Replication of bacteriophage M13: specificity of the Escherichia coli dnaB function for replication of double-stranded M13 DNA

Hijacking the self-replicating machine of bacteriophage for PCR-based cascade signal amplification in detecting SARS-CoV-2 viral marker protein in serum

In this work, the nucleic acid detection of SARS-Cov-2 is extended to protein markers of the virus, utilizing bacteriophage. Specifically, the phage display technique enables the main protease of SARS-Cov-2 to control the self-replication of m13 phage, so that the presence of the viral protease can be amplified by phage replication as the first round of signal amplification. Then, the genome of replicated phage can be detected using polymer chain reaction (PCR), as the second round of signal amplification. Based on these two types of well-established biotechnology, the proposed method shows satisfactory sensitivity and robustness in the direct serum detection of the viral protease. These results may point to clinical application in the near future.

Investigation of the Relation between Temperature and M13 Phage Production via ATP Expenditure

M13 bacteriophage is a promising biomolecule capable of various bionano and material science applications. The biomaterial can self-assemble into matrices to fabricate bioscaffolds using high phage concentration and high phage purity. Previous studies aimed to acquire these conditions in large-scale phage production and have identified the optimal culture temperature range at 28–31 °C. However, explanations as to why this temperature range was optimal for phage production is absent from the work. Therefore, in this study, we identified the relation between culture temperature and M13 phage production using ATP expenditure calculations to comprehend the high yield phage production at the optimal temperature range. We extended a coarse-grained model for the evaluation of phage protein and ribosomal protein synthesis with the premise that phage proteins (a ribosomal protein) are translated by bacterial ribosomes in E. coli through expenditure of ATP energy. By comparing the ATP energy for ribosomal protein synthesis estimated using the coarse-grained model and the experimentally calculated ATP expenditure for phage production, we interpreted the high phage yield at the optimal temperature range and recognized ATP analysis as a reasonable method that can be used to evaluate other parameters for phage production optimization.

Replisome structure suggests mechanism for continuous fork progression and post-replication repair

What happens to DNA replication when it encounters a damaged or nicked DNA template has been under investigation for five decades. Initially it was thought that DNA polymerase, and thus the replication-fork progression, would stall at road blocks. After the discovery of replication-fork helicase and replication re-initiation factors by the 1990s, it became clear that the replisome can "skip" impasses and finish replication with single-stranded gaps and double-strand breaks in the product DNA. But the mechanism for continuous fork progression after encountering roadblocks is entangled with translesion synthesis, replication fork reversal and recombination repair. The recently determined structure of the bacteriophage T7 replisome offers the first glimpse of how helicase, primase, leading-and lagging-strand DNA polymerases are organized around a DNA replication fork. The tightly coupled leading-strand polymerase and lagging-strand helicase provides a scaffold to consolidate data accumulated over the past five decades and offers a fresh perspective on how the replisome may skip lesions and complete discontinuous DNA synthesis. Comparison of the independently evolved bacterial and eukaryotic replisomes suggests that repair of discontinuous DNA synthesis occurs post replication in both.

Optimization of fermentation parameters in phage production using response surface methodology

Previously, we used computer-controlled fermentation technology to improve the yield of filamentous phage produced in Escherichia coli by 10-fold (Grieco et al., Bioprocess Biosyst Eng 32:773-779, 2009). In the current study, three major fermentation parameters (temperature, dissolved oxygen [DO], and pH) were investigated using design of experiments (DOE) methodology. Response surface methodology (RSM) was employed to create a process model and determine the optimal conditions for maximal phage production. The experimental data fitted best to a quadratic model (p < 0.0001). Temperature and pH, but not DO, proved to be significant variables. The model predicted a theoretical optimal condition for maximal bacteriophage production at temperature of 28.1 °C and pH 6.9. A validation run resulted in phage production [3.49 × 10(11) transducing units (TU)/mL] comparable to the predicted value (2.86 × 10(11) TU/mL). This represented a 7-fold increase in phage production above that obtained without optimization, resulting in a 70-fold increase above that achieved by shake flask culture alone.

Enzymatic synthesis of bacteriophage fd viral DNA

An enzyme system with requirements similar to those for replication of phage fd replicative form (RF) DNA in bacteriophage fd-infected cells has been reconstituted with purified fd gene 2 protein, and DNA polymerase III holoenzyme, DNA binding protein I and rep-protein (rep-helicase) of Escherichia coli. The system generates viral circular single strands, which are infective for E. coli spheroplasts. Parental and newly synthesized DNA are covalently connected in early stages of replication, as expected for DNA replication using the rolling circle mechanism. Single-stranded tails of the rolling circle intermediates are cleaved after a full round of replication by gene 2 protein and circularized by the same enzyme molecule.

