T4 DNA polymerase: Rates and processivity on single-stranded DNA templates

Three different methods have been used to determine the rate at which an individual bacteriophage T4 DNA polymerase molecule moves when synthesizing DNA on a single-stranded DNA template chain. These methods agree in suggesting an in vitro rate for this enzyme of about 250 nucleotides per second at 37 °C. This rate is close to the rate at which bacteriophage T4 replication forks move in vivo (about 500 nucleotides per second). Comparison with the overall amount of DNA synthesis seen in in vitro reactions reveals that only a small fraction of the T4 DNA polymerase molecules present are synthesizing DNA at any one time. This is explicable in terms of the limited processivity of the enzyme in these reactions, along with its capacity for non-productive DNA binding to the DNA template molecules.     

Function of the bacteriophage T4 transfer RNA's

Maximum growth of bacteriophage T4 requires the phage complement of transfer RNA. tRNA-deficient T4 grown on laboratory strains of Escherichia coli showed a moderate decrease in burst size that correlated with a decrease in the rate of synthesis of the major structural proteins of the T4 tail fiber. Some tRNA-defieient T4 mutants showed a 20-fold reduction in burst size on one of a number of E. coli strains isolated from hospital patients. We consider it most likely that the T4 tRNA's function to ensure optimum rates of protein synthesis in the maximum number of hosts by supplementing the reading capacity for those codons used more commonly in the virus than in the host.     

Rotating Magnetic Field-Assisted Reactor Enhances Mechanisms of Phage Adsorption on Bacterial Cell Surface

Growing interest in bacteriophage research and use, especially as an alternative treatment option for multidrug-resistant bacterial infection, requires rapid development of production methods and strengthening of bacteriophage activities. Bacteriophage adsorption to host cells initiates the process of infection. The rotating magnetic field (RMF) is a promising biotechnological method for process intensification, especially for the intensification of micromixing and mass transfer. This study evaluates the use of RMF to enhance the infection process by influencing bacteriophage adsorption rate. The RMF exposition decreased the t₅₀ and t₇₅ of bacteriophages T4 on Escherichia coli cells and vb_SauM_A phages on Staphylococcus aureus cells. The T4 phage adsorption rate increased from 3.13 × 10⁻⁹ mL × min⁻¹ to 1.64 × 10⁻⁸ mL × min⁻¹. The adsorption rate of vb_SauM_A phages exposed to RMF increased from 4.94 × 10⁻⁹ mL × min⁻¹ to 7.34 × 10⁻⁹ mL × min⁻¹. Additionally, the phage T4 zeta potential changed under RMF from −11.1 ± 0.49 mV to −7.66 ± 0.29 for unexposed and RMF-exposed bacteriophages, respectively.     

Outer Membrane Proteins Ail and OmpF of Yersinia pestis Are Involved in the Adsorption of T7-Related Bacteriophage Yep-phi

Yep-phi is a T7-related bacteriophage specific to Yersinia pestis, and it is routinely used in the identification of Y. pestis in China. Yep-phi infects Y. pestis grown at both 20°C and 37°C. It is inactive in other Yersinia species irrespective of the growth temperature. Based on phage adsorption, phage plaque formation, affinity chromatography, and Western blot assays, the outer membrane proteins of Y. pestis Ail and OmpF were identified to be involved, in addition to the rough lipopolysaccharide, in the adsorption of Yep-phi. The phage tail fiber protein specifically interacts with Ail and OmpF proteins, and residues 518N, 519N, and 523S of the phage tail fiber protein are essential for the interaction with OmpF, whereas residues 518N, 519N, 522C, and 523S are essential for the interaction with Ail. This is the first report to demonstrate that membrane-bound proteins are involved in the adsorption of a T7-related bacteriophage. The observations highlight the importance of the tail fiber protein in the evolution and function of various complex phage systems and provide insights into phage-bacterium interactions.     

Bacteriophage adsorption efficiency and its effect on amplification

Existing models for bacteriophage adsorption are modified with the addition of a new term, adsorption efficiency, and applied to a T4–Escherichia coli system. The adsorption efficiency is the fraction of phage that adsorbs irreversibly to the host. Adsorption kinetics were modeled using the adsorption rate constant (k) and the adsorption efficiency (ε). Experimental data demonstrated that the adsorption rate constant depends strongly on the condition of the host while the adsorption efficiency is a property of the bacteriophage population. The adsorption efficiency exhibited a marked dependence on the concentration of l-tryptophan. The system was used to study the effect of adsorption kinetics on bacteriophage amplification. Increasing adsorption efficiency had an effect similar to increasing the initial multiplicity of infection; the number of phages produced during amplification decreased. Optimizing the adsorption efficiency by manipulating the l-tryptophan concentration yielded a 14-fold increase in the number of phages produced.     

