New late gene, dar, involved in the replication of bacteriophage T4 DNA. III. DNA replicative intermediates of T4 dar and a gene 59 mutant suppressed by dar

Enhancement of platinum biosorption by surface-displaying EC20 on Escherichia coli

To increase the platinum adsorption capacity of Escherichia coli (E. coli) biomass, we fused EC20 protein to the E. coli cell surface using an InaKN-based display system, which is the N-terminal region of ice nucleation protein that can be employed as a cell surface display motif. The media and culture conditions were optimized for EC20 (a phytochelatin analogue with 20 repeating units of glutamate and cysteine) expression and Pt (IV) biosorption. Furthermore, the adsorption process was elucidated from aspect of adsorption kinetics and equilibrium, and the characterization of blank and Pt-loaded cells were analyzed using SEM, AFM, TEM, FT-IR and XPS. Our study demonstrated that E. coli strain, which had InaKN-EC20 protein expressed on the cell surface, showed a great enhancement in Pt (IV) adsorption under optimized condition when comparing with that of original E. coli strain. The SEM-EDX analysis revealed that the cellular morphology has been changed in Pt-loaded cells, and the weight percent of platinum in the surface of E.coli increased substantially after displaying EC20 protein. Furthermore, intracellular platinum accumulation was detected in Pt-loaded EC20 cells since a clear peak of platinum exhibited, implying that cytoplasmic EC20 protein might also contribute to platinum accumulation. FTIR analysis revealed that the predominant functional groups in platinum adsorption were amine, carboxyl and phosphate groups.

Bacteriophage T4 helicase loader protein gp59 functions as gatekeeper in origin-dependent replication in vivo

Bacteriophage T4 initiates origin-dependent replication via an R-loop mechanism in vivo. During in vitro reactions, the phage-encoded gp59 stimulates loading of the replicative helicase, gp41, onto branched intermediates, including origin R-loops. However, although gp59 is essential for recombination-dependent replication from D-loops, it does not appear to be required for origin-dependent replication in vivo. In this study, we have analyzed the origin-replicative intermediates formed during infections that are deficient in gp59 and other phage replication proteins. During infections lacking gp59, the initial replication forks from two different T4 origins actively replicated both leading- and lagging-strands. However, the retrograde replication forks from both origins were abnormal in the gp59-deficient infections. The lagging-strand from the initial fork was elongated as a new leading-strand in the retrograde direction without lagging-strand synthesis, whereas in the wild-type, leading- and lagging-strand synthesis appeared to be coupled. These results imply that gp59 inhibits the polymerase holoenzyme in vivo until the helicase-primase (gp41-gp61) complex is loaded, and we thereby refer to gp59 as a gatekeeper. We also found that all origin-replicative intermediates were absent in infections deficient in the helicase gp41 or the single-strand-binding protein gp32, regardless of whether gp59 was present or absent. These results argue that replication from the origin in vivo is dependent on both the helicase and single-strand-binding protein and demonstrate that the strong replication defect of gene 41 and 32 single mutants is not caused by gp59 inhibition of the polymerase.

UvsW protein regulates bacteriophage T4 origin-dependent replication by unwinding R-loops

The UvsW protein of bacteriophage T4 is involved in many aspects of phage DNA metabolism, including repair, recombination, and recombination-dependent replication. UvsW has also been implicated in the repression of origin-dependent replication at late times of infection, when UvsW is normally synthesized. Two well-characterized T4 origins, ori(uvsY) and ori(34), are believed to initiate replication through an R-loop mechanism. Here we provide both in vivo and in vitro evidence that UvsW is an RNA-DNA helicase that catalyzes the dissociation of RNA from origin R-loops. Two-dimensional gel analyses show that the replicative intermediates formed at ori(uvsY) persist longer in a uvsW mutant infection than in a wild-type infection. In addition, the inappropriate early expression of UvsW protein results in the loss of these replicative intermediates. Using a synthetic origin R-loop, we also demonstrate that purified UvsW functions as a helicase that efficiently dissociates RNA from R-loops. These and previous results from a number of studies provide strong evidence that UvsW is a molecular switch that allows T4 replication to progress from a mode that initiates from R-loops at origins to a mode that initiates from D-loops formed by recombination proteins.

