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PubMed1969

Complementary fractions of denatured DNA of coliphage T3 as templates for transcription.

This paper discusses the evidence that two fractions obtained by the chromatography of denatured DNA of phage T3 on columns of methylated albumin-kieselguhr represent the complementary strands. This evidence derives from a variety of temperature-absorbance measurements and from the base composition of the RNA products synthesized by RNA polymerase under the direction of the two single-stranded DNA templates.

Centrifugation, Density Gradient↗
PubMed1969

Photohydration of uridine in the RNA of coliphage R17. I. Reductive assay for uridine photohydration.

Photohydration of uridine in the RNA of E. coli bacteriophage R17 has been investigated with the help of a new chemical method which avoids digestion of the irradiated polymer. The uridine photohydrates are reductively cleaved with sodium borotritiide and the radioactively labeled fragment, 1,3-propane-diol-(3)H(alpha), (3)H(alpha), (3)H(gamma), formed in this reaction is isolated and used as a measure for the extent of uridine photohydration in the irradiated RNA. The influence of the conformational state of R17-RNA on the cross section of uridine photohydration (sigma(H)) was investigated. The cross section for irradiation at 280 mmu at 25 degrees was largest in 6 M urea (sigma(H) = 0.053), slightly smaller in low salt (<10(-3)M Na(+); sigma(H) = 0.050), and substantially smaller in 0.15 M Na(+) (sigma(H) = 0.038). The closeness of the values for sigma(H) in urea and low salt indicates that a majority of the uridine residues in R17-RNA in the low salt medium at 25 degrees are not hydrogen bonded and destacked. The significant suppression of photohydration in 0.15 M Na(+) on the other hand shows that a substantial portion of the uridine residues in R17-RNA are participating in base pairing and base stacking under these conditions. Our results demonstrate that studies of uridine photohydration may, beyond their importance to photobiology, yield information specifically about the conformational state of the uridine-rich regions of a RNA, information which cannot be readily obtained by other techniques.

Coliphages↗
PubMed1970

Photohydration of uridine in the RNA of coliphage R17. II. The relationship between ultraviolet inactivation and uridine photohydration.

Uridine photohydrates (6-hydroxy-5,6-dihydrouridine) are the major products formed upon irradiation of the RNA bacteriophage R17 with ultraviolet light at 280 mmu, while cyclobutane-type pyrimidine dimerization does not occur to an appreciable extent. The suppression of dimerization may indicate that the RNA inside the phage is held in a rigid conformation in close contact with the phage protein. A value of 0.94 (+/-0.10) uridine photohydrates per biological hit is obtained from a correlation of the fraction of phage surviving with the number of photohydrates formed as a function of ultraviolet dose. It is concluded that uridine photohydrates represent a major part of the lethal damage caused by ultraviolet light in bacteriophage R17. An efficient system for dark repair of uridine photohydration seems to be lacking in E. coli.

Coliphages↗
PubMed1976

Antiviral effect on MS-2 coliphage obtained with a synthetic antigen.

The coat protein of bacteriophage MS-2 was cleaved with cyanogen bromide to yield three fragments, possessing the sequence 1-88 (P1), 89-108 (P2), and 109-129 (P3), respectively. The mixture of peptides P2 and P3, which could not be separated, was found capable of inhibiting the neutralization of the phage by antiserum to the whole MS-2. The peptides corresponding to P2 and P3 were therefore synthesized. The synthetic P3 had no capacity to interfere with neutralization of MS-2, not did its macromolecular conjugate with multichain poly(DL-alanine) elicit neutralizing antibodies. On the other hand, the synthetic P2 was very efficient in inhibiting the inactivation of the phage by the antiserum against phage. Furthermore, a synthetic antigen prepared by attachment of P2 to multichain poly(alanine) incuded antiserum in rabbits that was capable of neutralizing MS-2 activity almost as efficiently as the antiserum prepared against the intact coat protein. This inactivation is specific, because it can, in turn, be totally inhibited by P2 peptide.

Antibodies, Viral↗
PubMed1977

Filamentous coliphage M13 as a cloning vehicle: insertion of a HindII fragment of the lac regulatory region in M13 replicative form in vitro.

A HindII restriction fragment comprising the Escherichia coli lac regulatory region and the genetic information for the alpha peptide of beta-galactosidase (beta-D-galactosidegalactohydrolase, EC. 3.2.1.23) has been inserted into 1 of the 10 Bsu I cleavage sites of M13 by blunt end ligation. A stable hybrid phage was isolated and identified by its ability to complement the lac alpha function. Further characterization of the hybrid phage includes retransformation studies, agarose gel electrophoresis, DNA-DNA hybridization, and heteroduplex mapping. The insertion point has been localized at 0.083 map unit on thewild-type circular map-i.e., within the intergenic region. The results prove that part of the intergenic region is nonessential and that the phage can be used as a cloning vehicle.