Use of Tetrahymena thermophila To Study the Role of Protozoa in Inactivation of Viruses in Water

The ability of a ciliate to inactivate bacteriophage was studied because these viruses are known to influence the size and diversity of bacterial populations, which affect nutrient cycling in natural waters and effluent quality in sewage treatment, and because ciliates are ubiquitous in aquatic environments, including sewage treatment plants. Tetrahymena thermophila was used as a representative ciliate; T4 was used as a model bacteriophage. The T4 titer was monitored on Escherichia coli B in a double-agar overlay assay. T4 and the ciliate were incubated together under different conditions and for various times, after which the mixture was centrifuged through a step gradient, producing a top layer free of ciliates. The T4 titer in this layer decreased as coincubation time increased, but no decrease was seen if phage were incubated with formalin-fixed Tetrahymena. The T4 titer associated with the pellet of living ciliates was very low, suggesting that removal of the phage by Tetrahymena inactivated T4. When Tetrahymena cells were incubated with SYBR gold-labeled phage, fluorescence was localized in structures that had the shape and position of food vacuoles. Incubation of the phage and ciliate with cytochalasin B or at 4°C impaired T4 inactivation. These results suggest the active removal of T4 bacteriophage from fluid by macropinocytosis, followed by digestion in food vacuoles. Such ciliate virophagy may be a mechanism occurring in natural waters and sewage treatment, and the methods described here could be used to study the factors influencing inactivation and possibly water quality.     

Phage-Encoded Colanic Acid-Degrading Enzyme Permits Lytic Phage Infection of a Capsule-Forming Resistant Mutant Escherichia coli Strain

In this study, we isolated a bacteriophage T7-resistant mutant strain of Escherichia coli (named S3) and then proceeded to characterize it. The mutant bacterial colonies appeared to be mucoid. Microarray analysis revealed that genes related to colanic acid production were upregulated in the mutant. Increases in colanic acid production by the mutant bacteria were observed when l-fucose was measured biochemically, and protective capsule formation was observed under an electron microscope. We found a point mutation in the lon gene promoter in S3, the mutant bacterium. Overproduction of colanic acid was observed in some phage-resistant mutant bacteria after infection with other bacteriophages, T4 and lambda. Colanic acid overproduction was also observed in clinical isolates of E. coli upon phage infection. The overproduction of colanic acid resulted in the inhibition of bacteriophage adsorption to the host. Biofilm formation initially decreased shortly after infection but eventually increased after 48 h of incubation due to the emergence of the mutant bacteria. Bacteriophage PBECO4 was shown to infect the colanic acid-overproducing mutant strains of E. coli. We confirmed that the gene product of open reading frame 547 (ORF547) of PBECO4 harbored colanic acid-degrading enzymatic (CAE) activity. Treatment of the T7-resistant bacteria with both T7 and PBECO4 or its purified enzyme (CAE) led to successful T7 infection. Biofilm formation decreased with the mixed infection, too. This procedure, using a phage cocktail different from those exploiting solely receptor differences, represents a novel strategy for overcoming phage resistance in mutant bacteria.     

The interaction of the 7,8-dihydrodiol-9, 10-oxides of benzo(a) pyrene with bacteriophages R17 and T7

Dose-survival curves for bacteriophages R17 and T7 treated with the syn- and anti-isomers for 7,8-dihydroxy-9,10-epoxy-7,8,9,10-tetrahydrobenzo(a)pyrene in 0.02 M phosphate buffer, pH 7.0, have been determined. In both cases the anti-isomer proved to be the more toxic: mean lethal dose for R17; syn- 3 μg/ml, anti- 2 μg/ml: and for T7, syn- 3 μg/ml, anti- 0.3 μg/ml. With both reagents reaction with bacteriophage or loss by solvolysis were complete within minutes. Physico-chemical studies of the RNA failed to detect any degradation 1 and 24 h after the addition of the reagents to the bacteriophage and no change in survival of the bacteriophage occurred during this period. In experiments with bacteriophage T7 and T7-DNA reaction did not, in the first hour, introduce any significant number of alkali-labile sites in the nucleic acid. These results suggest that no reaction occurs with the phosphate groups of the nucleic acids. Following the initial loss of infectivity when bacteriophage T7 was treated with the syn-isomer there was a further, progressive loss of biological activity over 4 days which was associated with the development of alkali labile lesions. It seems probable that these latter effects are due to the loss of alkylated bases from the DNA, a process similar to the depurination reactions observed following the reaction of DNA with e.g. methylating agents.     

