Effect of dark repair on ultraviolet sensitivity of bacteriophage-infected bacteria

Feiner, R. R. (Columbia University, New York, N.Y.), and R. F. Hill. Effect of dark repair on ultraviolet sensitivity of bacteriophage-infected bacteria. J. Bacteriol. 91:1239-1247. 1966.-Changes in ultraviolet (UV) sensitivity of phage-host complexes during phage development have been studied for the following systems: T1 and Escherichia coli B, T1 and E. coli K-12S, lambda and E. coli K-12S. Complexes were formed with bacterial strains differing in ability to dark-repair UV damage to deoxyribonucleic acid and, after irradiation, were plated on bacteria differing similarly. In the first half of the latent period, the resistance of complexes formed with nonrepairing bacteria increased considerably; with T1 and E. coli B hcr(-), in 4 min the resistance became the same as that of complexes formed with repairing bacteria. The repair ability of plating bacteria affected survival curves only upon irradiation in the second half of the latent period after mature phages were present in the initial complex. Use of nonrepairing bacteria both for initial infection and for plating of late complexes resulted in a series of survival curves showing for all three systems the same pattern of change originally reported for T2-E. coli B complexes. Thus, a hitherto unexplained difference between radiation survival curves for T-even and T-odd phages seems due to repair of T-odd phages by the host.     

Ambivalent bacteriophages of different species active on Escherichia coli K12 and Salmonella sps. strains

A study was made of several bacteriophages (including phages U2 and LB related to T-even phages of Escherichia coli) that grow both on E. coli K12 and on some Salmonella strains. Such phages were termed ambivalent. T-even ambivalent phages (U2 and LB) are rare and have a limited number of hosts among Salmonella strains. U2 and LB are similar to canonical E. coli-specific T-even phages in morphological type and size of the phage particle and in reaction with specific anti-T4 serum. Phages U2 and LB have identical sets of structural proteins, some of which are similar in size to structural proteins of phages T2 and T4. DNA restriction patterns of phages U2 and LB differ from each other and from those of T2 and T4. Still, DNAs of all four phages have considerable homology. Unexpectedly, phages U2 and LB grown on Salmonella bungori were unstable during centrifugation in a CsCl gradient. Ambivalent bacteriophages were found in species other than T-even phages and were similar in morphotype to lambdoid and other E. coli phages. One of the ambivalent phages was highly similar to well-known Felix01, which is specific for Salmonella. Ambivalent phages can be used to develop a new set for phage typing in Salmonella. An obvious advantage is that ambivalent phages can be reproduced in the E. coli K12 laboratory strain, which does not produce active temperate phages. Consequently, the resulting typing phage preparation is devoid of an admixture of temperate phages, which are common in Salmonella. The presence of temperate phages in phage-typing preparations may cause false-positive results in identifying specific Salmonella strains isolated from the environment or salmonellosis patients. Ambivalent phages are potentially useful for phage therapy and prevention of salmonellosis in humans and animals.     

Amplification and Purification of T4-Like Escherichia coli Phages for Phage Therapy: from Laboratory to Pilot Scale

We investigated the amplification and purification of phage preparations with respect to titer, contamination level, stability, and technical affordability. Using various production systems (wave bags, stirred-tank reactors, and Erlenmeyer flasks), we obtained peak titers of 10⁹ to 10¹⁰ PFU/ml for T4-like coliphages. Phage lysates could be sterilized through 0.22-μm membrane filters without titer loss. Phages concentrated by differential centrifugation were not contaminated with cellular debris or bacterial proteins, as assessed by electron microscopy and mass spectrometry, respectively. Titer losses occurred by high-speed pelleting of phages but could be decreased by sedimentation through a sucrose cushion. Alternative phage concentration methods are prolonged medium-speed centrifugation, strong anion-exchange chromatography, and ultrafiltration, but the latter still allowed elevated lipopolysaccharide contamination. T4-like phages could not be pasteurized but maintained their infectivity titer in the cold chain. In the presence of 10 mM magnesium ions, phages showed no loss of titer over 1 month at 30°C.     

A physiological role for tRNA nucleotidyltransferase during bacteriophage infection

Bacteriophage infection of E. coli cells deficient in the enzyme tRNA nucleotidyltransferase (cca mutants) resulted in greatly decreased production of viable progeny phage compared to wild type cells. This decrease amounted to as much as 90% in the case of T-even bacteriophages, and 50-65% for T-odd bacteriophages. However, infection by the RNA phages, Qbeta and f2, was unaffected by the cca mutation. Examination of T4 infection of cca hosts indicated that phage development proceeded normally, that near-normal numbers of progeny particles were formed, but that most of these particles were non-viable. Possible functions for E. coli tRNA nucleotidyltransferase during bacteriophage infection are discussed.     

