Synthesis of 5-hydroxymethyldeoxyuridine triphosphate in extracts of SP10c phage-infectedBacillus subtilis W23

A hypermodified nucleotide partially replaced deoxythymidylate in mature DNA ofBacillus subtilis phage SP10c. Studies with crude extracts of SP10c-infected cells revealed that deoxythymidylate synthetase activity declined by 70% during the program and was replaced by deoxyuridylate hydroxymethyltransferase. In addition, extracts of infected cells were able to phosphorylate 5-hydroxymethyldeoxyuridylate to the corresponding triphosphate, but these same extracts could not phosphorylate the hypermodified deoxynucleoside monophosphate. It is suggested that deoxythymidylate and the hypermodified nucleotide in mature SP10c DNA are derived by postreplicational modification of 5-hydroxymethyldeoxyuridylate in newly replicated DNA.     

Lysogenization by bacteriophage lambda: II. - Identification of genes involved in the multiplicity dependent processes

We previously showed that, under conditions of rapid exponential growth, lysogenization of E. coli cells by phage λ requires that the cell is infected by at least 2 phages able to replicate their DNA, or 3 or 4 phages unable to replicate their DNA [ref. 4]. Since genes dealing with prophage integration appear not to be involved in these multiplicity dependent processes, a determination was made as to whether more than one copy of the genes involved in repressor synthesis or its activation are needed for lysogenization. The complementation patterns which we obtained indicate multiplicity effects involving gene cII (and, perhaps, cIII) in lysogenization by both phage able or unable to replicate. In the former case, we propose that cII protein (and, perhaps, cIII) both induces repressor synthesis and inhibits phage DNA replication. In lysogenization by phage unable to replicate, the data suggest that the expression of early phage genes and repressor synthesis in the course of lysogenization are mutually exclusive processes which do not take place on the same phage chromosome.     

New Deoxyribonucleic Acid Polymerase Induced by Bacillus subtilis Bacteriophage PBS2

The deoxyribonucleic acid (DNA) of Bacillus subtilis phage PBS2 has been confirmed to contain uracil instead of thymine. PBS2 phage infection of wild-type cells or DNA polymerase-deficient cells results in an increase in the specific activity of DNA polymerase. This induction of DNA polymerase activity is prevented by actinomycin D and chloramphenicol. In contrast to the major B. subtilis DNA polymerase, which prefers deoxythymidine triphosphate (dTTP) to deoxyuridine triphosphate (dUTP), the DNA polymerase in crude extracts of PBS2-infected cells is equally active whether dTTP or dUTP is employed. This phage-induced polymerase may be responsible for the synthesis of uracil-containing DNA during PBS2 phage infection.     

Deoxythymidine nucleotide metabolism in Bacillus subtilis W23 infected with bacteriophage SP1Oc: preliminary evidence that dTMP in SP10c DNA is synthesized by a novel, bacteriophage-specific mechanism.

Despite the fact that mature SP10c DNA contains dTMP, the acid-soluble fraction of infected cells contained no dTTP during the interval of phage replication. However, infected cells contained normal cellular levels of dATP, dGTP, and dCTP. Upon infection of deoxythymidine-starved Bacillus subtilis M160 (a deoxythymidine-requiring mutant of B. subtilis W23), mature phage DNA with a normal dTMP content was made. SP10c codes for an enzyme that seems to catalyze the tetrahydrofolate-dependent transfer of 1-carbon fragments to the 5 position of dUMP. The transfer of 1-carbon fragments is not accompanied by oxidation of tetrahydrofolage to dihydrofolate, implying that the enzyme in question is not a dTMP synthetase. It is proposed that dTMP in mature SP10c DNA is derived by the postreplicational modification of some other nucleotide and not by the direct incorporation of dTTP into DNA.     

A determination of the efficiency of uptake of SP50 DNA by competent cells of B. subtilis

Summary Phage SP50 excludes phage SPP1 both in infection and in transfection of B. subtilis. The dependence of the efficiency of exclusion on the concentration of SP50 DNA shows that one SP50 DNA molecule within a competent cell is sufficient to exclude SPP1 phage development. The concentration dependence allows a determination of the efficiency of uptake of SP50 DNA by competent cells. Only 1 out of 200 SP50 DNA molecules in the transfection mixture will become biologically active in excluding SPP1 phage development in the competent cell.     

