THE COURSE OF INFECTION WITH ABNORMAL BACTERIOPHAGE T4 CONTAINING NON-GLUCOSYLATED DNA ON ESCHERICHIA COLI STRAINS

Interaction of phages, bacteria, and the human immune system: Evolutionary changes in phage therapy

Phages and bacteria are known to undergo dynamic and co-evolutionary arms race interactions in order to survive. Recent advances from in vitro and in vivo studies have improved our understanding of the complex interactions between phages, bacteria, and the human immune system. This insight is essential for the development of phage therapy to battle the growing problems of antibiotic resistance. It is also pivotal to prevent the development of phage-resistance during the implementation of phage therapy in the clinic. In this review, we discuss recent progress of the interactions between phages, bacteria, and the human immune system and its clinical application for phage therapy. Proper phage therapy design will ideally produce large burst sizes, short latent periods, broad host ranges, and a low tendency to select resistance.

Conflicts targeting epigenetic systems and their resolution by cell death: novel concepts for methyl-specific and other restriction systems

Epigenetic modification of genomic DNA by methylation is important for defining the epigenome and the transcriptome in eukaryotes as well as in prokaryotes. In prokaryotes, the DNA methyltransferase genes often vary, are mobile, and are paired with the gene for a restriction enzyme. Decrease in a certain epigenetic methylation may lead to chromosome cleavage by the partner restriction enzyme, leading to eventual cell death. Thus, the pairing of a DNA methyltransferase and a restriction enzyme forces an epigenetic state to be maintained within the genome. Although restriction enzymes were originally discovered for their ability to attack invading DNAs, it may be understood because such DNAs show deviation from this epigenetic status. DNAs with epigenetic methylation, by a methyltransferase linked or unlinked with a restriction enzyme, can also be the target of DNases, such as McrBC of Escherichia coli, which was discovered because of its methyl-specific restriction. McrBC responds to specific genome methylation systems by killing the host bacterial cell through chromosome cleavage. Evolutionary and genomic analysis of McrBC homologues revealed their mobility and wide distribution in prokaryotes similar to restriction–modification systems. These findings support the hypothesis that this family of methyl-specific DNases evolved as mobile elements competing with specific genome methylation systems through host killing. These restriction systems clearly demonstrate the presence of conflicts between epigenetic systems.

Episome-mediated Transfer of Drug Resistance in Enterobacteriaceae X. Restriction and Modification of Phages by fi R Factors

Watanabe, Tsutomu (Keio University, Tokyo, Japan), Toshiya Takano, Toshihiko Arai, Hiroshi Nishida, and Sachiko Sato. Episome-mediated transfer of drug resistance in Enterobacteriaceae. X. Restriction and modification of phages by fi(-) R factors. J. Bacteriol. 92:477-486. 1966.-An fi(-) R factor, which restricts phages lambda, T1, and T7 without modifying them, was found to restrict and not to modify an F(-)-specific phage, W-31, in Escherichia coli K-12, but not to restrict phage P-22 in Salmonella typhimurium LT-2, whereas other fi(-) R factors restricted and modified P-22 but not W-31; fi(+) R factors did not restrict these phages. Transduction and lysogenization with phages lambda and P-22 were reduced by these fi(-) R factors in K-12 and LT-2, respectively, and the transducing phages lambda and P-22 were modified by these fi(-) R factors. Spontaneous as well as ultraviolet-induced production of phage P-22 and zygotic induction of phage lambda were not significantly affected by any R factor. Injection of the nucleic acids of phages T1 and lambda was not affected by R factors, but the injected phage nucleic acids were rapidly broken down in the bacteria carrying fi(-) R factors. The nucleic acids of the modified phages were not broken down in these bacteria. It was assumed from these results that the mechanism of restriction of phages by fi(-) R factors is due to the breakdown of the injected phage nucleic acids by a deoxyribonuclease(s), presumably located near the cell surface in the cells carrying fi(-) R factors. The deoxyribonuclease(s), formed in the cells carrying the nonmodifying fi(-) R factor, is considered to be different from that synthesized in the cells carrying the modifying fi(-) R factors. It was further shown that the average burst sizes of the unmodified as well as modified phages are slightly reduced by the presence of the fi(-) R factors.