Ambivalent bacteriophages of different species active on Escherichia coli K12 and Salmonella sp. strains

A study was made of several bacteriophages (including phages U2 and LB related to T-even phages of Escherichia coli) that grow both on E. coli K12 and on some Salmonella strains. Such phages were termed ambivalent. T-even ambivalent phages (U2 and LB) are rare and have a limited number of hosts among Salmonella strains. U2 and LB are similar to canonical E. coli-specific T-even phages in morphological type and size of the phage particle and in reaction with specific anti-T4 serum. Phages U2 and LB have identical sets of structural proteins, some of which are similar in size to structural proteins of phages T2 and T4. DNA restriction patterns of phages U2 and LB differ from each other and from those of T2 and T4. Still, DNAs of all four phages have considerable homology. Unexpectedly, phages U2 and LB grown on Salmonella bongori were unstable during centrifugation in a CsCl gradient. Ambivalent bacteriophages were found in species other than T-even phages and were similar in morphotype to lambdoid and other E. coli phages. One of the ambivalent phages was highly similar to well-known Felix01, which is specific for Salmonella. Ambivalent phages can be used to develop a new set for phage typing in Salmonella. An obvious advantage is that ambivalent phages can be reproduced in the E. coli K12 laboratory strain, which does not produce active temperature phages. Consequently, the resulting typing phage preparation is devoid of an admixture of temperate phages, which are common in Salmonella. The presence of temperate phages in phage-typing preparations may cause false-positive results in identifying specific Salmonella strains isolated from the environment or salmonellosis patients. Ambivalent phages are potentially useful for phage therapy and prevention of salmonellosis in humans and animals.     

Functional interactions of the genomes of Shigella sonnei phages and Escherichia coli phage T4 in mixed infection]

A comparative study of Shigella sonnei phages U and G and Escherichia coli phage T4 has shown that enzymes coded for by the Sh. sonnei phages can functionally substitute for some T4-coded products. This finding in indicative of an evolutionary relationship between T-even phages and disenteric phages U and G. The U phage is uncapable to compensate amber mutants for the genes that control the conversion of cytosine into 5-hydroxymethyl cytosine (5-HMC) and the glucosylation of the latter, which agrees with our earlier finding that the U phage DNA contains no 5-HMC. U and G phages are also found to exclude the T4 phage in the course of mixed infection.     

Pretreatment to reduce somatic salmonella phage interference with FRNA coliphage assays: successful use in a one-year survey of vulnerable groundwaters

Somatic salmonella (SS) phages were commonly found in higher numbers than F-specific RNA (FRNA) coliphages in a multi-site survey of contamination-vulnerable groundwaters. The relative abundance of SS phages required that a pretreatment procedure be implemented to reduce the SS phage content of samples before FRNA coliphage assay with Salmonella typhimurium WG49. Pretreatment involved selective SS phage removal by Salm. typhimurium WG45 cells. This pretreatment proved effective in producing interference-free samples throughout the one-year survey period and in seeded evaluation, was shown not to affect the detection of representative FRNA coliphage MS2. During the survey, 30 groundwater sites located in the continental United States, Puerto Rico and the Virgin Islands were examined for FRNA coliphages and SS phages at monthly intervals. FRNA coliphages were detected at six of the 30 sites and in 33 of 329 monthly samples. SS phages were also detected at six sites and in 28 of 329 monthly samples. Five of the phage-positive sites were positive for both phage groups. At those five sites, 58 monthly samples were collected during the survey period. Those 58 samples yielded an average FRNA coliphage concentration of 140 pfu per 100 1 of groundwater as compared to an average SS phage concentration of 565 pfu per 100 1 of groundwater. Twenty of the 58 samples were positive for both FRNA coliphages and SS phages. In those samples, FRNA coliphages were more abundant in five samples; SS phages were more abundant in 15 samples. Because these results demonstrate that SS phage levels may often exceed FRNA coliphage levels in environmental waters, it is clear that SS phage removal procedures will greatly enhance the effectiveness of the WG49-based FRNA coliphage assay.     