Cloning and Physical Mapping of an Early Region of the Bacteriophage T4 Genome

We have cloned DNA restriction fragments from the largely nonessential region of bacteriophage T4 located between genes 39 and 56. The cloned DNA fragments were used to construct a precise map of the sites in this region recognized by eight restriction endonucleases. This restriction map allowed us to compare the cytosine-containing T4 DNA used for cloning with the hydroxymethylcytosine-containing DNA of wild-type T4; there were no detectable rearrangements in the region tested. We were also able to determine the physical locations of several deletion end points and of several genes.     

Incorporation of T4 bacteriophage in electrospun fibres

Aims

Antibacterial food packaging materials, such as bacteriophage‐activated electrospun fibrous mats, may address concerns triggered by waves of bacterial food contamination. To address this, we investigated several efficient methods for incorporating T4 bacteriophage into electrospun fibrous mats.

Methods and Results

The incorporation of T4 bacteriophage using simple suspension electrospinning led to more than five orders of magnitude decrease in bacteriophage activity. To better maintain bacteriophage viability, emulsion electrospinning was developed where the T4 bacteriophage was pre‐encapsulated in an alginate reservoir via an emulsification process and subsequently electrospun into fibres. This resulted in an increase in bacteriophage viability, but there was still two orders of magnitude drop in activity. Using a coaxial electrospinning process, full bacteriophage activity could be maintained. In this process, a core/shell fibre structure was formed with the T4 bacteriophage being directly incorporated into the fibre core. The core/shell fibre encapsulated bacteriophage exhibited full bacteriophage viability after storing for several weeks at +4°C.

Conclusions

Coaxial electrospinning was shown to be capable of encapsulating bacteriophages with high loading capacity, high viability and long storage time.

Significance and Impact of the Study

These results are significant in the context of controlling and preventing bacterial infections in perishable foods during storage.     

Effect of thermoinduced changes in T4 bacteriophage structure on the process of molecular recognition of 'host' cells.

By means of high-precision acoustic measurements and by methods of fluorescent and electron microscopy, investigations have been performed of thermoinduced conformational changes in T4 bacteriophage and its thermolabile mutants altered in baseplate proteins (gene products 7, 8, 10). A relationship was found between the conformational changes in T4 bacteriophage structure in the temperature range of 33-45 degrees C and the efficiency of bacteriophage adsorption and the changes in the orientation of long tail fibers. The possibility of heat regulation of 'recognition' of 'host' cells by bacterial viruses is suggested.     

The function of tail fibers in triggering baseplate expansion of bacteriophage T4

Normal particles of bacteriophage T4 have six long tail fibers attached to a hexagonal baseplate. T4 particles having various complements of tail fibers were prepared by in vitro addition of fibers to fiberless particles, and the infectivity of the particles was determined. Particles having fewer than six fibers (partially fibered) were found to have a decreased probability of infection. Partially fibered particles having T4 fibers were completed by addition of T6 fibers, and the infectivity was determined on a host that lacked the T6 tail fiber receptor. Attachment of the additional fibers increased the infectivity even though the T6 fibers could not bind to the host cell. The infectivity of particles having mixtures of T4 and T6 fibers was determined on cells having only one type of receptor. The results indicated that particles bound by only three fibers have a low probability of infection. The effect of thermolabile baseplate mutations was also examined. Studies of partially fibered particles and particles with mixtures of fibers indicated that particles with altered baseplates have a less stringent requirement for binding of the tail fibers for infection.     

Electron microscopy of a eukaryotic single-stranded DNA binding protein-DNA complex

The single-stranded DNA binding protein of Ustilago maydis decreases the contour length of φX174 DNA. When DNA complexes were prepared with subsaturating amounts of the protein, its distribution on the DNA was markedly non-random, indicating a high degree of co-operativity in its binding to single-stranded DNA. The analagous Escherichia coli, Salmonella typhimurium and bacteriophage T7 binding proteins also reduced DNA contour lengths to a similar extent, whereas the bacteriophage T4 gene 32 protein, as shown previously, increased the contour length. Despite the fact that the U. maydis protein efficiently denatures poly[d(A-T) · d(A-T)], it appears to initiate denaturation of native bacteriophage λ DNA rather inefficiently.     