Cell death upon epigenetic genome methylation: a novel function of methyl-specific deoxyribonucleases

BACKGROUND

Alteration in epigenetic methylation can affect gene expression and other processes. In Prokaryota, DNA methyltransferase genes frequently move between genomes and present a potential threat. A methyl-specific deoxyribonuclease, McrBC, of Escherichia coli cuts invading methylated DNAs. Here we examined whether McrBC competes with genome methylation systems through host killing by chromosome cleavage.

RESULTS

McrBC inhibited the establishment of a plasmid carrying a PvuII methyltransferase gene but lacking its recognition sites, likely through the lethal cleavage of chromosomes that became methylated. Indeed, its phage-mediated transfer caused McrBC-dependent chromosome cleavage. Its induction led to cell death accompanied by chromosome methylation, cleavage and degradation. RecA/RecBCD functions affect chromosome processing and, together with the SOS response, reduce lethality. Our evolutionary/genomic analyses of McrBC homologs revealed: a wide distribution in Prokaryota; frequent distant horizontal transfer and linkage with mobility-related genes; and diversification in the DNA binding domain. In these features, McrBCs resemble type II restriction-modification systems, which behave as selfish mobile elements, maintaining their frequency by host killing. McrBCs are frequently found linked with a methyltransferase homolog, which suggests a functional association.

CONCLUSIONS

Our experiments indicate McrBC can respond to genome methylation systems by host killing. Combined with our evolutionary/genomic analyses, they support our hypothesis that McrBCs have evolved as mobile elements competing with specific genome methylation systems through host killing. To our knowledge, this represents the first report of a defense system against epigenetic systems through cell death.

Sedimentation velocity of DNA in isokinetic sucrose gradients: calibration against molecular weight using fragments of defined length

The relationship between sedimentation coefficient and molecular weight for DNA sedimenting in preformed alkaline and neutral sucrose gradients was determined using absolute molecular weight standards (restriction fragments of plasmid pBR322 and phage lambda DNA). The range of calibration for alkaline gradients was extended to small DNA fragments (652 base-pairs) for the first time. The exponent b in the equation S20 degrees, w = aMb was found to be 0.380 in neutral gradients and 0.410 in alkali. The latter value differs significantly from previous estimates. The gradients were isokinetic, and the distance sedimented was shown to be directly proportional to the sedimentation coefficient at all times.

Evidence for a near UV-induced photoproduct of 5-hydroxymethylcytosine in bacteriophage T4 that can be recognized by endonuclease V

Non-photoreactivable endonuclease V-sensitive sites have been detected in the DNA of wild type bacteriophage T4 irradiated with near UV light (320 nm). Such sites were not detected in the DNA of (a) wild type T4 irradiated with far UV (254 nm) or (B) in T4 mutants in which non-glucosylated 5-hydroxy-methylcytosine (5HMC) or cytosine replaces glucosylated 5HMC normally present in T4, irradiated with 320 nm or 254 nm light. Although the non-photoreactivable sites accounted for approximately 50% of the endonuclease V-sensitive sites in the DNA of glucosylated T4 irradiated with near UV, there was very little difference in the sensitivities of T4 containing glucosylated 5HMC, non-glucosylated 5HMC and cytosine to near UV (313 nm). We propose that the photoproduct responsible for the non-photoreactivable, but endonuclease V-sensitive, sites in glucosylated DNA is formed from glucosylated 5HMC and that a similar photoproduct is formed from non-glucosylated 5HMC or cytosine in the appropriate phage strains. We further propose that the glucosylated 5HMC photoproduct is non-photoreactivable whereas the cytosine and non-glucosylated 5HMC photoproducts are photoreactivable and are therefore possibly cyclobutane dimers.

Mechanism localisation and control of restriction cleavage of phage T4 and lambda chromosomes in vivo

The primary action of restriction endonuclease, cleaving infecting DNA, has been demonstrated in vivo. This primary cleavage is followed rapidly by hydrolysis of the cleaved DNA at its newly exposed termini. Infecting viruses can inactivate cytoplasmic and membrane restriction endonucleases to prevent cleavage of unmodified DNA replicas.

Complementation by restricted phage T1

The ability of restricted phage T1hr to complement stocks of T1am mutants carrying the P1 modification has been tested in mixed infection of Escherichia coli B(P1). Of the 18 genes tested, 15 could be complemented to give successful infection of approximately 10 to 25% of the cells, and 2 other genes consistently gave at least 5% complementation. The progeny phage produced in these infections was predominantly of the hr(+)am genotype. A mutant in gene 12 could be complemented very poorly, if at all. With one double mutant stock, the complementation obtained was nearly as good as the more poorly complemented of the two corresponding single mutants.