Biosynthesis of 5-(4''5''-dihydroxypentyl) uracil as a nucleoside triphosphate in bacteriophage SP15-infected Bacillus subtilis.

The nucleoside triphosphate of 5-(4',5'-dihydroxypentyl)uracil (DHPU) was detected in the acid-soluble extract from bacteriophage SP15-infected Bacillus subtilis W23. No uracil was found in the DNA of either replicating or mature phage. Labeled thymidine added during phage DNA synthesis was incorporated into phage DNA. The presence of DHPU as a nucleoside triphosphate in the acid-soluble pool and the incorporation of thymidine into phage DNA suggest that both DHPU and thymine are incorporated into SP15 DNA via their nucleoside triphosphates. 5-Fluorodeoxyuridine inhibited biosynthesis of SP15 DNA, and this inhibition was reversed by thymidine, resulting in the synthesis of a DNA containing reduced amounts of fully modified DHPU. It is proposed that 5-fluorodeoxyuridine, or its metabolic product, inhibits a step in the biosynthetic pathway to the nucleoside triphosphate of DHPU.     

Molecular interactions involving Escherichia coli nucleoside diphosphate kinase

Nucleoside diphosphate kinase plays a distinctive metabolic role as the enzyme poised between the last reaction of deoxyribonucleoside triphosphate (dNTP) biosynthesis and the DNA polymerization apparatus. In bacteriophage T4 infection, NDP kinase is one of very few enzymes of host cell origin to participate in either dNTP synthesis or DNA replication. Yet NDP kinase forms specific contacts with phage-coded proteins of dNTP and DNA synthesis. This article summarizes work from our laboratory that identifies and characterizes these interactions. Despite these specific interactions, the enzyme appears to be dispensable, both for T4 replication and for growth of the host, Escherichia coli, because site-specific disruption of ndk, the structural gene for NDP kinase, does not interfere with growth of the host cell and only partly inhibits phage replication. However, ndk disruption unbalances the dNTP pools and stimulates mutagenesis. We discuss our attempts to understand the basis for this enhanced mutagenesis.     

DNA Synthesis and Gene Expression in Bacillus subtilis Infected with Wild-Type and Hypermodification-Defective Bacteriophage SP10

A hypermodified base (Y-Thy) replaces 20% of the thymine (Thy) in mature DNA of Bacillus subtilis phage SP10. Two noncomplementing hypermodification-defective (hmd) mutants are described. At 30°C, hmd phage carried out a normal program, but at temperatures of ≥37°C, the infection process was nonproductive. When cells were infected at 37°C with hmd phage, DNA synthesis started at its usual time (12 min), proceeded at about half the normal rate for 6 to 8 min, and then stopped or declined manyfold. All, or nearly all, of the DNA made under hmd conditions consisted of fully hypermodified parental DNA strands H-bonded to unhypermodified nascent strands. The reduced levels of DNA synthesis observed under hmd conditions were accompanied by weak expression of late genes. A sucrose gradient analysis of SP10 hmd⁺ replicating DNA intermediates was made. Two intermediates, called VG and F, were identified. VF consisted of condensed DNA complexed to protein; VF also contained negatively supercoiled domains covalently joined to relaxed regions. F was composed of linear concatenates from which mature DNA was cleaved. None of those intermediates was evident in cells infected at 37°C with hmd phage. Shiftup experiments were performed wherein cells infected with hmd phage at 30°C were shifted to 37°C at a time when replication was well under way. DNA synthesis stopped or declined manyfold 10 min after shiftup. The hmd DNA made after shiftup was conserved as a form sedimentationally equivalent to the F intermediate, but little mature DNA was evident. It is proposed that Y-Thy is required for replication and DNA maturation because certain key proteins involved with these processes interact preferentially with hypermodified DNA.     

