The biosynthesis of 5-hydroxymethyldeoxyuridylic acid in bacteriophage-infected Bacillus subtilis

Specificity of hydroxylmethyluracil-containing DNA for transcription factor 1: structural insights

The genomic materials from some Bacillus subtilis bacteriophages are found to contain 5-(hydroxymethyl)-2'-deoxyuridine in place of thymine. Phage-encoded proteins such as transcription factor 1 specifically and preferentially bind to the minor grooves of these hmU-containing DNA but not to thymine-containing DNA. Data from electrophoretic mobility shift assays suggest that the inherent, localized flexibility of hmU-DNA, which is sequence-specific, is responsible for its discriminative binding. We discuss here, from the NMR-derived structural point of view, how differential DNA flexibility can contribute to specific binding of TF1 to hmU-DNA.

The DNA polymerase genes of several HMU-bacteriophages have similar group I introns with highly divergent open reading frames

A previous report described the discovery of a group I, self-splicing intron in the DNA polymerase gene of the Bacillus subtilis bacteriophage SPO1 (1). In this study, the DNA polymerase genes of three close relatives of SPO1: SP82, 2C and phi e, were also found to be interrupted by an intron. All of these introns have group I secondary structures that are extremely similar to one another in primary sequence. Each is interrupted by an open reading frame (ORF) that, unlike the intron core or exon sequences, are highly diverged. Unlike the relatives of Escherichia coli bacteriophage T4, most of which do not have introns (2), this intron seems to be common among the relatives of SPO1.

Genetic effects of 5-hydroxymethyl-2'-deoxyuridine, a product of ionizing radiation

Ionizing radiation causes formation of heterogeneous types of damage to DNA. Among those, 5-hydroxymethyl-2'-deoxyuridine (HMdU) was identified as a major thymidine derivative in gamma-irradiated HeLa cells [G.W. Teebor, K. Frenkel and M.S. Goldstein (1984) Proc. Natl. Acad. Sci. (U.S.A.), 81, 318-321]. We report here that HMdU is a strong inducer of lambda prophage in Escherichia coli WP2s(lambda) and is highy mutagenic in Salmonella typhimurium. HMdU causes his+ revertants in strains TA100, which reverts predominantly by base-pair substitution at G-C sites, and TA97, which reverts mainly by frameshift mutation at G-C sites. It does not cause reversion in TA98, another frameshift-sensitive strain, nor in strains TA1535 and TA1537. Of those tested, only the last two strains do not contain pkM101, a plasmid which enhances mutagenic effects of ionizing radiation. HMdU also causes reversion in strains TA102 and TA104, which detect oxidative damage and can revert by base-pair substitution at A-T base pairs at the hisG428 site. We show that HMdU can be incorporated into DNA of TA100 and that, in addition to causing point mutations, it causes suppressor mutations as well. The ability of HMdU to induce lambda prophage and its strong mutagenicity in Salmonella typhimurium provide evidence that the presence of HMdU in DNA is biologically significant and may play a major role in the genetic consequences of ionizing radiation and other types of oxidative damage.

Ordered distribution of modified bases in the DNA of a dinoflagellate

In DNA of the dinoflagellate Crypthecodinium cohnii, 38% of the thymine is replaced by the modified base 5-hydroxymethyluracil, and approximately 3% of the cytosine is replaced by 5-methylcytosine. Both of the modified bases are non-randomly distributed in the DNA. Determinations of 3' nearest neighbors show that HOMeU is preferentially located in the dinucleotides HOMeUpA and HOMeUpC. Pyrimidine tract analysis shows that HOMeU is also greatly enriched in the trinucleotide purine-HOMeU-purine. As in other eukaryotes, methylcytosine in C. cohnii DNA occurs predominantly in the dinucleotide MeCpG. By analysis of restriction endonuclease digestion patterns of C. cohnii total DNA and ribosomal DNA, we have found that the central CpG dinucleotides in the sites for the enzymes Hpa II (CCGG) and Hha I (GCGC) are extensively methylated in both total DNA and ribosomal DNA. Results of digestion with Ava I, however, indicated that not all CpG dinucleotides in the sequence CCTCGGAG are methylated in C. cohnii DNA.

