Evolution of phi-chi 174. Isolation of four new phi-chi-like phages and comparison with phi-chi 174

Microviruses: A World Beyond phiX174

Two decades of metagenomic analyses have revealed that in many environments, small (∼5 kb), single-stranded DNA phages of the family Microviridae dominate the virome. Although the emblematic microvirus phiX174 is ubiquitous in the laboratory, most other microviruses, particularly those of the gokushovirus and amoyvirus lineages, have proven to be much more elusive. This puzzling lack of representative isolates has hindered insights into microviral biology. Furthermore, the idiosyncratic size and nature of their genomes have resulted in considerable misjudgments of their actual abundance in nature. Fortunately, recent successes in microvirus isolation and improved metagenomic methodologies can now provide us with more accurate appraisals of their abundance, their hosts, and their interactions. The emerging picture is that phiX174 and its relatives are rather rare and atypical microviruses, and that a tremendous diversity of other microviruses is ready for exploration.

Whole-genome synthesis and characterization of viable S13-like bacteriophages

Background

Unprecedented progresses in high-throughput DNA sequencing and de novo gene synthesis technologies have allowed us to create living organisms in the absence of natural template.

Methodology/Principal Findings

The sequence of wild-type S13 phage genome was downloaded from GenBank. Two synonymous mutations were introduced into wt-S13 genome to generate m1-S13 genome. Another mutant, m2-S13 genome, was obtained by engineering two nonsynonymous mutations in the capsid protein coding region of wt-S13 genome. A chimeric phage genome was designed by replacing the F capsid protein open reading frame (ORF) from phage S13 with the F capsid protein ORF from phage G4. The whole genomes of all four phages were assembled from a series of chemically synthesized short overlapping oligonucleotides. The linear synthesized genomes were circularized and electroporated into E.coli C, the standard laboratory host of S13 phage. All four phages were recovered and plaques were visualized. The results of sequencing showed the accuracy of these synthetic genomes. The synthetic phages were capable of lysing their bacterial host and tolerating general environmental conditions. While no phenotypic differences among the variant strains were observed when grown in LB medium with CaCl₂, the S13/G4 chimera was found to be much more sensitive to the absence of calcium and to have a lower adsorption rate under calcium free condition.

Conclusions/Significance

The bacteriophage S13 and its variants can be chemically synthesized. The major capsid gene of phage G4 is functional in the phage S13 life cycle. These results support an evolutional hypothesis which has been proposed that a homologous recombination event involving gene F of quite divergent ancestral lineages should be included in the history of the microvirid family.

Chemical synthesis of bacteriophage G4

Background

Due to recent leaps forward in DNA synthesis and sequencing technology, DNA manipulation has been extended to the level of whole-genome synthesis. Bacteriophages occupy a special niche in the micro-organic ecosystem and have potential as a tool for therapeutic agent. The purpose of this study was to carry out chemical synthesis of the bacteriophage G4 and the study of its infectivity.

Methodology/Principal Findings

Full-sized genomes of bacteriophage G4 molecules were completed from short overlapping synthetic oligonucleotides by direct assembly polymerase chain reaction and ligase chain reaction followed by fusion polymerase chain reaction with flanking primers. Three novel restriction endonuclease sites were introduced to distinguish the synthetic G4 from the wild type. G4 particles were recovered after electroporation into Escherichia coli and were efficient enough to infect another strain. The phage was validated by electron microscope. Specific polymerase chain reaction assay and restriction analyses of the plaques verified the accuracy of the chemical synthetic genomes.

Conclusions

Our results showed that the bacteriophage G4 obtained is synthetic rather than a wild type. Our study demonstrated that a phage can be synthesized and manipulated genetically according to the sequences, and can be efficient enough to infect the Escherichia coli, showing the potential use of synthetic biology in medical application.