Preparation of Photoreactive Oligonucleotide Duplexes and Their Application to Photoaffinity Modification of DNA-Binding Proteins

To introduce photoreactive dNMP residues to the 3"-end of a mononucleotide gap, base-substituted photoreactive deoxynucleoside triphosphate derivatives, (5-[N-(2,3,5,6-tetrafluoro-4-azidobenzoyl)-trans-3-aminopropenyl-1]- and 5-{N-[N-(4-azido-2,5-difluoro-3-chloropyridine-6-yl)-3-aminopropionyl]-trans-3-aminopropenyl-1}-2"-deoxyuridine 5"-triphosphates, were used as substrates in the DNA polymerase -catalyzed reaction. The resulting nick, containing a modified base at the 3"-end, was sealed by T4 phage DNA ligase. This approach enables the preparation of DNA duplexes bearing photoreactive groups at a predetermined position of the nucleotide chain. Using the generated photoreactive DNA duplexes, the photoaffinity modifications of DNA polymerase and human replication protein A (hRPA) were carried out. It was shown that DNA polymerase and hRPA subunits were modified with the photoreactive double-stranded DNA considerably less effectively than by the nicked DNA. In the case of double-stranded DNA, the hRPA p70 subunit was preferentially labeled, implying a crucial role of this subunit in the protein–DNA interaction.     

An Haemophilus influenzae mutant which inhibits the growth of HP1c1 phage

Summary A strain of Haemophilus influenzae, called hpm ^- inhibits the growth of phage HP1c1 but not S2. This inhibition is overcome by HP1c1ph mutants. Phage HP1c1 adsorbs normally to hpm ^- cells but only a small fraction of infected cells produce phage with a normal burst size or become lysogenic. When hpm ^- strains lysogenic for HP1c1 are induced, 100% of the cells yield phage. There is no degradation of phage DNA after infection of hpm ^- cells and HP1c1 can normally grow when its DNA is introduced into hpm ^- by transfection. The most probable explanation is that in hpm ^- cells the penetration of phage DNA is blocked. The hpm ^- property behaves as as unstable mutation.     

Biological Activity of 5-Hydroxymethyluracil and Its Deoxynucleoside in Noninfected and Phageinfected Bacillus subtilis

(14)C-hydroxymethyldeoxyuridine (dHMU) is specifically incorporated into the deoxyribonucleic acid (DNA) of bacteriophage SP8. Incorporation experiments demonstrate that the initiation of phage SP8 DNA synthesis occurs between 12.5 to 15 min after infection. Incorporation into host DNA does not occur. (14)C-dHMU can be used as an analytical tool for screening conditionally lethal phage mutants containing hydroxymethyluracil in their DNA to select those that are defective in DNA synthesis under restrictive conditions. The pyrimidine, (14)C-hydroxymethyluracil (HMU), is not incorporated into bacterial or phage DNA. Neither HMU nor dHMU can replace thymine as a growth requirement for Bacillus subtilis 168 Ind(-) Thy(-). HMU does not inhibit the utilization of thymine. Although dHMU inhibits deoxythymidine utilization, the inhibition is not competitive.     

Deoxythymidine sugars are not direct precursors of DNA-thymine.

A theoretical model for the kinetics of uptake of a putative precursor molecule into nucleotide pools and into replicating DNA has been developed. The relationship between the accumulation of radioactively labeled precursors in the pool and the appearance of radioactivity in DNA is then derived. Experiments have been carried out in bacteria to compare the uptake of radioactive thymine into deoxythymidine triphosphate, deoxythymidine diphosphate sugars, and DNA to test the suitability of either compound as the direct precursor of thymine in DNA. New one-dimensional, thin-layer chromatographic procedures were used to determine the specific activity of deoxythymidine triphosphate and deoxythymidine triphosphate and deoxythymidine diphosphate sugars in growing cultures of 32PO4-labeled Escherichia coli during pulse labeling with [3H]-thymine. A comparison of the experimental data with our theoretical model supports the hypothesis that deoxythymidine triphosphate, but not deoxythymidine sugar, is the direct precursor of thymine in normally replicating DNA in vivo.     

Mutation induction in yeast by deoxythymidine monophosphate: A model

Summary High concentrations of deoxythymidine monophosphate (dTMP) induce mutations in Saccharomyces cerevisiae. Strains defective in the RAD6 gene-thought to be involved in error-prone DNA repair-do not show dTMP-induced mutation. We propose a model to explain these findings and suggest that fluxes of thymidine nucleotides may diminish the fidelity of DNA replication.     