Bacteriophage T4 UvsW protein is a helicase involved in recombination, repair and the regulation of DNA replication origins

Bacteriophage T4 UvsW protein is involved in phage recombination, repair and the regulation of replication origins. Here, we provide evidence that UvsW functions as a helicase. First, expression of UvsW allows growth of an (otherwise inviable) Escherichia coli recG rnhA double mutant, consistent with UvsW being a functional analog of the RecG helicase. Second, UvsW contains helicase sequence motifs, and a substitution (K141R) in the Walker 'A' motif prevents growth of the E.coli recG rnhA double mutant. Third, UvsW, but not UvsW-K141R, inhibits replication from a T4 origin at which persistent RNA-DNA hybrids form and presumably trigger replication initiation. Fourth, mutations that inactivate UvsW and endonuclease VII (which cleaves DNA branches) synergistically block repair of double-strand breaks. These in vivo results are consistent with a model in which UvsW is a DNA helicase that catalyzes branch migration and dissociation of RNA-DNA hybrids. In support of this model, a partially purified GST/UvsW fusion protein, but not a GST/UvsW-K141R fusion, displays ssDNA-dependent ATPase activity and is able to unwind a branched DNA substrate.

Recombination apparatus of T4 phage

The substantial process of general DNA recombination consists of production of ssDNA, exchange of the ssDNA and its homologous strand in a duplex, and cleavage of branched DNA to maturate recombination intermediates. Ten genes of T4 phage are involved in general recombination and apparently encode all of the proteins required for its own recombination. Several proteins among them interact with each other in a highly specific manner based on a protein-protein affinity and constitute a multicomponent protein machine to create an ssDNA gap essential for production of recombinogenic ssDNA, a machine to supply recombinogenic ssDNA which has a free end, or a machine to transfer the recombinogenic single strand into a homologous duplex.

Studies on the recombination genes of bacteriophage T4: suppression of uvsX and uvsY mutations by uvsW mutations

Genes uvsW, uvsX and uvsY are dispensable for T4 growth but are implicated in recombination and in the repair of damaged DNA. We found that large-plaque mutants arose efficiently from small-plaque uvsX and uvsY mutants at 42 degrees and were pseudorevertants containing a new mutation in uvsW. Using reconstructed double mutants, we confirmed that a mutation in uvsW partially increases the burst size and UV resistance of uvsX and uvsY mutants. At 41 degrees the uvsW mutation completely restores the arrest in DNA synthesis caused by mutations in genes uvsX, uvsY and 46, but at 30 degrees it only partially restores DNA synthesis in a gene 46 mutant and does not restore DNA synthesis in uvsX and uvsY mutants. Restored DNA synthesis at 41 degrees was paralleled by the overproduction of single-stranded DNA and gene 32 protein. Based on these findings, we propose that the uvsW gene regulates the production of single-stranded DNA and we discuss the phenotype of uvsW mutants and their suppression of some uvsX and uvsY phenotypes. Infection of restrictive cells with am uvsW mutants revealed a defect in the synthesis of a protein of molecular weight 53,000 daltons, suggesting that this protein is the uvsW gene product.

Topoisomerase II and other DNA-delay and DNA-arrest mutations impair bacteriophage T4 DNA packaging in vivo and in vitro

A survey of DNA packaging in vivo and in vitro during infections caused by T4 DNA-delay and DNA-arrest amber mutants revealed a common DNA packaging-deficient phenotype. Electron microscopy revealed high proportions of proheads partially filled with DNA in vivo, indicating normal initiation but incomplete encapsidation. In contrast, exogenous mature T4 DNA was packaged in vitro by several early-gene mutant extracts. Detailed analysis of gene ts39 mutants (subunit of topoisomerase II) showed that in vivo packaging is defective, yet expression of late proteins appeared normal and the concatemeric DNA was not abnormally short or nicked. Although g39 amber mutant extracts packaged DNA in vitro, two of three ts39 mutant extracts prevented encapsidation of the exogenous DNA. The temperature-sensitive (ts) gp39 in a mutant topoisomerase II complex may have interfered with packaging in vivo and in vitro by interacting with DNA in an anomalous fashion, rendering it unfit for encapsidation. These results support the hypothesis that T4 DNA packaging is sensitive to DNA structure and discriminates against encapsidation of some types of defective DNA.