Methods for studying aquatic bacteriophage ecology

Methods are described for enumerating the different kinds of bacteriophage present in virus concentrates prepared from 120 liters of water. Although developed specifically for use with coliphages, they should be applicable to viruses infecting other hosts. These methods involve mixed indicators, equilibrium buoyant-density centrifugation, use of enzymes or inhibitors or both, and specific hybridization probes, either alone or in combination. With these methods, it was possible to specifically enumerate filamentous and isometric male-specific (F-specific) phages, the different classes of P-group plasmid-specific phages, phiX174-like phages, and lambda-like phages. Some applications of these methods, including measurement of virus inactivation in the environment and the extent of fecal pollution, are discussed.

Horizontal gene transfer and the evolution of microvirid coliphage genomes

Bacteriophage genomic evolution has been largely characterized by rampant, promiscuous horizontal gene transfer involving both homologous and nonhomologous source DNA. This pattern has emerged through study of the tailed double-stranded DNA (dsDNA) phages and is based upon a sparse sampling of the enormous diversity of these phages. The single-stranded DNA phages of the family Microviridae, including phiX174, appear to evolve through qualitatively different mechanisms, possibly as result of their strictly lytic lifestyle and small genome size. However, this apparent difference could reflect merely a dearth of relevant data. We sought to characterize the forces that contributed to the molecular evolution of the Microviridae and to examine the genetic structure of this single family of bacteriophage by sequencing the genomes of microvirid phage isolated on a single bacterial host. Microvirids comprised 3.5% of the detectable phage in our environmental samples, and sequencing yielded 42 new microvirid genomes. Phylogenetic analysis of the genes contained in these and five previously described microvirid phages identified three distinct clades and revealed at least two horizontal transfer events between clades. All members of one clade have a block of five putative genes that are not present in any member of the other two clades. Our data indicate that horizontal transfer does contribute to the evolution of the microvirids but is both quantitatively and qualitatively different from what has been observed for the dsDNA phages.

Interfaces of the yeast killer phenomenon

A new prophylactic and therapeutic antimicrobial strategy based on a specific physiological target that is effectively used by killer yeasts in their natural ecological competition is theorized. The natural system exploited is the yeast killer phenomenon previously adopted as an epidemiological marker for intraspecific differentiation of opportunistic yeasts, hyphomycetes, and bacteria. Pathogenic microorganisms (Candida albicans) may be susceptible to the activity of yeast killer toxins due to the presence of specific cell wall receptors. On the basis of the idiotypic network, we report that antiidiotypic antibodies, produced against a monoclonal antibody bearing the receptor-like idiotype, are in vivo protecting animals immunized through idiotypic vaccination and in vitro mimicking the antimicrobial activity of yeast killer toxins, thus acting as antibiotics.

Interaction between phage G13 and its oligosaccharide receptor studied by equilibrium dialysis

The reversible binding of phage G13, a phi X174-like single-strand DNA phage, to a 3H-labelled nonasaccharide from the lipopolysaccharide of its natural host Escherichia coli C was studied with equilibrium dialysis. The binding constant (Ka) was determined to 1.3 x 10(7) M-1 in Scatchard and Lineweaver-Burk plots. Approximately one saccharide bound per G13 phage particle which suggests that only one of the 12 spikes in each G13 virion was engaged in the phage/receptor saccharide interaction. Equilibrium dialysis inhibition experiments with saccharides from lipopolysaccharides of an isogenic series of Salmonella typhimurium mutants showed that hepta- and pentasaccharides from two G13-sensitive bacteria, i.e., with efficiencies of plating of 0.1-1.0 compared to E. coli C, were efficient inhibitors with Ka-values greater than or equal to 1.2 x 10(7) M-1. The octa- and hexasaccharides from two G13 resistant strains, with efficiency of plating less than or equal to x 10(-4), were either greater than 1000-fold or greater than 15-fold less efficient as inhibitors with Ka-values less than or equal to 8.8 x 10(5) M-1. The results show that phage G13 binds in a specific and reversible way to penta-, hepta-, and nonasaccharides from G13 sensitive bacteria with the specificity residing in the hexose and heptose region of the core lipopolysaccharide.