Variable transforming activity of nonglucosylated and fragmented T4 DNA

Nonglucosylated and fragmented T4 DNA shows a gene-specific variation in transformation efficiency.

Analysis of host range restriction in Escherichia coli treated with toluene

Escherichia coli cells treated with toluene replicate DNA when they are provided with deoxyribonucleoside 5'-triphosphates, ATP, Mg(++), and K(+). However, when deoxycytidine 5'-triphosphate is replaced by hydroxymethyl deoxycytidine 5'-triphosphate, incorporation of nucleotides into acid-precipitable material by toluenetreated strains restrictive to nonglucosylated T-even phage is reduced to less than 5% of that normally observed. Even when dCTP is present in the reaction mixture, a similar effect of the hydroxymethyl analogue on DNA replication is observed. In contrast, toluene-treated E. coli K12r6(-)r2,4(-), a strain permissive to the nonglucosylated T-even phage, incorporates hydroxymethyl deoxycytosine into its DNA, and replication proceeds at only a slightly reduced rate in the presence of the hydroxymethyl deoxycytidine 5'-triphosphate. The presence of the hydroxymethyl deoxycytidine 5'-triphosphate in the reaction mixture does not lead to degradation of preexisting DNA of the restrictive host, but it does lead to an irreversible inhibition of further DNA replication; the inhibition is observed only when the hydroxymethyl deoxycytidine 5'-triphosphate is present during replication. Thus phage-specific enzymes are not necessary for the incorporation of hydroxymethylcytosine into phage DNA, and the restrictive mechanism, present in the host cell before infection, can recognize hydroxymethylcytosine residues in its own DNA, as well as the DNA of the T-even phage.

Abortive infection of sporulating Bacillus subtilis 168 by phi 2 bacteriophage

Bacteriophage phi2 is unable to replicate in Bacillus subtilis 168. Although some phage deoxyribonucleic acid (DNA) synthesis can occur, the DNA made is not biologically active and sedimentation analysis reveals that it is smaller in size than that of mature DNA or DNA isolated from phi2-infected permissive hosts. Messenger ribonucleic acid hybridizable with phi2 DNA is also synthesized in phi2-infected cells of 168. Mutants of 168 which are permissive hosts for phi2 have been isolated. These mutants are defective in sporulation and possess the phenotype of "early sporulation mutants." The majority map in two locations, one near the lys locus opposite the trp locus (spoA locus) and the other tightly linked to a phe locus.

Inhibition of T4 bacteriophage multiplication by superinfecting ghosts and the development of tolerance after bacteriophage infection

Simultaneous addition of T4 phage and ghosts to host cells prevents infective center formation. Cells which have been infected with phage for less than 2 min are also inhibited by superinfecting ghosts. After this time, a chloramphenicol-inhibitable reaction occurs which causes the phage-infected cells to become increasingly tolerant of added ghosts.

Biological activity of bacteriophage ghosts and "take-over" of host functions by bacteriophage

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Biological effects of substituting cytosine for 5-hydroxymethylcytosine in the deoxyribonucleic acid of bacteriophage T4

