acid synthesis in thy- cultures of Escherichia coli is stimulated after a period of thymine starvation is shown to be a function of the concentration of thymine present as well as of the culture doubling time. Inhibition of deoxyribonucleic acid synthesis by nalidixic acid yields comparable results. Periods of thymine starvation exceeding one doubling time appear to cause an irreversible inactivation of a fraction of the replication forks in the culture.     

Transport of DNA from Lymphocytes to Fibroblasts in Culture

The exchange of radioactivity between lymphocytes, labelled with (³H) thymidine after stimulation with Concanavalin A, and recipient V79 fibroblasts in culture was studied. The radioactive material involved in this exchange was macromolecular deoxyribonucleic acid as well as its breakdown products. This deoxyribonucleic acid from lymphocytes localised in the nuclei of the host cells soon after contact between donor and recipients. This occurred even when the V79 fibroblasts were confluent at high cell density, and thus in a steady, non-growing state with respect to cell numbers.
The fate of the radioactive donor lymphocyte deoxyribonucleic acid, substituted with bromodeoxyuridine, was followed in the recipient cells by analysing its buoyant density in caesium chloride gradients. This deoxyribonucleic acid was found to become associated with the nuclear deoxyribonucleic acid of the host cells, involving both retention of relatively intact donor deoxyribonucleic acid as well as its breakdown and re-utilisation for host cell deoxyribonucleic acid synthesis. Nongrowing recipient cells were found to retain the donor deoxyribonucleic acid in relatively intact form for much longer periods than when the same cells were in logarithmic growth phase.     

Plasmid deoxyribonucleic acid replication in Streptomyces griseus

A series of electron micrographs showing the presence of different molecular forms representing various replication stages of plasmid deoxyribonucleic acid from Streptomyces griseus was obtained. Based upon an analysis of these electron micrographs, a tentative model for plasmid deoxyribonucleic acid replication in S. griseus is proposed.     

The Isolation and Characterization of Adenosine Monophosphate-rich Polynucleotides Synthesized by Soybean Hypocotyl Cells: Their Relation to Messenger Ribonucleic Acid

Plant ribonucleic acids which have high adenosine monophosphate concentrations were studied. Purified deoxyribonucleic acid-like ribonucleic acid and tenaciously bound ribonucleic acid fractions both contained poly-adenosine monophosphate sequences (those from the latter being longer than those from the former); without these poly-adenosine monophosphate sequences their base compositions were the same. The average poly-adenosine monophosphate sequence from purified tenaciously bound ribonucleic acid was 160 residues long, as measured by gel electrophoresis. However, base hydrolysis and chromatography indicated one 3′-nucleoside (adenosine) per 71 nucleotides, giving a chain length of 72 residues. The dominant species in the cytoplasm, as measured by radioactive precursor incorporation, was tenaciously bound ribonucleic acid, whereas deoxyribonucleic acid-like ribonucleic acid was present in greater amounts in the nucleus. This work provides evidence that deoxyribonucleic acid-like ribonucleic acid and tenaciously bound ribonucleic acid represent forms of messenger ribonucleic acid in soybean, with deoxyribonucleic acid-like ribonucleic acid residing in the nucleus, perhaps as the messenger ribonucleic acid precursor, and tenaciously bound ribonucleic acid residing, as the active messenger ribonucleic acid, in the cytoplasm.     

Merodiploid ribosomal loci arising by transformation and mutation in pneumococcus

Merodiploid states have been detected in the ery and str loci of the pneumococcal genome. They are associated with particular mutations (ery-r10 and str-d2) which add to, rather than replace their homologous sites during deoxyribonucleic acid (DNA)-mediated transformation. Markers at linked sites do not become diploid at the same time. The heterozygous condition thus produced is maintained during cell reproduction. However, in the case of the ery merodiploid at least, segregation of haploid types does occasionally occur. The transforming properties of DNA isolated from the merodiploids, taken together with the segregation patterns of the merodiploids, reveal the heterozygous condition. The merodiploid condition can be transferred via a single molecule of DNA, which can be explained by assuming that both alleles at the diploid site are integrated into the linear continuity of the bacterial chromosome. In the case of the ery merodiploid, two distinct, relatively stable but interconvertible states are recognizable. Their interconvertibility, as well as the segregation of hapliod descendants, can be explained as the result of occasional pairing of the duplicated regions with loss of one of these duplicated regions by recombination.     