Bacteriophage phi W-14-infected Pseudomonas acidovorans synthesizes hydroxymethyldeoxyuridine triphosphate

The infection of Pseudomonas acidovorans with bacteriophage phi W-14 leads to the gradual disappearance of dTTP from the cells and to the appearance of hydroxymethy dUTP (hmdUTP). Infected-cell contain dUMP hydroxymethylase and activities converting hmdUMP to humdUDP and hmdUTP. Hydroxymethylase appears immediately after infection, reaching a maximum 20 min later. Thymidylate synthase activity decreases to less than 10% of the preinfection level during the initial 40 min after infection. Newly replicated DNA contains 2 to 3% hydroxymethyluracil. Although uracil is released from newly replicated DNA by acid hydrolysis, uracil is not incorporated as such into phi W-14 DNA, and dUTP is not present in the acid-soluble pool of infected cells. It is concluded that the thymine and alpha-putrescinylthymine in phi W-14 DNA are formed from hydroxymethyluracil at the polynucleotide level and that an intermediate in one or both of these conversions is degraded to uracil by acid hydrolysis. The modification of hydroxymethyluracil is coupled tightly to replication.

Characterization of deoxycytidylate methyltransferase in Xanthomonas oryzae infected with bacteriophage Xp12

Three methods, chromatographic, spectrophotometric and tritium-release assay, were used and compared for the assay of deoxycytidylate methyltransferase. All three methods can be used for assay of this enzyme but the tritium-release assay appears to be the most simple and convenient. With the help of this assay the deoxycytidylate methyltransferase has been isolated and purified from sonically disrupted cells of Xp12-infected Xanthomonas oryzae. Using a procedure that involves fractionation with streptomycin sulfate and ammonium sulfate, filtration through Sephadex G-100 and chromatography on DEAE-cellulose, a 214-fold increase in specific activity was obtained. The enzyme displays a narrow pH optimum at 6.0 Among the buffers tested, 6-morpholinoethane sulfonate with the addition of Mg2 is the best. The enzyme can utilize dCMP as a substrate. The enzyme can also convert tetrahydrofolic acid into dihydrofolic acid. The Km value for dCMP is 31.3 micrometer and the Km value for tetrahydrofolic acid is 71.4 micrometer. There is no absolute requirement of ions for the activity of the enzyme; however, the presence of ions causes stimulating or inhibiting effects on enzyme activity that are dependent on the variety and concentration of ions used.

Modified bases in the DNAs of unicellular eukaryotes: an examination of distributions and possible roles, with emphasis on hydroxymethyluracil in dinoflagellates

The occurrence of small amounts of one or more of several modified bases in the DNA of an organism is widespread in nature. Prominent among these bases are 5-methylcytosine, N6-methyladenine and 5-hydroxymethyluracil. All can be found in varying amounts in DNA of viral, prokaryotic and eukaryotic origin. In some organisms, modified nucleotides comprise a large fraction of DNA nucleotides and in others there is complete replacement of one of the common four nucleotides by a modified one. This article discusses the distributions and possible roles of the several modified bases found in prokaryote and eukaryote DNAs. Emphasis is given (1) methylcytosine in a broad variety of eukaryotes, (2) methyladenine in certain protozoa and protophyta and (3) hydroxymethyluracil in dinoflagellates. Attention is focused on the phenomenology and the possible consequences of the presence of hydroxymethyluracil in DNA.

Induction of mutations in B. subtilis phage SPP1 by growth on host cells carrying a mutator DNA polymerase III

Phage SPP1 infecting a mutator strain of B. subtilis (BD337) which carries a defective DNA polymerase III is mutagenized. This effect is absent in phages SPO2, SP82G and øe. The results confirm previous observations that SPP1 uses host DNA polymerase III for its DNA synthesis.

Hydroxymethyluracil in eukaryote DNA: a natural feature of the pyrrophyta (dinoflagellates)

Analysis of the DNA of several diverse dinoflagellates and other algae has revealed that the presence of the base hydroxymethyluracil (HOMeU) is a feature common among the DNA's of dinoflagellates; this base has not been found in any other group of eukaryotes that has been examined. Among examined members of the dinoflagellates, the ratio of the base pairs HOMeU-A to T-A, where A is adenine and T is thymine, ranges from 0.14 to 2.13. In addition to hydroxymethyluracil, the DNA of one dinoflagellate contains methylcytosine, and that of another contains methyladenine, while the DNA of other dinoflagellates contains no detectable amounts of either of these two bases.