Genetic analysis of dar, uvsW, and uvsY in bacteriophage T4: dar and uvsW are alleles

A genetic study of the T4 dar (DNA arrested synthesis restoration) mutations was performed by two- and three-factor crosses. The dar mutations restore the viability of gene 59 mutants. Mapping studies of the dar mutations indicated that the dar gene extended over 16 map units. This high recombination frequency is attributed to an increased level of recombination in the dar region. Two other mutations, uvsY and uvsW, known to be located in the vicinity of dar, were studied. These studies indicated that the uvsY and dar mutations were located in separate genes but that dar and uvsW were allelic. The genes are ordered as follows: gene 24, dar(uvsW), uvsY, and gene 25 in clockwise order.

The coupling of DNA repair-recombination functions with DNA replication in bacteriophage T4: a new DNA repair mutant

The requirement of DNA repair-recombination functions for T4 phage DNA replication has been known for some time but the underlying basis for this relationship has been unclear. This report is concerned with a new uv-sensitive gene [uvsU], whose function appears to bridge these two major activities of DNA. The [uvsU] mutant fails to complement [uvsX] mutants but uvsU maps in a region distinct from uvsX. Furthermore, the uvsU mutation specifically suppressed the DNA replication defect but not the uv sensitivity of the uvsX mutation. The previously discovered uvsW gene, whose mutations suppress the DNA replication defects of gene 59, 46, and 47 mutations, seems to have an analogous role. As a possible explanation for these observations, it is suggested that the uvsW and uvsU gene products (gps) couple the DNA repair-recombination and replication functions by controlling the entry of DNA intermediates from the replication pool into the DNA repair-recombination pathway. Furthermore the suppression data are interpreted to suggest that the gps uvsW, 59, 46, and 47 function together. Similarly the gps uvsU and uvsX may form a functional unit.

Properties of the nonlethal recombinational repair deficient mutants of bacteriophage T4. III. DNA replicative intermediates and T4w

The rate at which 3H thymidine is incorporated into DNA is increased in T4w-infected cells compared to wild-type when measured late in infection under conditions of low thymidine concentration. This increased DNA synthesis is sensitive to hydroxyurea but not to mitomycin C, and can be prevented by the addition of chloramphenicol early in infection. Also, DNA replicative intermediates isolated from T4w-infected cells late in infection sediment significantly faster than those isolated from wild-type-infected cells. In contrast, DNA replicative intermediates isolated from T4x- or T4y-infected cells sediment more slowly than those produced by wild-type T4. Cells coinfected with wild-type T4+ and T4x, y or w; or T4w and T4x or y, produce wild-type DNA replicative intermediates. Cells coinfected with T4x and T4y produce more slowly sedimenting DNA replicative intermedites. Cells coinfected with T4w and wild-type T4 show wild-type rates of DNA synthesis while cells coinfected with T4w and T4x or T4y show increased rates of DNA synthesis over that observed with wild-type alone.

New late gene, dar, involved in the replication of bacteriophage T4 DNA. II. Overproduction of DNA binding protein (gene 32 protein) and further characterization

We have previously shown that the arrested DNA synthesis of mutant defective in T4 phage gene 59 can be reversed by a mutation in dar. In this paper, we have examined the effect of the dar mutation on the kinetics of gene 32 protein (DNA binding protein) synthesis, DNA packaging, progeny formation, and several other porcesses. Several lines of evidence are presented showing that the regulation of synthesis of gene 32 protein is abnormal in dar 1-infected cells. In these cells, gene 32 protein, an early protein, is also expressed late in the infectious cycle. Our data also indicate that the packaging og DNA into T4 phage heads is delayed in dar mutant-infected cells, and this in turn results in a 6- to 8-min delay in intracellular progeny formation, although the synthesis of late proteins appears to be normal, as shown by gel electrophoresis. We have also studied the phenotypes of the double mutant dar-amC5 (gene 59). The increased sensitivity to hydroxyurea caused by a mutation in the dar gene can be alleviated by a second mutation in gene 59, but an increased sensitivity to UV irradiation caused by a mutation in gene 59 cannot be alleviated by a second mutation in the dar gene. Therefore, the double mutant still exhibits abnormalities in the repair of UV lesions.