Previous work from this laboratory has shown that the cytosine-containing T4 deoxyribonucleic acid (DNA) made by deoxycytidine triphosphatase (dCTPase) amber mutants is extensively degraded, and that nucleases controlled by genes 46 and 47 participate in this process. In this paper, we examine other consequences of a defective dCTPase. Included are studies of DNA synthesis and phage production, and of the control of both early and late protein synthesis after infection of Escherichia coli B with various T4 mutants defective in genes 56 (dCTPase), 42 (dCMP hydroxymethylase), 1 (deoxynucleotide kinase), 43 (DNA polymerase), 30 (polynucleotide ligase), 46 and 47 (DNA breakdown) or e(lysozyme). By varying the temperature of infection with a temperature-sensitive dCTPase mutant, we have been able to control intracellular dCTPase activity, and thus vary the cytosine content of the phage DNA. We have produced and characterized viable T4 phage in which cytosine replaces 20% of the 5-hydroxymethylcytosine (HMC) in the DNA. We present evidence which suggests that intact, cytosine-containing T4 DNA is much less efficient than is normal T4 DNA in directing the synthesis of tail-fiber antigen. Lysozyme production is much less affected by progressively decreasing dCTPase activity; however, complete substitution of cytosine is correlated with a depression of lysozyme synthesis greater than expected from the defective synthesis of DNA. Low but significant lysozyme synthesis is observed late after infection of E. coli B with T4 amber mutants defective in a number of genes controlling DNA synthesis. The "20% cytosine" T4 phage, once produced, can initiate an apparently normal infection at permissive temperatures; the synthesis of early enzymes, DNA, and phage does not appear to be impaired. Two roles for HMC in T4 DNA have been indicated previously: (i) involvement in host-controlled restriction of the phage, in which glucosylation of the hydroxymethyl group plays a crucial role (16, 29, 53, 58), and (ii) protection of vegetative DNA against phage-controlled nucleases, a protection not dependent on glucosylation (41, 66, 67). A third role is suggested by our present results: transcription of at least some late genes can occur only from HMC-containing DNA and not from cytosine-containing DNA.

Abortive infection of Shigella dysenteriae P2 by T2 bacteriophage

We have investigated some of the biochemical events that accompany the abortive infection by T2 of Shigella dysenteriae lysogenized with the temperate phage P2. After infection with T2, protein and RNA synthesis continued for 3 to 5 min. The virus-induced enzyme, deoxycytidylate hydroxymethylase was produced in reduced amounts (15% of normal), and the extent of deoxyribonucleic acid (DNA) synthesis was 0.1% of that found with a nonlysogenic strain. Measurements of the production of acid-soluble fragments and sedimentation analyses failed to detect enzymatic degradation of the infecting viral DNA which could be specifically related to the presence of the prophage P2. Each interaction between T2 and a bacterium resulted in the death of the cell. This observation is consistent with results obtained with other types of bacteria which show that only when a nucleolytic attack occurs on T2 DNA does the cell have an increased capacity to survive after adsorption of T2.

Infection by bacteriophage P1 and development of host-controlled restriction and modification and of lysogenic immunity

Shigella dysenteriae cells were infected with phage P1 or P1cl. The outcome of superinfection of these cells with phage T1.Sh or T1.Sh(P1) or P1cl was studied as a function of time after the initial infection. Cells undergoing either a lytic response or a lysogenic response to the primary infection develop the ability to specifically restrict T1.Sh between 30 and 45 min. Between 15 and 30 min, the cells seem to develop the ability to produce T1.Sh(P1) after infection by T1.Sh. However, reasons are given for believing that this apparent time difference is consistent with a simultaneous development of the two capacities (restriction and modification) within the cell. This development occurs between 30 and 45 min. Cells infected with P1cl and superinfected 45 or more min later with T1.Sh(P1) can yield both P1cl and T1. Cells infected with P1 become resistant to infection by P1cl within 5 to 10 min. It is argued that this early immunity is not necessarily different in mechanism from true lysogenic immunity.

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.

Chemistry and structure of nucleic acids of bacteriophages. Many forms of nucleic acids of bacteriophages show the ways that information is stored and reproduced

The nucleic acids of bacteriophages are characterized by a surprising multiformity. RNA and DNA may occur, the latter in single- or double-stranded form, circular or linear, with or without breaks or single-strand ends. Terminal redundancy may exist and the populations of linear phages may be uniform or randomly permuted. A double-stranded circular DNA does not occur in extracellular bacteriophage, but is often if not always formed after infection of the bacterial host. Phage DNA may be glucosylated or methylated to a certain extent, and the glucose and methyl residues may influence the stability of the DNA inside the host.

The effect of various physiological conditions on host-controlled restriction in Escherichia coli K(P1)

Growth of K(P1) bacteria under conditions which lead to a reduction in the level of nucleases also leads to a reduction of their ability to restrict the growth of λ.C. Experiments designed to estimate the time after adsorption at which restriction takes place indicate that phage DNA is probably restricted by a nuclease while passing through the periplasm.

On the localization of a factor responsible for host-controlled restriction in Escherichia coli K(P1)

The restriction of phage λ.C by K(P1) cells is reduced when the cells are subjected to an EDTA cold-wash treatment which has been shown to remove surface-localized enzymes. We conclude that a surface-localized enzyme plays an essential role in host-controlled restriction.