Coliphages↗
PubMed1978

Protein Ia and the lamB protein can replace each other in the constitution of an active receptor for the same coliphage.

Protein Ia and the lamB protein are both located in the outer membrane of Escherichia coli K-12. The lamB protein is known to be the receptor for phage lambda. Datta et al. [Datta, D. B., Arden, B. & Henning, U. (1977) J. Bacteriol. 131, 821--829] recently isolated a phage called TuIa that uses protein Ia for its adsorption. While phage TuIa fails to grow on ompB mutants, which lack protein Ia, we show here that host-range mutants of TuIa can be isolated that do grow on ompB strains. These host-range mutants fail to grow on ompB lamB double mutants, but retain the ability of the parental phage to grow on ompB+ lamB strains. They are therefore apparently able to use either protein Ia or the lamB protein for their adsorption. Genetic evidence suggests that essentially the same site on the lamB protein may be interacting with phage lambda or the host-range mutants of phage TuIa.

Bacterial Proteins↗
PubMed1975

Gamma-ray-induced thymine damage in the DNA in coliphage phi chi 174 and in E. coli.

The radiation chemical reactivity of thymine residues has been compared for single-stranded phi chi 174 DNA free in solution and in the intact bacteriophage, as well as for native E. coli DNA in solution and inside the cell. The gamma-ray-induced release of [3H]H2O from thymine-methyl[3H] was measured to assess the reactivity of the thymine methyl group. Formation of ring-saturated products of the 5,6-dihydroxy-dihydrothymine type (see article) was determined by an alkali-acid degradation assay. It was observed that the formation of that the formation of [3H]H2O was suppressed by a factor of 9 in intact phi chi 174 bacteriophage compared to phi chi 174 DNA, whereas the formation of (see article) was only slightly suppressed in the phage. For E. coli cells the formation of [3H]H29 was reduced 790-fold compared with free E. coli DNA, and (see article) formation was reduced 140-fold. The extents of survival after gamma-irradiation of phi chi 174 phage plaque-forming ability and E. coli colony-forming ability were also determined. Under the conditions used in these experiments, a linear relationship was observed between the loss of biological activity and the formation of thymine damage for both phi chi 174 phage and E. coli cells.

Cesium Isotopes↗
PubMed1988

Analysis of the complete nucleotide sequence of the group IV RNA coliphage SP.

We report the nucleotide sequence of the Group IV RNA bacteriophage SP. The entire sequence is 4276 nucleotides long. Four cistrons have been identified by comparison with the related Group III phage Q beta. The maturation protein contains 449 amino acids, the coat protein contains 131 amino acids, the read-through protein contains 330 amino acids and the replicase beta-subunit contains 575 amino acids. SP is 59 nucleotides longer than Q beta. We have analyzed both sequence and structural conservation between SP and Q beta and shown that the sequences for the coat and central region of the replicase are strongly conserved between the two genomes. We also show that the S and M replicase binding sites of Q beta are strongly conserved in SP. Interestingly, the base composition of SP and Q beta differ significantly from one another, and most of the differences can be accounted for by a strong preponderance of U in the third position of each codon of Q beta relative to SP. We also compare conserved hairpins associated with potential coat protein and replicase binding sites.

Base Sequence↗
PubMed1987

Codon contexts in enterobacterial and coliphage genes.

This investigation of the codon context of enterobacteria, plasmid, and phage protein genes was based on a search for correlations between the presence of one base type at codon position III and the presence of another base type at some other position in adjacent codons. Enterobacterial genes were compared with eukaryotic sequences for codon context effects. In enterobacterial genes, base usage at codon position III is correlated with the third position of the upstream adjacent codon and with all three positions of the downstream codon. Plasmid genes are free of context biases. Phage genes are heterogeneous: MS2 codons have no biased context, whereas lambda genes partly follow the trends of the host bacterium, and T7 genes have biased codon contexts that differ from those of the host. It has been reported that two successive third-codon positions tend to be occupied by two purines or two pyrimidines in Escherichia coli genes of low expression level. Here, the extent to which highly expressed protein genes can modulate base usage at two successive codon positions III, given the constraints on codon usage and protein sequence that act on them, was quantified. This demonstrates that the above-mentioned favored patterns are not a characteristic of weakly expressed genes but occur in all genes in which codon context can vary appreciably. The correlation between successive third-codon positions is a distinct feature of enterobacteria and of some phages, one that may result from adaptation of gene structure to translational efficiency. Conversely, codon context in yeast and human genes is biased--but for reasons unrelated to translation.

Animals↗