Invasion by bacteriophage T5. II. Dissociation of calcium-independent and calcium-dependent processes

Characterization of an unusual bipolar helicase encoded by bacteriophage T5

Bacteriophage T5 has a 120 kb double-stranded linear DNA genome encoding most of the genes required for its own replication. This lytic bacteriophage has a burst size of ∼500 new phage particles per infected cell, demonstrating that it is able to turn each infected bacterium into a highly efficient DNA manufacturing machine. To begin to understand DNA replication in this prodigious bacteriophage, we have characterized a putative helicase encoded by gene D2. We show that bacteriophage T5 D2 protein is the first viral helicase to be described with bipolar DNA unwinding activities that require the same core catalytic residues for unwinding in either direction. However, unwinding of partially single- and double-stranded DNA test substrates in the 3′–5′ direction is more robust and can be distinguished from the 5′–3′ activity by a number of features including helicase complex stability, salt sensitivity and the length of single-stranded DNA overhang required for initiation of helicase action. The presence of D2 in an early gene cluster, the identification of a putative helix-turn-helix DNA-binding motif outside the helicase core and homology with known eukaryotic and prokaryotic replication initiators suggest an involvement for this unusual helicase in DNA replication initiation.

Is the in vitro ejection of bacteriophage DNA quasistatic? A bulk to single virus study

Bacteriophage T5 DNA ejection is a complex process that occurs on several timescales in vitro. By using a combination of bulk and single phage measurements, we quantitatively study the three steps of the ejection-binding to the host receptor, channel-opening, and DNA release. Each step is separately addressed and its kinetics parameters evaluated. We reconstruct the bulk kinetics from the distribution of single phage events by following individual DNA molecules with unprecedented time resolution. We show that, at the single phage level, the ejection kinetics of the DNA happens by rapid transient bursts that are not correlated to any genome sequence defects. We speculate that these transient pauses are due to local phase transitions of the DNA inside the capsid. We predict that such pauses should be seen for other phages with similar DNA packing ratios.

CALCIUM ION REQUIREMENT FOR PROLIFERATION OF BACTERIOPHAGE PHI MU-4

Shafia, Fred (University of Nebraska, Lincoln), and T. L. Thompson. Calcium ion requirement for proliferation of bacteriophage phimu-4. J. Bacteriol. 88:293-296. 1964.-Divalent ions are essential for proliferation of phage phimu-4. Small amounts of citrate interfere with efficient adsorption of phage to the host cells. Penetration of phage material into the cell is strictly dependent on divalent ions and is inhibited by low levels of citrate. Inhibition of infection can be partially reversed, in early latent period, by calcium ions. Synthesis of new phage particles is also dependent on divalent ions. Addition of citrate to infected cell suspensions significantly reduced the number of phage progeny produced. Chelates such as phosphate and citrate rapidly inactivated the free phage particles at 65 C. Chelate inactivation of phage is not reversible; however, it can be prevented to some degree by calcium ions.

Calcium controls phage T5 infection at the level of the Escherichia coli cytoplasmic membrane

Phage T5 requires 0.1 mM calcium to produce phage progeny in Escherichia coli cells. Decreasing calcium below 0.1 mM at time phage DNA was transferred depleted the bacteria of K+, caused membrane depolarization, perturbation of phage DNA transfer and resulted in a low internal ATP level. Our data suggest that calcium controls the conformation of the channel involved in the transfer of phage DNA through the host envelope and that below 0.1 mM calcium the channel remains open. This creates an energetic state of the host unfavorable to the synthesis of phage components and leads to abortion of the infectious process.

Proportion of phage-insensitive and phage-sensitive cells within pure strains of lactic streptococci, and the influence of calcium

It is of industrial importance to investigate the interaction ofStreptococcus lactiswith phages. Although it has been long recognized that in phage–bacterial relationships the phage-carrier state can occur (Hunter, 1947), relatively little study has been done on this subject. The terras ‘phage-carrier state’ and ‘pseudolysogeny’ have been used synonymously to describe bacterial cultures which are persistently infected with a virus (Barksdale & Arden, 1974, Lawrenceet al.1976). The phagecarrier state differs from lysogenesis in that the bacteria are easily separated from the bacteriophage by a simple plating and re-isolation procedure (Grahamet al.1952). Süssmuth & Tayran (1986) showed that after lysis of one single strain, phage and phage-insensitive bacteria coexist. This work investigates the proportion of phage-insensitive bacteria remaining after lysis of otherStr. lactisstrains, the effect of calcium on this proportion, and the number of generations required to return to a normal sensitive population.