Bacteriophage-induced Inhibition of Host Functions: II. Evidence for Multiple, Sequential Bacteriophage-induced Deoxyribonucleases Responsible for Degradation of Cellular Deoxyribonucleic Acid

Degradation of bacterial deoxyribonucleic acid (DNA) after infection with T4 bacteriophage was studied in an endonuclease I-deficient host. The kinetics of degradation were similar to those seen in other hosts with a normal level of this enzyme. Irradiation of extracellular phage with ultraviolet (UV) destroyed the capacity of the infecting virus to induce extensive breakdown of host DNA, which was, however, converted to high-molecular-weight material. Addition of chloramphenicol to T4-infected cells provided data which can be interpreted to indicate the involvement of at least two endodeoxyribonucleases and one exodeoxyribonuclease having a high degree of specificity. A model is proposed showing the sequential action of two endodeoxyribonucleases followed by an exodeoxyribonuclease in the degradation of host DNA. The appearance of these hydrolytic enzymes requires protein synthesis. Infections leading to partial degradation only (UV-irradiated phages, gene 46 mutants) effectively inhibited the synthesis of bacterial messenger ribonucleic acid and of beta-galactosidase.     

Modulation of gene expression by drugs affecting deoxyribonucleic acid gyrase.

Nalidixic acid (Nal), a drug which affects deoxyribonucleic acid gyrase activity, inhibits the expression of catabolite-sensitive genes: the three maltose operons, the lactose and galactose operons, and the tryptophanase gene. A correlation between the degree of sensitivity to Nal and that to catabolite repression has been observed. The expression of the threonine and tryptophan operons, insensitive to catabolite repression, is insensitive to Nal. The expression of the lacZ gene under the control of the IQ promoter is activated by Nal. Strains carrying a mutation in the nalA locus are resistant to these effects. Novobiocin, which inhibits the negative supercoiling activity of deoxyribonucleic acid gyrase, affects expression of the operons similarly to Nal. The involvement of promoters in Nal and novobiocin action, as well as a possible role of in vivo negative supercoiling in the selectivity of gene expression, are discussed.     

Segregation of Deoxyribonucleic Acid in Bacteria: Association of the Segregating Unit with the Cell Envelope

Cells of the gram-positive organism Lactobacillus acidophilus R-26 were labeled with ³H-thymine to measure the segregation of radioactive deoxyribonucleic acid (DNA) into daugher cells. Such cells were found to contain 8 conserved units of DNA which would correspond to two replicating chromosomes per cell. Fluorescent antibody (FA) against this organism was used to demonstrate that portions of the cell surface (2 to 4 units per cell) were conserved during growth and division. The permanent association of DNA with these conserved cell surface units was measured by combining autoradiography with FA techniques. DNA synthesized immediately before FA labeling was not associated with the fluorescent cell surface, whereas DNA synthesized a generation previously was. The results are consistent with a model in which DNA becomes permanently fixed to the cell surface when it is first used as a template.     

Newly proposed node segregation index is not suitable for analyzing unimode food webs

Strona and Veech (2015) developed a new node segregation (or node overlap) index for analysing ecological network structure based on the Veech (2013)’s species co-occurrence probabilistic model, which was originally applied to species-site matrices. However, a species-site matrix for analysing species co-occurrence patterns and an adjacency matrix for characterising unimode network structures are different. Directly applying Veech’s species co-occurrence probabilistic model to adjacency matrices in unimode food webs is problematic. The central critical problem is related to the number of free species (or nodes/vertices) in the unimode network that can be the neighbors (have links to connect) of a focused species or a focused pair of species. This number is typically less than the total number of species in real food webs. That is, species are not independent from each other in unimode networks. For a simple undirected unimode network without self-loops, based on the criterion whether there is a link between two species for a focused pair, a correct probabilistic model is developed to accurately compute the probability of observing some shared neighbors for a pair of species in the network. Numerical simulation show that the node overlap calculated using the correct and original probabilistic models present remarkable differences, especially when a unimode network is nested and contains generalists. In summary, The correct probabilistic model should be used if ones want Strona and Veech (2015)’s node segregation index to work for unimode food webs.     

Effect of gyrB-mediated changes in chromosome structure on killing of Escherichia coli by ultraviolet light: experiments with strains differing in deoxyribonucleic acid repair capacity.

Mutations at the gyrB locus were found to decrease the degree of supercoiling of the Escherichia coli chromosome. The effect of a gyrB mutation on the repair of ultraviolet-induced deoxyribonucleic acid damage was studied by following the killing of strains of E. coli K-12 proficient and deficient in deoxyribonucleic acid repair. The effectiveness of both excision and postreplication types of deoxyribonucleic acid repair was found to be altered by this mutation, the former being apparently enhanced and the latter impaired.     