Initiation of DNA synthesis on the isolated strands of bacteriophage f1 replicative-form DNA

Viral and complementary strand circular DNA molecules were isolated from intracellular bacteriophage f1 replicative-form DNA. Soluble protein extracts of Escherichia coli were used to examine the initiation of DNA synthesis on these DNA templates. The initiation of DNA synthesis on f1 viral strand DNA was catalyzed by E. coli DNA-dependent RNA polymerase, as was initiation of f1 viral strand DNA isolated from mature phage particles. The site of initiation was the same as that used in vivo. In contrast, no de novo initiation of DNA synthesis was detected on f1 complementary strand DNA. Control experiments demonstrated that the E. coli dnaB, dnaC, and dnaG initiation proteins were active under the conditions employed. The results suggest that the viral strand of the f1 replicative-form DNA molecule carries the same DNA synthesis initiation site as the viral strand packaged in mature phage, whereas the complementary strand of the replicative-form DNA molecule carries no site for de novo primer synthesis. These in vitro observations are consistent with the simple rolling circle model for f1 DNA replication in vivo proposed by Horiuchi and Zinder.

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.

Replication of bacteriophage M13 IX. Requirement of the Escherichia coli dnaG function for M13 duplex DNA replication

Temperature-shift experiments with an Escherichia coli dnaG strain indicate a requirement for the dnaG function for M13 phage production only at an early stage of infection. Mutant cells infected at nonpermissive temperature form the parental RF (SS leads to RF) but do not replicate further. A shift to nonpermissive temperature after infection inhibits RF leads to RF replication but not RF leads to SS synthesis. The synthesis of both strands of the duplex RF was inhibited equally after a temperature shift during RF leads to RF replication. We infer that the dnaG protein is required for M13 production only during RF replication and that it is required for the synthesis of both strands of the RF.

Growth of a capsid mutant of bacteriophage phi X174 in a temperature-sensitive strain of Escherichia coli

A capsid mutant of phiX174 is capable of forming replicative form and synthesizing single strands at the restrictive temperature in a dnaB mutant of Escherichia coli. Under similar conditions, the wild-type bacteriophage is incapable of either step in viral synthesis.

Inhibition of bacteriophage phi chi 174 DNA replication in dnaB mutants of Escherichia coli C

Bacteriophage phiX174 DNA replication was examined in temperature-sensitive dnaB mutants of Escherichia coli C to determine which stages require the participation of the product of this host gene. The conversion of the infecting phage single-stranded DNA to the double-stranded replicative form (parental RF synthesis) is completely inhibited at the nonpermissive temperature (41 C) in two of the three dnaB mutants tested. The efficiency of phage eclipse and of phage DNA penetration of these mutant host cells at 41 C is the same as that of the parent host strain. The defect is most likely in the synthesis of the complementary strand DNA. The semiconservative replication of the double-stranded replicative form DNA (RF replication) is inhibited in all three host mutants after shifting from 30 to 41 C. Late in infection, the rate of progeny single-stranded phage DNA synthesis increases following shifts from 30 to 41 C. Approximately the same amounts of phage DNA and of infectious phage particles are made following the shift to 41 C as in the control left at 30 C. The simplest interpretation of our data is that the product of the host dnaB gene is required for phiX174 parental RF synthesis and RF replication, but is not directly involved in phage single-stranded DNA synthesis once it has begun. The possible significance of the synthesis of parental RF DNA at 41 C in one of the three mutants is discussed.

Synthesis of bacteriophage M13-specific proteins in a DNA-dependent cell-free system. II. In vitro synthesis of biologically active gene 5 protein

It is shown that gene 5 protein of bacteriophage M13 is one of the major proteins synthesized in vitro under the direction of M13 replicative-form DNA. By means of DNA-cellulose chromatography, this protein has been purified to homogeneity and its biological characteristics have been compared with those of its native counterpart. Like native gene 5 protein, the purified, in vitro-synthesized protein binds tightly and selectively to single-stranded, but not to double-stranded, DNAs. These results suggest that truly functional gene 5 protein is made in the cell-free system.