Evidence for heterogeneity in populations of T5 bacteriophage. II. Some particles are unable to inject their second-step-transfer DNA

A new class of bacteriophage was characterized in purified T5 stocks. Regardless of the host cell, these phages were irreversibly blocked at the first-step-transfer stage under conditions in which whole DNA injection normally takes place. However, they expressed their first-step-transfer functions. These observations confirmed the previously established heterogeneity of T5 bacteriophage populations and provided a new way to define a phage function necessary to release the blocking of T5 DNA injection at the first-step-transfer stage.

Electron microscopic analysis of in vitro transcriptional complexes: mapping of promoters of the coliphage T5 genome

Transcriptional complexes formed in vitro with coliphage T5 DNA as template were analyzed by electron microscopy and the number and location of starting sites utilized by E. coli RNA polymerase were determined. Of the 40 promoters characterized in this way, 6 map in the two terminal "pre-early" regions, 29 in the "early" and 5 in the "late" region. The direction of transcription within the different regions determined in this study agrees with earlier findings derived from RNA synthesized in vivo.

Bacteriophage P22 virion protein which performs an essential early function. II. Characterization of the gene 16 function

P16 is a virion protein and, as such, is incorporated into the phage head as a step in morphogenesis. The role of P16 in assembly is not essential since particles are formed without this protein which appear normal by electron microscopy. P16 is essential when the particle infects a cell in the following cycle of infection. In the absence of functional P16, the infection does not appear to proceed beyond release of phage DNA from the capsid. No known genes are expressed, no DNA is transcribed, and the host cell survives the infection, continuing to grow and divide normally. The P16 function is required only during infection for the expression of phage functions. Induction in the absence of P16 proceeds with the expression of early and late genes and results in particle formation. P16 must be incorporated during morphogenesis into progeny particles after both infection and induction for the progeny to be infectious. The P16 function is necessary for transduction as well as for infection. Its activity is independent of new protein synthesis and it is not under immunity control. P16 can act in trans, but appears to act preferentially on the phage or phage DNA with which it is packaged. The data from complementation studies are compatible with P16 release from the capsid with the phage DNA. In the absence of P16 the infection is blocked, but the phage genome is not degraded. The various roles which have been ruled out for P16 are: (i) an early regulatory function, (ii) an enzymatic activity necessary for phage production, (iii) protection of phage DNA from host degradation enzymes, (iv) any generalized alteration of the host cell, (v) binding parental DNA to the replication complex, and (vi) any direct involvement in the replication of P22 DNA. P16 can be responsible for: (i) complete release of the DNA and disengagement from the capsid, (ii) bringing the released DNA to some necessary cell site or compartment such as the cytoplasm, (iii) removal of other virion proteins from the injected DNA, and (iv) alterations of the structure of the injected DNA.

Transfection of Escherichia coli spheroplasts. IV. Transfection of rec+ and rec minus spheroplasts by native, denatured, and renatured T5 bacteriophage DNA after repair of single-strand breaks by polynucleotide ligase

Transfection of Escherichia coli spheroplasts by native T5 phage DNA was not affected by treatment with polynucleotide ligase. Denatured T5 phage DNA infectivity, only 0.1% of the native DNA level, was increased slightly by polynucleotide ligase treatment. Renatured T5 phage DNA infectivity was also increased slightly by polynucleotide ligase treatment. To form an infective center with rec(+) spheroplasts, 1.6 to 2.1 native T5 phage DNA molecules were required; however, 1.4 T5 phage DNA molecules were required to form an infective center with recA(-)B(-) spheroplasts, and one molecule was sometimes sufficient for rec B(-) spheroplasts. Polynucleotide ligase treatment of T5 phage DNA had no effect on these parameters. Thus, the single-strand interruptions of T5 phage DNA are probably not essential to the survival of the parental T5 phage DNA, and T5 phage DNA, especially the denatured form, is highly sensitive to some nucleases in E. coli spheroplasts.

In vivo repair of the single-strand interruptions contained in bacteriophage T5 DNA

Bacteriophage T5 is known to contain several unique single-strand interruptions in only one strand of the duplex DNA. Analysis of labeled parental phage DNA from infected Escherichia coli shows that these nicks are repaired in vivo to yield intact double-stranded molecules. Sealing begins at about 6 min after infection and is independent of DNA replication. Repair may be an ordered process that starts at a unique end of the molecule.

Requirement of a phage-induced 5'-exonuclease for the expression of late genes of bacteriophage T5

Amber mutants of bacteriophage T5 defective in gene D15, which codes for a 5'-exonuclease, do not express late genes. Electrophoretic separation in sodium dodecyl sulfate-polyacrylamide gels of the proteins induced by this mutant in nonpermissive Escherichia coli show a virtual absence of late proteins. Synthesis of lysozyme and serum-blocking power is very low whereas the extent of synthesis of an early enzyme, deoxyribonucleoside monophosphokinase, is similar to that in wild-type infections. It is proposed that one requirement for the expression of late T5 genes is the introduction of gaps or nicks in the T5 DNA so that late transcription can occur.