The asymmetric dimeric polymerase hypothesis: a progress report

In 1983, my laboratory first proposed that the DNA polymerase III holoenzyme is an asymmetric dimer with distinguishable leading and lagging strand polymerases. Here, I review progress by my laboratory and others in testing this hypothesis. To date, the hypothesis is supported by our demonstration of (i) an asymmetry in function of two populations of holoenzyme in solution in their ability to use the ATP analog, ATP gamma S, to support initiation complex formation, (ii) the stabilization of a dimeric polymerase structure by the tau subunit, (iii) allosteric communication between polymerase halves and (iv) the coexistence of gamma and the tau, subunits which share common sequences, within the same holoenzyme assemblies. This latter observation may provide a structural basis for holoenzyme asymmetry. I discuss the implications of the asymmetric dimer hypothesis to the solution of problems encountered by polymerases at the replication fork and delineate further tests required before the hypothesis can be firmly established.

Recovery of DNA fragments specifically bound by monoclonal anti-DNA antibody

A method to recover and identify DNA fragments that were specifically bound by a monoclonal anti-DNA antibody has been developed. A mixture of DNA fragments digested by restriction enzymes was first incubated with a murine monoclonal anti-DNA antibody and then reacted with anti-murine immunoglobulin-conjugated Sepharose 4B. The resulting complex was washed to remove unbound DNA by low-speed centrifugation. The bound DNA fragment was released from antibody by alkaline dimethyl sulfoxide solution or extracted by phenol treatment. The recovered DNA was analyzed by electrophoresis on a polyacrylamide gel.

DNA requirements at the bacteriophage G4 origin of complementary-strand DNA synthesis

An in vivo assay was used to define the DNA requirements at the bacteriophage G4 origin of complementary-strand DNA synthesis (G4 origin). This assay made use of an origin-cloning vector, mRZ1000, a defective M13 recombinant phage deleted for its natural origin of complementary-strand DNA synthesis. The minimal DNA sequence of the G4 genome sufficient for the restoration of normal M13 growth parameters was determined to be 139 bases long, located between positions 3868 and 4007. This G4-M13 construct was also found to give rise to proper initiation of complementary-strand synthesis in vitro. The cloned DNA sequence contains all the regions of potential secondary structure which have been implicated in primase-dependent replication initiation as well as additional sequence information. To address the role of one region which potentially forms a DNA secondary structure, the DNA sequence internal to the G4 origin was altered by site-directed mutagenesis. A 3-base insertion at the AvaII site as well as a 17-base deletion between the AvaI and AvaII sites both resulted in loss of origin function. The 17-base deletion was also generated within the G4 genome and found to dramatically reduce the infectious growth rate of the resulting phage. These results are discussed with respect to the role of the G4 origin as the recognition site for primase-dependent replication initiation and its possible role in stage II replication.

The binding of RecA protein to duplex DNA molecules is directional and is promoted by a single stranded region

RecA protein from E. coli binds more strongly to single stranded DNA than to duplex molecules. Using duplex DNA that contains single stranded gaps, we have studied the protection by RecA protein at various concentrations, of restriction sites as a function of their distance from the single stranded region. We show that the binding of RecA protein, initiated in the single stranded region, extends progressively along the adjoining duplex in the 5' to 3' direction with respect to the single stranded region. The strand exchange reaction is known to proceed in the same direction.

Isolation and construction of mutants of the G4 minus strand origin: analysis of their in vivo activity

An active, rifampicin-resistant primase-dependent bacteriophage G4 origin of complementary DNA strand synthesis has been cloned as a 274 bp fragment into the filamentous phase M13 and its secondary structure altered by deletion and insertion. It has been found that the entire 136 bp G4 intergenic region containing the secondary structure loops I and III is necessary for rifampicin-resistant conversion of SS----RF DNA in vivo. The secondary structures, however, can be widely separated by insertion between them of both random DNA sequences, and sequences that form strong additional secondary structure configurations and the origins still retain activity. Primase therefore probably recognises two DNA domains on loops I and III, the physical separation of which is not important.