Detection and identification of minor nucleotides in intact deoxyribonucleic acids by mass spectrometry

A mass spectral method is described for the detection and identification of unusual nucleotide residues present in DNAs. Analysis by this method of intact, underivatized DNA from salmon sperm, calf thymus, mouse L-cells, wheat germ, M. lysodeikticus, E. Coli, and the bacteriophages 0X-174, fd, and lamda, yields diagnostic ions for the four common components of DNA as well as characteristic ions for 5-methyldeoxycytidine residues. The spectrum from T2 DNA contains ions indicative of 5-hydroxymethyldeoxycytidine and 5-methyldoxycytidine components but no ions corresponding to deoxycytidine residues. The DNAs of phages fd and 0X-174 also display ion products indicative of N6-methyldeoxyadenosine residues. Additional series of ions in the spectra of all four bacteriophage DNAs suggest the presence of 5-substituted deoxyuridine residues. The detection method exhibits considerable sensitivity in that amounts of DNA as low as 0.01 A260nm units can be used in the analysis, and thus, the procedure should prove of some value in the detection and location of modified components in specific regions of the various genomes by analysis of the appropriate endonuclease restriction fragments.

Behavior of a temperate bacteriophage in differentiating cells of Bacillus subtilis

During the first 6 hr of sporulation, infection of Bacillus subtilis by by phi105 wild type or the clear-plaque mutant phi105 c30 was nonproductive, but phage DNA was trapped inside developing spores. After infection with either wild-type or mutant phage at early times of sporulation (T1-T3), phage DNA entered the developing spores in a heat-stable form, which may represent integration of the phage DNA into the host chromosome. Phage DNA in carrier spores produced by infection at later times (T4-T6) was much more heat sensitive. Spore preparations containing either phi105 wild type or phi105 c30 carrier spores gave rise to a spontaneous burst of phage during outgrowth, although the fraction of carried wild-type phage that chose lysis over lysogeny at germination has not been determined. Heat induction of the thermoinducible lysogen 3610 (phi105 cts23) was also abortive during sporulation. Furthermore, induction neither prevented eventual spore formation nor resulted in the conversion of prophage DNA to the carrier state; during outgrowth, the previously induced lysogenic spores remained stable lysogens. However, if the sporulating lysogenic cells were plated immediately after induction, they did not form colonies at high efficiency, as though transfer to fresh medium allowed sufficient phage expression to kill the host.

Bacteriophages of Bacillus subtilis

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Bacillus subtilis DNA polymerase III is required for the replication of the virulent bacteriophage phi e

The virulent phage phie of Bacillus subtilis which contains hydroxymethyluracil in its DNA requires host DNA polymerase III for its DNA replication. DNA polymerase III(ts) mutant cells infected with phie at restrictive temperatures do not support phage DNA synthesis. However, phie grows normally both at low and high temperatures in the mutant's parent strain and in spontaneous DNA polymerase III(+) revertants isolated from the mutant strain. Temperature-shift-down experiments with phie-infected cells having thermosensitive DNA polymerase III (pol III(ts)) indicate that at 48 C the thermolabile DNA polymerase III is irreversibly inactivated and has to be synthesized de novo after the shift to 37 C, before phage DNA synthesis can begin. Temperature-shift-up experiments with phie-infected mutant cells show that phage replication is arrested immediately after the temperature shift and indicate that phie requires DNA polymerase III throughout its replication stage.

Mutants of Bacillus subtilis bacteriophage phi e defective in dTTP-dUTP nucleotidohydrolase

Mutants of bacteriophage phie inducing only 1 to 5% of wild-type levels of dTTP-dUTP nucleotidohydrolase give normal bursts of viable progeny phage whose DNA contains 5 to 10% thymine (but no uracil) in place of 5-hydroxymethyluracil. The relative heat lability of one phage mutant enzyme solubilized from the membrane fraction of infected cells suggests that a phie gene codes for the induced dTTPase-dUTPase.

Early biochemical events occurring after infection of Bacillus cereus 569-SP1 with bacteriophage GSW

After infection of Bacillus cereus 569-SP1 with the 5-hydroxymethyluracil-containing phage GSW, new dTTPase, dUTPase, and dUMP-hydroxymethylase activities appear. No significant changes in activities of other pyrimidine ribonucleoside or 2'-deoxyribonucleoside triphosphate nucleotidohydrolases were detected. dUTP and dUMP inhibit the dTTPase activity, whereas dTTP failed to inhibit dUTPase activity. The K(m) value for the substrate dUTP is 10(-4) M and for dTTP is 4.85 x 10(-4) M. Thymidylate synthetase activity is inhibited only when cells are infected during the late lag or very early log phases of growth; when cells are infected with phage during mid-log, thymidylate synthetase activity is unaffected. The data support the suggestion that, although phage GSW may inhibit an otherwise expected increase in activity of thymidylate synthetase, it fails to affect the already existing activity. The data presented do not allow discrimination as to whether the phage specifies inhibition of de novo synthesis of thymidylate synthetase or the increase in activity of already existing but not fully expressed enzyme.