Mutants of the mini-F plasmid pML31 thermosensitive in replication.

Hydroxylamine mutagenesis was used for the induction of thermosensitive replication mutants of the mini-F plasmid pML31. Replication mutants were characterized by studying the segregation kinetics and the incorporation of [3H]-thymidine into plasmid deoxyribonucleic acid at the nonpermissive temperature. Based on these experiments two types of mutants could be distinguished. Mutants of type I are fast segregating with the kinetics expected if plasmid replication was blocked immediately. Double-label experiments showed a rapid shut-off of replication in these mutants at 42 degrees C. Mutants of type II segregate slower, showing only a partial inhibition of plasmid deoxyribonucleic acid synthesis at the nonpermissive temperature. The label incorporated at 42 degrees C was predominantly found in open circular plasmid molecules.     

Inhibition of deoxyribonucleic acid replication in Bacillus brevis by ribonucleic acid polymerase inhibitors.

The incorporation of [3H]thymidine into deoxyribonucleic acid by exponentially growing cells of Bacillus brevis was inhibited by streptolydigin and rifampin in the same concentration range in which these drugs inhibit ribonucleic acid synthesis. Complete inhibition occurred within one-third generation time after drug addition, suggesting an effect on deoxyribonucleic acid chain elongation.     

Changing proportions of DNA components in Euglena gracilis

The ratios of satellite deoxyribonucleic acid components to chromosomal deoxyribonucleic acid in Euglena gracilis Z were measured by analytical density gradient ultracentrifugation. Chloroplast deoxyribonucleic acid with a buoyant density of 1.685 g/cm³ exhibited a constant ratio to chromosomal deoxyribonucleic acid during exponential growth and increased twofold as the culture reached the end of the exponential growth phase. The quantity of a satellite deoxyribonucleic acid with a buoyant density of 1.691 g/cm³ was not sufficient to measure the ratio to chromosomal deoxyribonucleic acid during exponential growth but increased to approximately equal the quantity of chloroplast deoxyribonucleic acid as the culture approached the end of the exponential growth phase. The quantity of a deoxyribonucleic acid component with a buoyant density of 1.700 g/cm³ was not sufficient to measure the ratio to chromosomal deoxyribonucleic acid during exponential growth but represented approximately one-third of the total deoxyribonucleic acid as the culture entered the stationary phase of growth.     

SP02 particles mediating transduction of a plasmid containing SP02 cohesive ends

SP02 particles that mediate transduction of plasmid pPL1010, a 4.6-megadalton derivative of pUB110 containing an Eco RI endonuclease-generated fragment of SP02 deoxyribonucleic acid that spans the cohesive ends, exhibit three unusual features: the transducing particles have a lower buoyant density than infectious particles; the transduction of pPL1010 occurs at high efficiency; and the transducing activity of the particles is relatively resistant to ultraviolet irradiation when the recipient is recombination proficient. Evidence is presented which indicates that SP02(pPL1010) particles carry the plasmid predominantly as a linear multimer having a molecular mass comparable to that of infectious SP02 deoxyribonucleic acid (ca. 31 megadaltons). The plasmid monomers in the linear multimer appear oriented in the same polarity. The buoyant density difference between infectious and transducing particles appears to be due mainly to the buoyant density difference between pPL1010 (1.699 g/cm3) and SP02 deoxyribonucleic acid (1.702 gm/cm3).     

Genetic modifiers of the phenotypic level of deoxyribonucleic acid-conferred novobiocin resistance in Haemophilus

Leidy, Grace (Columbia University, New York, N.Y.), Iris Jaffee, and Hattie E. Alexander. Genetic modifiers of the phenotypic level of deoxyribonucleic acid-conferred novobiocin resistance in Haemophilus. J. Bacteriol. 92:1464-1468. 1966.-An apparent increase in novobiocin resistance in Haemophilus aegyptius after a second exposure to a particular H. influenzae transforming deoxyribonucleic acid was shown to be the result not of multi-step transformation but of the action of a gene functioning as an enhancement modifier. The modifier is very closely linked to a streptomycin resistance gene (which is linked to a novobiocin resistance marker); it affects the natural degree of resistance to both novobiocin and kanamycin to a measurable degree. Evidence of a repressor of the enhancement modifier is reported.