Nucleotide sequence and genome organization of bacteriophage S13 DNA

The complete sequence of bacteriophage S13 DNA has been determined. The molecule has 5386 nucleotides and differs from phi X174 by 87 transitions and 24 transversions. All the proteins, A,A*,B,C,D,E,F,G,H, J and K found in phi X174 are also present in S13. Due to changes in the H/A intergenic region of S13, the start of an additional protein, A', has been identified. Genes F and H coding for the capsid and spike proteins, respectively, are the least conserved in comparison to phi X174. Many of the silent changes, as well as some amino acid changes, are found in the same nucleotide sequence positions in phage G4, confirming the interrelationship between the three phages.

Mutations in the J-F intercistronic region of bacteriophages phi X174 and G4 affect the regulation of gene expression

The J-F intercistronic region of the genomes of bacteriophages phi X174 and G4 is transcribed but not translated. It contains the potential for a perfectly base-paired hairpin structure, which has been proposed to act as a terminator of transcription or as a regulatory region for mRNA turnover (or both). We measured phage-specific protein synthesis in mutants with modifications of the hairpin sequence and found a relative decrease in the expression of the upstream gene D as compared to the downstream genes F, G, and H in all mutants. The mutations also appeared to affect the efficiency of the gene F ribosome-binding site. These data strongly support the regulatory significance of the J-F intercistronic region and the putative hairpin structure therein.

Role of SSB protein in RecA promoted branch migration reactions

The RecA protein of Escherichia coli is essential for genetic recombination and postreplicational repair of DNA. In vitro, RecA protein promotes strand transfer reactions between full length linear duplex and single stranded circular DNA of phi X174 to form heteroduplex replicative form II-like structures (Cox and Lehman 1981 a0. In a similar way, it transfers one strand of a short duplex restriction fragment to a single stranded circle. Both reactions require RecA and single strand binding protein (SSB) in amounts sufficient to saturate the ssDNA. The rate and extent of strand transfer is enhanced considerably when SSB is added after preincubation of the DNA with RecA protein. In contrast, SSB protein is not required for RecA protein catalysed reciprocal strand exchanges between regions of duplex DNA. These results indicate that while SSB is necessary for efficient transfer between linear duplex and ssDNA to form a single heteroduplex, it is not required for branch migration reactions between duplex molecules that form two heteroduplexes.

Cloned bacteriophage phi X174 DNA sequence interferes with synthesis of the complementary strand of infecting bacteriophage phi X174

The insertion of a particular phi X DNA sequence in the plasmid pACYC177 strongly decreased the capacity of Escherichia coli cells containing such a plasmid to propagate bacteriophage phi X174. The smallest DNA sequence tested that showed the effect was the HindII fragment R4. This fragment does not code for a complete protein. It contains the sequence specifying the C-terminal part of the gene H protein and the N-terminal part of the gene A protein, as well as the noncoding region between these genes. Analysis of cells that contain plasmids with the "reduction sequence" showed that (i) the adsorption of the phages to the host cells is normal, (ii) in a single infection cycle much less phage is formed, (iii) only 10% of the infecting viral single-stranded DNA is converted to double-stranded replicative-form DNA, and (iv) less progeny replicative form DNA is synthesized. The reduction process is phi X174 specific, since the growth of the related G4 and St-1 phages was not affected in these cells. The effect of the recombinant plasmids on infecting phage DNA shows similarity to the process of superinfection exclusion.

Site-specific mutagenesis using oligodeoxyribonucleotides: isolation of a phenotypically silent phi X174 mutant, with a specific nucleotide deletion, at very high efficiency

A decadeoxyribonucleotide, pAAATCCCTCA, was synthesized to complement nucleotides 2920--2930 of coliphage phi X174 viral DNA except that the nucleotide corresponding to position 2925 is deleted. The phage DNA sequence in this region codes for the ribosome-binding site of gene H. The oligodeoxyribonucleotide was integrated into double-stranded phi X174 DNA by using it as a primer for DNA polymerase with wild-type DNA template followed by ligation. The resultant heteroduplex DNA was used to transfect Escherichia coli spheroplasts and progeny bacteriophage were isolated. The synthetic decadeoxyribonucleotide was then used to enrich mutant viral DNA from which nucleotide 2925 had been deleted. After three cycles of enrichment and spheroplast transfection only mutant DNA was detectable. The deletion of nucleotide 2925 from the phi X174 genome seriously disrupts a sequence complementary to the 3'-terminus of the 16S rRNA of E. coli and also eliminates a translation termination codon from that sequence. However, the mutant grows normally with no readily perceptible phenotype. Thus, a short synthetic oligodeoxyribonucleotide has been used to construct, and to isolate with 100% efficiency, a mutant for which there is no biological selection procedure.