Roles of copper and O(2) in the radiation-induced inactivation of T7 bacteriophage

The effect of copper on the radiation damage induced in T7 bacteriophage has been investigated. The phages were gamma-irradiated and the effects of copper(II) ions in the presence of various additives and radical scavengers were examined in an attempt to better understand the effect of transition metal ions on the role of free radicals, particularly superoxide, in biological damage. The present work extends a study previously done on isolated enzyme to a whole biological entity. Copper(II) ions even at very low concentrations enhanced the lethal effect of radiation. This sensitization was observed in both the presence and the absence of oxygen. The effect of copper could be reverted by chelating agents such as EDTA or 1,10-phenanthroline. Hydrogen peroxide enhanced the sensitizing effect of copper, though little if any protection was provided by catalase or SOD. High molecular weight scavengers of free radicals in the presence of both copper(II) and hydrogen peroxide had no protective effect. (This is in contrast to metal-free systems where, although such scavengers are incapable of penetrating the phages, they protect them against inactivation.) These scavengers, without added H2O2, afforded only slight protection to the irradiated phages in the presence of Cu. Low molecular weight scavengers of free radicals reduced but did not eliminate the sensitizing effect of copper. The sensitizing effect of copper was also observed with other T-odd phages, but not with the T-even series. Copper(II) ions under similar experimental conditions did not sensitize T4 or T2 phages but rather had a protective effect. The results are interpreted in terms of a site-specific Fenton mechanism according to which the binding of the metal ion to the phages is a prerequisite for the occurrence of the biological damage. The results also indicate that most of the copper effect is endogenous. This is in accord with the failure of copper to sensitize the T-even phages, which differ by the rigidity and permeability of their outer coat structures.     

Selection for lysis inhibition in bacteriophage

For Escherichia coli cells that have been infected by T-even bacteriophages (phages T2, T4, and T6), the adsorption of a second T-even phage results in an increase in the length of the original phage infection and an associated increase in the number of phages produced by the same infected cell. This is a phage encoded response called lysis inhibition. In this study the ecological significance of lysis inhibition is explored. In particular it is argued that lysis inhibition is an adaptive response to environments containing high concentrations of infected cells and low concentrations of uninfected cells.     

Factors influencing the replication of somatic coliphages in the water environment

The potential replication of somatic coliphages in the environment has been considered a drawback for their use as viral indicators, although the extent to which this affects their numbers in environmental samples has not been assessed. In this study, the replication of somatic coliphages in various conditions was assayed using suspensions containing naturally occurring somatic coliphages and Escherichia coli WG5, which is a host strain recommended for detecting somatic coliphages. The effects on phage replication of exposing strain WG5 and phages to a range of physiological conditions and the effects of the presence of suspended particles or other bacteria were also assayed. Phage replication was further tested using a strain of Klebsiella terrigena and naturally occurring E. coli cells as hosts. Our results indicate that threshold densities of both host bacterium and phages should occur simultaneously to ensure appreciable phage replication. Host cells originating from a culture in the exponential growth phase and incubation at 37 degrees C were the best conditions for phage replication in E. coli WG5. In these conditions the threshold densities required to ensure phage replication were about 10(4) host cells/ml and 10(3) phages/ml, or 10(3) host cells/ml and 10(4) phages/ml, or intermediate values of both. The threshold densities needed for phage replication were higher when the cells proceeded from a culture in the stationary growth phase or when suspended particles or other bacteria were present. Furthermore E. coli WG5 was more efficient in supporting phage replication than either K. terrigenae or E. coli cells naturally occurring in sewage. Our results indicate that the phage and bacterium densities and the bacterial physiological conditions needed for phage replication are rarely expected to be found in the natural water environments.     

DNA sequence heterogeneity in the genes of T-even type Escherichia coli phages encoding the receptor recognizing protein of the long tail fibers

Summary Genes (g) 36 and 37 code for the proteins of the distal half of the long tail fibers of phage T4, gene product (gp) 35 links the distal half to the proximal half of this fiber. The receptor, lipopolysaccharide, most likely is recognized by gp37. Using as probe a restriction fragment consisting of most of g36 and g37 of phage T4 the genes corresponding to g35, g36, and g37 of phages T2 and K3 (using the E. coli outer membrane proteins OmpF and OmpA, respectively, as receptors) have been cloned into plasmid pUC8. Partial DNA sequences of g37 of phage K3 have been determined. One area, corresponding to residues 157 to 210 of the 1026 residue gp37 of phage T4, codes for an identical sequence in phage K3. Another area corresponds to residues 767 to 832 of the phage T4 sequence. Amino acid residues 767 to 832 of the phage T4 sequence are almost identical in both phage proteins while the remainder is rather different. DNAs of T2, T4, T6, another T-even type phage using protein Tsx as a receptor, and 10 different T-even type phages using the OmpA protein as a receptor have been hybridized with restriction fragments covering various parts of the g37 area of phage K3. With probably only one exception all of the 13 phages tested possess unique genes 37 and within the majority of these, sequences highly homologous to parts of g37 of K3 are present in a mosaic type fashion. Other regions of these genes 37 did not show any homology with the K3 probes; in case of the OmpA specific phage M1 absence of homology was evident in most of its g37 even including the area that should serve for recognition of the cellular receptor. In sharp contrast to this situation it was found that a major part of the gene (g23) coding for the major capsid protein is rather highly conserved in all phages studied. The extreme variability in sequences existing in genes 37 might be a consequence of phages during evolution being able to more or less drastically change their receptor specifities.     