Arrangement on the chromosome of the known pre-early genes of bacteriophages T5 and BF23

Genetic crosses between mutants defective in the known pre-early genes of T5 and BF23 and the detection of putative N-terminal fragments have allowed the determination of the order of genes along the initially transferred 8% section of DNA of these phages.

Effect of rifampin on the growth of bacteriophage T5

A rifampin-resistant mutant of Escherichia coli F with an altered ribonucleic acid (RNA) polymerase was isolated and was shown to support the growth of phage T5 in the presence of rifampin. In contrast, wild-type, rifampin-sensitive cells of E. coli F did not support the growth of T5 in the presence of rifampin. We concluded, therefore, that no phage-specific RNA polymerase is essential to the development of phage T5. Rather, the host RNA polymerase, or at least that portion of the host RNA polymerase that is responsible for rifampin sensitivity, is required for the transcription of all essential regions of the T5 deoxyribonucleic acid. These conclusions are supported by in vitro measurements of the rifampin sensitivity of the RNA polymerase activities extracted from infected and uninfected cells. The rifampin sensitivity of the RNA polymerase activity extracted from uninfected cells was similar to the rifampin sensitivity of the RNA polymerase activity extracted 30 min after infection.

Genetic and physiological studies of bacteriophage T5. 3. Patterns of deoxyribonucleic acid synthesis induced by mutants of T5 and the identification of genes influencing the appearance of phage-induced dihydrofolate reductase and deoxyribonuclease

Patterns of deoxyribonucleic acid (DNA) metabolism in nonpermissive cells infected with amber mutants representing 29 genes of T5 are reported. A group of 7 contiguous genes are essential for the synthesis of phage DNA, whereas 20 other genes, when defective, permit varying degrees of phage DNA synthesis. Two further genes are essential for complete transfer of phage DNA to host cells, and therefore indirectly do not permit the synthesis of phage DNA. The structural genes for an early T5 deoxyribonuclease and for T5 DNA polymerase, as well as a gene that affects the synthesis of dihydrofolate reductase, have been identified in the genetic map of T5.

Location of single-strand interruptions in the DNA of bacteriophage T5

The positions of three single-strand interruptions in the DNA of phage T5(+) have been located by electron microscopy. All three interruptions were found in the same strand. Uneven base composition along the molecule is indicated by the preferential melting of certain regions. The data suggest a model according to which (1) the first-step-transfer DNA section is separated by a single-strand interruption from the rest of the phage genome, (2) the phage carries only one such section and therefore transfers the asymmetrical DNA molecule always in the same direction into the host cell, and (3) single-strand interruptions are points of preferred breakage.

Early abortive lysis by phage BF23 in Escherichia coli K-12 carrying the colicin Ib factor

Growth of phage BF23 was restricted in Escherichia coli K-12 strains carrying a colicin I factor (ColIb); most infected cells lysed early without producing progeny phages. Either addition of chloramphenicol before phage infection or ultraviolet irradiation of phage prevented early abortive lysis, an indication that certain phage functions are required for this phenomenon. Very little or no phage-induced lysozyme was synthesized in the infected ColI(+) cells. This result suggests that early abortive lysis was not due to the lysozyme action. A small fraction (0.05) of BF23-infected ColI(+) cells showed normal phage growth. This "escaped growth" may reflect the physiological state of the host bacteria rather than the heterogeneity of the infecting phage. Host-controlled modification was not observed. A phage mutant, BF23hI, able to grow on ColI(+) cells, was isolated and was characterized to be recessive to the wild-type BF23 in its ability to undergo early abortive lysis. Among the T series phages, T5 induced early abortive lysis, and growth of T5 was restricted upon infection to ColI(+) cells. These results and the other observations, including the occurrence of phenotypic mixing between BF23 and T5, suggest that these two phages are related to each other even though the receptor sites for BF23 and T5 are apparently different.

First-step-transfer deoxyribonucleic acid of bacteriophage T5

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Ultrastructure of bacteriophage and bacteriocins

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Bacteriophage T5 chromosome fractionation: genetic specificity of a DNA fragment

The bacteriophage T5 DNA fragments retained by a population of blended early complexes, formed under conditions of limited viral DNA transfer to host cells, appear to include only one of six tested cistrons. When complexes harboring wild-type fragments are infected with appropriate amber mutants, recombination occurs but apparently is not needed for productive infection.