Recognition of duplex DNA containing single-stranded regions by recA protein

Genetic recombination in Escherichia coli requires recA protein, the product of the recA+ gene. In this paper we show that purified recA protein, which binds strongly to denatured DNA, cooperatively recognizes DNA containing short single-stranded regions. The interaction of varying amounts of recA protein with DNA molecules was investigated by measuring its DNA-dependent ATPase activity. In 3mM Mg2+, the ATPase activity was stimulated by excess single-stranded DNA and was minimal with either intact circular or blunt-ended linear duplexes. Single-strand gaps of about 30 nucleotides were sufficient to increase the ATPase activity to a level almost as great as that observed with single-stranded DNA. Sedimentation studies at neutral pH showed cooperative binding of recA protein to single-stranded DNA or to duplex DNA containing single-stranded regions. In the presence of ATP, an intermediate rate of sedimentation was observed; in contrast, adenosine 5'-gamma-thiotriphosphate (ATP[S]) caused the formation of fast-sedimenting DNA-protein complexes. Gapped plasmid DNA plus recA protein and ATP[S] formed large aggregates containing thousands of molecules. Complex formation and stimulation of the ATPase activity of recA protein with duplex DNA containing single-stranded regions indicates that recA protein may change the conformation of the normally duplex molecules to a conformation prepared for homologous pairing.

The enzymatic replication of DNA

Enzymatic mechanisms of DNA replication have been investigated using small bacteriophages as probes to illuminate the cellular systems upon which they must rely during infection. Conversion of the circular, single-stranded DNAs of phages M13, G4, and phi X174 to their duplex forms has revealed the participation of diverse ways to start a new chain and a complex DNA polymerase III holoenzyme upon which all these systems depend for chain elongation. The phi X174 system, which is the most exacting and revealing of the host chromosomal replication pattern, includes at least twenty polypeptides for making the viral DNA into a duplex and multiplying the duplex. Resolution and purification of these numerous proteins is in train and their reconstitution into a "replisome"-like structure is envisioned.

Nucleotide sequence of bacteriophage G4 DNA

The 5,577 nucleotide long sequence of bacteriophage G4 DNA has been determined using the 'plus and minus' and chain termination methods of DNA sequencing. This sequence has been compared with that of the closely related bacteriophage phiX174 (refs 1, 55). In the coding regions there is an average of 33.1% nucleotide sequence differences between the two genomes, but the distribution of these changes is not random and the sequence of some genes is more conserved than others. There is less sequence similarity between the untranslated intergenic regions of G4 and phiX174, but despite this the sequences of the J/F, F/G and H/A untranslated spaces in both genomes have similar sized hairpin loops, which may be related to their function.

Replication of bacteriophage G13 DNA in dna mutants of Escherichia coli

Host functions required for replication of microvirid phage G13 DNA were investigated in vivo, using thermosensitive dna mutants of Escherichia coli. In dna+ bacteria, conversion of viral single-stranded DNA into double-stranded replicative form (stage I synthesis) was resistant to 150 microgram/ml of chloramphenicol or 200 microgram/ml of rifampicin. Although multiplication of G13 phage was severely inhibited at 42--43 degrees C even in dna+ host, considerable amount of parental replicative form was synthesized at 43 degrees C in dna+, dnaA or dnaE bacteria. In dnaB and dnaG mutants, however, synthesis of parental replicative form was severely inhibited at the restrictive temperature. Interestingly enough, stage I replication of G13 DNA was, unlike that of phiX174, dependent on host dnaC(D) function. Moreover, the stage I synthesis of G13 DNA in dnaZ was thermosensitive in nutrient broth but not in Tris/casamino acids/glucose medium. In contrast with the stage I replication, synthesis of G13 progeny replicative form was remarkably thermosensitive even in dna+ or dnA cells.