Susceptibility of Different Coliphage Genomes to Host-controlled Variation

Twenty-eight coliphages were studied for their susceptibility to four systems of host control variation in Escherichia coli. Both temperate and virulent phages were studied, including phages with ribonucleic acid, double- and single-stranded deoxyribonucleic acid (DNA) and glucosylated DNA. The systems examined were E. coli C-K, K-B, B-K, and K-K(P1). The C-K, K-B, and B-K systems affected temperate phages and nonlysogenizing mutants derived from temperate phages. In general, these systems did not restrict virulent phages. Phage 21e, a variant of phage 21, lost the ability to undergo restriction in the C-K and B-K systems, but retained susceptibility to the K-B and K-K(P1) systems. This suggests that the genetic site(s) on the phage, as well as in the host, determines susceptibility to host-controlled variation. Both temperate and dependent virulent phages were susceptible to the host control system resulting from the presence of prophage P1. The autonomous and small virulents were not susceptible. In a given system, the various susceptible phages differed widely in their efficiency of plating on the restricting host. If the few infections that occur arise in rare special cells, then different populations of special cells are available to different phage species. For most phage types, when a susceptible phage infected a nonrestricting host, the progeny showed the specificity appropriate to that host. Behavior of T3 was exceptional, however. When T3 obtained from E. coli K infected E. coli C or B, some of the progeny phages retained K host specificity, whereas others acquired the specificity of the new host.     

Photodynamic activity of dyes with different DNA binding properties II. T4 phage inactivation.

The photosensitizing efficiency of six dyes--proflavine, 9-aminoacridine, ethidium bromide, thiopyronine, pyronine and acridine red--have been compared on the basis of the inactivation of sensitized T4 phage caused by light irradiation. This reaction was only measurable after diffusion of the dye through the phage capsid and was not observed in the presence of either chloroquine or quinacrine; it followed a single-hit kinetics as a function of the irradiation time. With each dye, a double reciprocal plot of the inactivation constant versus the dye concentration present gave rise to a linear relationship. From this relation, parameters were deduced which expressed the relative photosensitizing efficiencies. Dye-binding to the phages was measured and the proflavine-mediated inactivation appeared to be related to the amount of strongly bound molecules. Such a conclusion could not be reached in the case of 9-aminoacridine and ethidium bromide, which were much less efficient photosensitizers than proflavine, but which were also strongly bound to the phages. Thiopyronine was weakly bound to the phages; it had, however, the highest photosensitizing activity observed. These results indicate that various mechanisms are involved when the phage photosensitization is due to one dye or another.     

The first recognized epigenetic signal: DNA glucosylation of T-even bacteriophages.

Host-induced modification of phage T2 to T*2 was discovered in 1952. This phenomenon, a reversible alteration in viral host range resulting from a single growth cycle in certain bacterial hosts, is an ‘epigenetic’ change. In 1963 the chemical basis for the T* modification was shown to be the loss of DNA glucosylation, which resulted from T-even phage growth in cells lacking the glucosyl donor UDPG. Thus, DNA glucosylation of T-even phages was the first recognized epigenetic signal.     

Partial Exclusion between T-Even Bacteriophages; an Incipient Genetic Isolation Mechanism

Conditional lethal mutant systems developed in T-even bacteriophages T2, T4 and T6 have been used to study the partial exclusion which characterizes mixed infections of these phages. In bacteria mixedly infected with T2 and T4, the dominant phage (T4) acts against localized exclusion sensitivity determinants in the genome of the excluded phage (T2). These determinants are clustered near genes controlling early functions; the determinants themselves do not appear among the progeny, but markers located close to them appear infrequently, by recombination. The excluding action of T4 does not depend on the action of any gene so far identified by conditional lethal mutations, nor does it depend on differences in DNA glucosylation between infecting phages. Regardless of mechanism, the genetic consequence of this partial exclusion is to limit genetic exchange between T2 and T4 in the region of the genome controlling early functions, while retaining the capacity for extensive exchange in other regions; in short, partial exclusion constitutes a localized genetic isolating mechanism. Related forms of partial exclusion characterize mixed infections of other T-even phages, including those of some phages newly isolated from nature.     