Studies on the biosynthesis of alpha-putrescinylthymine in bacteriophage phi W-14-infected Pseudomonas acidovorans

The alpha-putrescinylthymine (putThy) in bacteriophage phiW-14 DNA is synthesized at the mononucleotide level: it is labeled by uracil or deoxyuridine but not by thymidine, and it appears in the acid-soluble pool of infected cells before the onset of phage DNA synthesis. The methylene group at the C-5 position of the pyrimidine moiety of putThy is derived in vivo from a C(1) unit. Extracts of a phage infected thymidine auxotroph of the host, Pseudomonas acidovorans, apparently contain a phage-specific thymidylate synthetase and a phage-specific activity which forms 5-hydroxymethyl dUMP from N(5), N(10)-methylene-tetrahydrofolate and dUMP.

Synthesis of the unusual DNA of Bacillus subtilis bacteriophage SP-15

Cultures of Bacillus subtilis infected with phage SP-15 were examined to investigate the metabolic origin of two of the unique components of the phage DNA: the component responsible for the unusually high buoyant density in CsCl and the unusual pyrimidine, 5-(4', 5'-dihydroxypentyl) uracil (DHPU). Newly synthesized pulse-labeled DNA was light in buoyant density and shifted to the high density of mature phage DNA upon further incubation. Parental DNA was converted to a light-density intermediate form prior to replication. When labeled uracil, thymidine, or DHPU were added to infected cells, it was found that only uracil served as the precursor to DHPU and thymine in phage DNA. Analysis of the bases from hydrolyzed DNA of labeled phage or infected cells indicated that the uracil was incorporated into the DNA as such (presumably via deoxyuridine triphosphate) and later converted to DHPU and thymine at the macromolecular level. The sequence of events after phage infection appeared to be: (i) injection of parental DNA; (ii) conversion of parental DNA to a light form; (iii) DNA replication, yielding light DNA containing uracil; (iv) conversion of uracil to DHPU and thymine; and (v) addition of the heavy component.

Thymidine triphosphate nucleotidohydrolase and deoxyuridylate hydroxymethylase induced by mutants of Bacillus subtilis bacteriophage SP82G

Assays on extracts of Bacillus subtilis infected by temperature-sensitive mutants of bacteriophage SP82G indicate that thymidine triphosphate nucleotidohydrolase may not be an essential SP82G enzyme and that deoxyuridylate hydroxymethylase is an essential enzyme coded for by SP82G gene 2.

Structure of Bacillus subtilis bacteriophage phi25 and phi25 deoxyribonucleic acid

The structure of Bacillus subtilis bacteriophage phi25 and phi25 deoxyribonucleic acid (DNA) were studied by electron microscopy. The head of phi25 is a regular polyhedron measuring 75 nm in diameter. The uncontracted tail of phi25 is 130 nm in length and includes a large, complex tail plate. Phage phi25 DNA is double-stranded and has a molecular weight of approximately 100 million as determined by electron microscopic length measurements and analytical band sedimentation in CsCl. The complementary strands of phi25 DNA contain numerous random interruptions. Chemical analysis of phi25 DNA demonstrated that 5-hydroxymethyluracil replaces thymine and that the DNA has a mole per cent (guanine plus cytosine) of 42.

Suppressor system in Bacillus subtilis 168

Multiple auxotrophic strains of Bacillus subtilis 168 were tested for joint one-step reversion of two or more auxotrophic markers to the wild-type phenotype. Mu8u5u5, a strain requiring leucine, methionine, and threonine, yielded revertants that grew without added methionine or threonine and proved to have a suppressor gene. When transferred by transformation with deoxyribonucleic acid, this suppressor gene also suppressed the adenine mutation in another strain, Mu8u5u6. The one-step double revertants fell into two distinct classes: strains of class su(+) (I) grow well in broth; strains of class su(+) (II) grow poorly. Strains su(+) (II) tend to revert frequently to the su(+) (I) or su(-) state. Conditional lethal mutants of phage phie were isolated which can grow on the su(+) and not on the su(-) strains.

Biological activity of 5-hydroxymethyluracil and its deoxynucleoside in noninfected and phage-infected 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.