Evolution of bacteriophage phi C174. V. Alignment of the phi X174, G4, and St-1 restriction enzyme cleavage maps

The restriciton enzyme cleavage maps of bacteriophage phiS174, G4, and St-1 were aligned by two-dimensional filter hybridization. These studies show that the basic genome structure of phiX174 is conserved in the other two bacteriophage. However, the data also suggest the existence of regions of nonhomology.

Conversion of bacteriophage G4 single-stranded viral DNA to double-stranded replicative form in dna mutants of Escherichia coli

Host functions involved in synthesis of parental replicative form of bacteriophage G4 were investigated using various replication mutants of Escheria coli. In dna+ bacteria, conversion of single-stranded viral DNA to replicative form DNA was insensitive to 200 microng/ml of rifampicin or 25 microng/ml of chloramphenicol. At high temperature, synthesis of parental replicative form was unaffected in mutants thermosensitive for dnaA, dnaB, dnaC(D), dnaE or dnaH. In dnaG or dnaZ mutants, however, parental replicative from DNA synthesis was clearly thermosensitive at 43 degrees C. Although the host rep product was essential for viral multiplication, the conversion of single stranded to replicative form was independent of the rep function.

Bacterial rep- mutations that block development of small DNA bacteriophages late in infection

Several related mutants of Escherichia coli C have been isolated that block the growth of the small icosahedral DNA phages phiX174 and S13 late in infection. Phage G6 is also blocked, at a stage not yet known. Growth of the filamentous phage M13, though not blocked, is affected in these strains. These host mutations co-transduce with ilv at high frequency, as do rep- mutations. However, the new mutants, designated groL-, differ from previously studied rep- mutants in that they permit synthesis of progeny replicative-form DNA. The groL- mutants are blocked in synthesis of stable single-stranded DNA of phiX174 and related phages. They are gro+ for P2. Evidence that groL- mutations and rep- mutations are in the same gene is presented. Spontaneous mutants (ogr) of phiX174, S13, and the G phages can grow on groL- strains. The ogr mutations are located in the phage's major capsid gene, F, as determined by complementation tests. There are numerous sites for mutation to ogr. Some mutations in genes A and F interfere with the ogr property when combined with an ogr mutation on the same genome. The ogr mutations are cis acting in a groL- cell; i.e., an ogr mutant gives very poor rescue of a non-ogr mutant. The wild-type form of each G phage appears to be naturally in the ogr mutant state for one or more groL- strains. It is suggested that a complex between F and rep proteins is involved in phage maturation. The A protein appears to interact with this complex.

Recombination promoted by superhelical DNA and the recA gene of Escherichia coli

When a mixture of superhelical DNA (RFI) of phage phiX174 am3 and fragments of single-stranded DNA from wild-type phiX174 was added to spheroplasts of E. coli carrying an amber suppressor, several percent of the progeny phage were recombinant. The yield of wild-type progeny was 10(3) to 10(4) times lower when the fragments came from phiX174 am3 or phage G4 am+, or when fragments were absent. Fewer recombinants were produced in proportion to the decrease in the fraction of RFI in samples treated with S1 nuclease, whereas the total yield of phage did not decrease. Transfection by fragments and superhelical DNA produced 20 to 100 times more recombinants than transfection by fragments and either nicked circular DNA or relaxed closed circular DNA. Transfection of a recA- strain by RFI DNA and fragments yielded 5-10% as many recombinants as transfection of a rec+ strain. This partial requirement for recA was bypassed by transfection with complexes of RFI AM3 DNA and am+ fragments made in vitro.