Host-controlled Restriction of T-even Bacteriophages: Relation of Endonuclease I and T-even-induced Nucleases to Restriction

Restriction of nonglucosylated T2 phage (T(*)2) as a function of bacterial growth state was the same for endonuclease I-containing and endonuclease I-deficient strains of Escherichia coli B. Furthermore, E. coli strains with various levels of restriction for T2 had comparable endonuclease I activities. It was also found that a T4 mutant temperature-sensitive for gene 46 and 47 functions was fully restricted at 42 C. It therefore appears that neither endonuclease I nor the phage-induced nucleases whose activities are blocked by mutations in genes 46 and 47 catalyze the initial event in restriction of nonglucosylated T-even phages.     

Concentration of coliphages from large volumes of water and wastewater.

Membrane filter adsorption-elution technology has been extensively used for the concentration and detection of animal viruses from large volumes of water. This study describes the development of positively charged microporous filters (Zeta Plus) for the concentration of coliphages from large volumes of water and wastewater. Four different coliphages were studied: MS-2, phi X174, T2, and T4. Positively charged microporous filters were found to efficiently adsorb these coliphages from tap water, sewage, and lake water at neutral pH. Adsorbed viruses were eluted with a 1:1 mixture of 8% beef extract and 1 M sodium chloride at pH 9. Using this method, coliphages could be concentrated from 17-liter volumes of tap water with recoveries ranging from 34 to 100%. Coliphages occurring naturally in raw and secondarily treated sewage were recovered with average efficiencies of 56.5 and 55.0%, respectively. This method should be useful in isolation of rare phages, the ecology of phages in natural waters, and the evaluation of water quality.     

Isolation of Escherichia coli bacteriophages from the stool of pediatric diarrhea patients in Bangladesh

A 3-week coliphage survey was conducted in stool samples from 140 Bangladeshi children hospitalized with severe diarrhea. On the Escherichia coli indicator strain K803, all but one phage isolate had 170-kb genomes and the morphology of T4 phage. In spot tests, the individual T4-like phages infected up to 27 out of 40 diarrhea-associated E. coli, representing 22 O serotypes and various virulence factors; only five of them were not infected by any of these new phages. A combination of diagnostic PCR based on g32 (DNA binding) and g23 (major capsid protein) and Southern hybridization revealed that half were T-even phages sensu strictu, while the other half were pseudo-T-even or even more distantly related T4-like phages that failed to cross-hybridize with T4 or between each other. Nineteen percent of the acute stool samples yielded T4-like phages, and the prevalence was lower in convalescent stool samples. T4-like phages were also isolated from environmental and sewage water, but with low frequency and low titers. On the enteropathogenic E. coli strain O127:K63, 14% of the patients yielded phage, all of which were members of the phage family Siphoviridae with 50-kb genomes, showing the morphology of Jersey- and beta-4 like phages and narrow lytic patterns on E. coli O serotypes. Three siphovirus types could be differentiated by lack of cross-hybridization. Only a few stool samples were positive on both indicator strains. Phages with closely related restriction patterns and, in the case of T4-like phages, identical g23 gene sequences were isolated from different patients, suggesting epidemiological links between the patients.     

Synthesis of Indicator Strains and Density of Ribonucleic Acid-Containing Coliphages in Sewage

Escherichia coli strains freshly isolated from natural sources are inefficient indicators of coliphages present in sewage. Four E. coli strains recently isolated from clinical specimens were mutagenized to obtain lac(-) mutants. Such mutants were infected with an F'lac(+) sex factor of E. coli K-12. Pairs of isogenic lac(-) and lac(-)/F'lac(+) strains were used as indicators of coliphages present in sewage, and it was found that such strains can be effectively used for a direct and almost selective enumeration of F-specific coliphage contents of sewage samples. Serological tests were applied to a number of F-specific phages isolated. All the isolates that were tested fell into two distinguishable antigenic classes: members of one class being related to ribonucleic acid (RNA) phage MS2 and those of the other being related to another RNA phage, namely, Qbeta. MS2-related phages have been found to be more widely distributed than the Qbeta related phages. Most habitats sampled were found to yield only one or the other kind of phage. Single-stranded deoxyribonucleic acid-containing F-specific phages were not detectable by the methods employed by us.