Three <Emphasis Type="Italic">Bacillus anthracis</Emphasis> Bacteriophages from Topsoil

Three Bacillus anthracis bacteriophages from Iowa topsoil are characterized as to latent period, morphology, structural proteins, DNA size, and restriction endonuclease digestion. Electron micrographs indicate that the three isolates include two members of the Myoviridae and one smaller phage belonging to the Podoviridae. Phages Nk and DB resemble Myoviridae phage SP50 in morphology, but host range studies, protein, and DNA analysis indicate that both differ from SP50. Phage MH is very similar to phage φ29, but differs in terms of host range, structural protein, and DNA characteristics. Received: 21 June 2002 / Accepted: 13 September 2002     

The pool size of deoxyguanosine 5′-triphosphate and deoxycytidine 5′-triphosphate in phytohemagglutinin-stimulated and non-stimulated human lymphocytes

Requirements and optimal conditions have been studied for measurements of dGTP and dCTP in cellular extracts using the copolymer [d(1 − C)] as primer in a reaction catalysed by the large fragment of DNA polymerase from E. coli. The pool size of dGTP and dCTP in the human lymphocytes in the absence of PHA was found to be about 0.1 and 0.15 pmoles/10⁶ cells, respectively. After treatment with PHA the pool size of both deoxynucleotides increased. The pool size of dCTP reached a maximum after 67 h simultaneously with the peak value of labelled deoxythymidine incorporation into DNA and the variation in these two parameters was very similar. The variation in the dGTP pool, however, was not so distinctly related to deoxythymidine incorporation as in the dCTP pool, since the increase in the dGTP pool was very small from 52–67 h. During transformation the dGTP pool was found to be the smallest pool. The relative cellular content of mono-, di- and triphosphate esters of deoxyadenosine, deoxyguanosine and deoxycytidine was studied.     

In vitro studies on the role of phage T7 gene 4 product in DNA replication

Summary A soluble enzyme fraction prepared from T7-infected E. coli is able to initiate DNA synthesis on circular single-stranded phage DNA. The product synthesized in vitro is a full-length linear complementary strand as judged by alkaline sucrose gradient analysis. DNA synthesis requires the products of the phage genes 4 and 5, Mg⁺⁺, dNTPs and rNTPs; however, ATP by itself can almost completely satisfy the rNTP requirement. The gene 4 product is essential for DNA chain initiation on unprimed single-stranded DNA, but is dispensable for the replication of a X174 DNA-RNA hybrid. The enzyme system from T7-infected cells does not discriminate between the DNA templates from phages X174, M13 or fd and is also capable of replicating native T7 DNA. However, a striking difference with regard to the template DNA is revealed by complementation analysis. Extracts of T7 mutant-infected cells complement each other only with T7 DNA but not with X174 DNA as template.Abbreviations rNTP ribonucleoside triphosphate - dNTP deoxyribonucleoside triphosphate - BSA bovine serum albumin     

Regulation of replication of λ phage and λ plasmid DNAs at low temperature

It was previously demonstrated that while lysogenic development of bacteriophage λ in Escherichia coli proceeds normally at low temperature (20–25° C), lytic development is blocked under these conditions owing to the increased stability of the phage CII protein. This effect was proposed to be responsible for the increased stimulation of the p _E promoter, which interferes with expression of the replication genes, leading to inhibition of phage DNA synthesis. Here we demonstrate that the burst size of phage λcIb2, which is incapable of lysogenic development, increases gradually over the temperature range from 20 to 37° C, while no phage progeny are observed at 20° C. Contrary to previous reports, it is possible to demonstrate that p _E promoter activation by CII may be more efficient at lower temperature. Using density-shift experiments, we found that phage DNA replication is completely blocked at 20° C. Phage growth was also inhibited in cells overexpressing cII, which confirms that CII is responsible for inhibition of phage DNA replication. Unexpectedly, we found that replication of plasmids derived from bacteriophage λ is neither inhibited at 20° C nor in cells overexpressing cII. We propose a model to explanation the differences in replication observed between λ phage and λ plasmid DNA at low temperature. Received: 30 December 1997 / Accepted: 25 February 1998