Host genes involved in the replication of single-stranded DNA phage phiK

Using various replication mutants of E. coli, the host genes that participate in the replication of some K12-specific single-stranded DNA phages have been determined. Functional products of dnaE, -F, -G and -Z genes are required for the multiplication of phiK, whereas dnaA, -B, -C(D), H, -I and -P are dispensable for viral replication. In contrast with polB, recA, B, C, or xth functions, host rep activity is essential for phiK. At the restrictive temperature, the yield of phiK was markedly reduced in the ligts7 mutant and partially decreased in a polAts strain. The phage phiK is thus less dependent on the host cells than phiX174 and phiA which require additionally the dnaB, -C(D) and -H functions. Replication of phage St-1 depends on dnaG and -Z gene products, but not on dnaP function. Although not much affected in polAts host, growth of St-1 was significantly diminished in dnaF or ligts7 mutants.

Host factor requirements and some properties of phiXtB. An evolutionary aspect of phiX-type phages

Replication of phiXtB, a capsid mutant of bacteriophage phiX174, depends on the host functions directed by the E.coli genes dnaE, dnaF, dnaG, dnaZ, lig and rep. The cellular products of dnaA, dnaB, dnaC(D), dnaI, dnaP, polA, polB and xth genes are, however, dispensable for the viral growth. In these host factor requirements, phiXtB resembles phages phiK and St-1 rather than phiX174. Host ranges of phiXtB, St-1 and phiK overlap considerably, and growth temperature of the three phages is somewhat higher than that of phiX174. Furthermore, phiXtB is, like phiK, inactivated by antiserum against St-1. phiXtB may thus fill an evolutionary gap between the phiX174 group and the St-1 group.

Bacteriophage G4 DNA synthesis in temperature-sensitive dna mutants of Escherichia coli

The synthesis of bacteriophage G4 DNA was examined in temperature-sensitive dna mutants under permissive and nonpermissive conditions. The infecting single-stranded G4 DNA was converted to the parental replicative form (RF) at the nonpermissive temperature in infected cells containing a temperature sensitive mutation in the dnaA, dnaB, dnaC, dnaE, or dnaG gene. The presence of 30 mug of chloramphenicol or 200 mug of rifampin per ml had no effect on parental RF synthesis in these mutants. Replication of G4 double-stranded RF DNA occurred at a normal rate in dnaAts cells at the nonpermissive temperature, but the rate was greatly reduced in cells containing a temperature-sensitive mutation in the dnaB, dnaC, dnaE, or dnaG gene. RF DNA replicated at normal rates in revertants of these dna temperature-sensitive host cells. The simplest interpretation of these observations is that none of the dna gene products tested is essential for the synthesis of the complementary DNA strand on the infecting single-stranded G4 DNA, whereas the dnaB, dnaC, dnaE, (DNA polymerase III), and dnaG gene products are all essential for replication of the double-stranded G4 RF DNA. The alternate possibility that one or more of the gene products are actually essential for G4 parental RF synthesis, even though this synthesis is not defective in the mutant hosts, is also discussed.

Isolation of an intermediate which precedes dnaG RNA polymerase participation in enzymatic replication of bacteriophage phi X174 DNA

Conversion of phi X174 single-stranded DNA to the duplex replicative form (RF) in vitro requires at least 10 purified proteins. Three stages - strand initiation, elongation, and termination - comprise this conversion. We now identify a separate stage in strand initiation which precedes dnaG RNA polymerase participation. Incubation of five proteins - protein i, protein n, DNA unwinding protein, dnaB protein, and dnaC protein - with ATP and phi X174 DNA forms an intermediate which enables subsequent stages measured by DNA synthesis to proceed 20 times faster. The intermediate can be isolated in quantitative yield by gel filtration or by ultracentrifugation. Protein i and protein n are required in less than stoichiometric amounts and appear to be absent from the isolated intermediate. Whereas formation of the intermediate is sensitive to antibody to protein i and to N-ethylmaleimide (an inhibitor of protein n and dnaC protein), the intermediate itself is resistant to these reagents. DNA unwinding protein complexes the DNA in a ratio of 60 molecules per circle. Synthesis of the intermediate appears to require stoichiometric quantities of dnaB protein and dnaC PROTEin but their presence in the intermediate has not been established as yet.