PilF is an outer membrane lipoprotein required for multimerization and localization of the Pseudomonas aeruginosa Type IV pilus secretin

Type IV pili (T4P) are retractile appendages that contribute to the virulence of bacterial pathogens. PilF is a Pseudomonas aeruginosa lipoprotein that is essential for T4P biogenesis. Phenotypic characterization of a pilF mutant confirmed that T4P-mediated functions are abrogated: T4P were no longer present on the cell surface, twitching motility was abolished, and the mutant was resistant to infection by T4P retraction-dependent bacteriophage. The results of cellular fractionation studies indicated that PilF is the outer membrane pilotin required for the localization and multimerization of the secretin, PilQ. Mutation of the putative PilF lipidation site untethered the protein from the outer membrane, causing secretin assembly in both inner and outer membranes. T4P-mediated twitching motility and bacteriophage susceptibility were moderately decreased in the lipidation site mutant, while cell surface piliation was substantially reduced. The tethering of PilF to the outer membrane promotes the correct localization of PilQ and appears to be required for the formation of stable T4P. Our 2.0-Å structure of PilF revealed a superhelical arrangement of six tetratricopeptide protein-protein interaction motifs that may mediate the contacts with PilQ during secretin assembly. An alignment of pseudomonad PilF sequences revealed three highly conserved surfaces that may be involved in PilF function.     

The generation and analysis of clones containing bacteriophage T4 DNA fragments

Cytosine-containing DNA of bacteriophage T4 was digested with three restriction endonucleases: endo R · EcoRI, endo R · HindIII and endo R · PstI, and each digestion ligated with a cloning vector to generate three independent collections of T4 DNA-containing clones. The T4 clones were screened for their T4 genetic content by recombinational analysis using amber mutants of T4. Complementation of T4 amber mutant growth and labeling of proteins in vivo provided evidence of expression of specific (g30, g39, g44 and g46) cloned T4 genes.     

Bacteriophage-based biosorbents coupled with bioluminescent ATP assay for rapid concentration and detection of Escherichia coli

Wild type T4 bacteriophage and recombinant T4 bacteriophages displaying biotin binding peptide (BCCP) and cellulose binding module (CBM) on their heads were immobilized on nano-aluminum fiber-based filter (Disruptor™), streptavidin magnetic beads and microcrystalline cellulose, respectively. Infectivity of the immobilized phages was investigated by monitoring the phage-mediated growth inhibition of bioluminescent E. coli B and cell lysis using bioluminescent ATP assay. The results showed that phage immobilization resulted in a partial loss of infectivity as compared with the free phage. Nevertheless, the use of a biosorbent based on T4 bacteriophage immobilized on Disruptor™ filter coupled with a bioluminescent ATP assay allowed simultaneous concentration and detection of as low as 6 × 10³ cfu/mL of E. coli in the sample within 2 h with high accuracy (CV = 1-5% in log scale). Excess of interfering microflora at levels 60-fold greater than the target organism did not affect the results when bacteriophage was immobilized on the filter prior to concentration of bacterial cells.     

The interaction of emetine with DNA and its effect on the adsorption of certain bacteriophages

The interaction of emetine with DNA in solution at low ionic strength did not bring about a detectable change of the spectrum of either DNA or emetine in the ultraviolet region but resulted in stabilization of the secondary structure of DNA. The irreversible interaction of emetine with DNA or bacteriophage coat, which would result in a loss of infectivity of the lambda cI 857, T7 or T4 BOI bacteriophages did not take place. However, emetine decreased the adsorption of the bacteriophage lambda cI 857 onEscherichia coli C 600, probably due to interaction with cellular receptors.     

The interaction of platinum II compounds with bacteriophages T7 and R17

The inactivation of the DNA-containing bacteriophage T7 and of the RNA-containing bacteriophage R17 by dichloro-ethylenediamine Pt II and by cis- and trans-dichloro-diammine Pt II has been studied under a variety of experimental conditions. It has been found that the mean lethal concentrations vary for T7 from 0.007 to 0.5 μg/ml and for R17 from 0.09 to 1.1 μg/ml depending upon which compound is used and the manner in which the experiment is performed. Experiments with the ¹⁴C-labelled ethylenediamine derivative have shown that inactivation is primarily related to the extent of reaction of the compound with the bacteriophage and that variations in inactivation observed under different experimental conditions simply reflect differences in the kinetics of the binding reactions. Quantitative comparisons have shown that at the mean lethal dose 1.5 molecules of platinum compound are bound to each R17 bacteriophage and 5 molecules to each T7.96% of the compound bound to R17 was bound to RNA and 76% of the compound bound to T7 was bound to the DNA.