The regulation of transcription in bacteriophage T5-infected Escherichia coli

T5-like phage BF23 evades host-mediated DNA restriction and methylation

Bacteriophage BF23 is a close relative of phage T5, a prototypical Tequintavirus that infects Escherichia coli. BF23 was isolated in the middle of the XXth century and was extensively studied as a model object. Like T5, BF23 carries long ∼9.7 kb terminal repeats, injects its genome into infected cell in a two-stage process, and carries multiple specific nicks in its double-stranded genomic DNA. The two phages rely on different host secondary receptors-FhuA (T5) and BtuB (BF23). Only short fragments of the BF23 genome, including the region encoding receptor interacting proteins, have been determined. Here, we report the full genomic sequence of BF23 and describe the protein content of its virion. T5-like phages represent a unique group that resist restriction by most nuclease-based host immunity systems. We show that BF23, like other Tequintavirus phages, resist Types I/II/III restriction-modification host immunity systems if their recognition sites are located outside the terminal repeats. We also demonstrate that the BF23 avoids host-mediated methylation. We propose that inhibition of methylation is a common feature of Tequintavirus and Epseptimavirus genera phages, that is not, however, associated with their antirestriction activity.

Novel Escherichia coli RNA Polymerase Binding Protein Encoded by Bacteriophage T5

The Escherichia coli bacteriophage T5 has three temporal classes of genes (pre-early, early, and late). All three classes are transcribed by host RNA polymerase (RNAP) containing the σ⁷⁰ promoter specificity subunit. Molecular mechanisms responsible for the switching of viral transcription from one class to another remain unknown. Here, we find the product of T5 gene 026 (gpT5.026) in RNAP preparations purified from T5-infected cells and demonstrate in vitro its tight binding to E. coli RNAP. While proteins homologous to gpT5.026 are encoded by all T5-related phages, no similarities to proteins with known functions can be detected. GpT5.026 binds to two regions of the RNAP β subunit and moderately inhibits RNAP interaction with the discriminator region of σ⁷⁰-dependent promoters. A T5 mutant with disrupted gene 026 is viable, but the host cell lysis phase is prolongated and fewer virus particles are produced. During the mutant phage infection, the number of early transcripts increases, whereas the number of late transcripts decreases. We propose that gpT5.026 is part of the regulatory cascade that orchestrates a switch from early to late bacteriophage T5 transcription.

Cloning, sequencing, and recombinational analysis with bacteriophage BF23 of the bacteriophage T5 oad gene encoding the receptor-binding protein

Binding of bacteriophage T5 to its receptor, the Escherichia coli FhuA protein, is mediated by tail protein pb5. In this article we confirm that pb5 is encoded by the T5 oad gene and describe the isolation, expression, and sequencing of this gene. In order to locate oad precisely, we analyzed recombinants between BF23, a T5-related phage with a different host range, and plasmid clones containing segments of the T5 chromosome. This analysis also showed that oad has little or no homology with hrs, the analogous BF23 gene. We were able to overproduce a protein that comigrates with pb5 after fusing a 2-kb segment containing oad to a phage T7 promoter. This segment contains an open reading frame that can encode a protein of the appropriate size. Its deduced amino acid sequence does not closely resemble that of any other protein in the database. The sequence upstream of the open reading frame shows typical characteristics of a promoter region with two overlapping, divergently orientated promoters.

Identity of genes A2 and A3 of bacteriophage BF23

The polypeptide coded by gene A3 of bacteriophage BF23 has been purified and its N-terminal amino acid sequence determined. This sequence is identical to the N-terminal sequence of the polypeptide coded by gene A2. The two gene products have identical molecular weight. We conclude that these two gene products are identical, and are coded by one and the same gene, namely gene A2-A3, which was previously thought to be two genes, A2 and A3.

Regulation of the temporal synthesis of proteins in bacteriophage BF23-infected cells

Regulation of temporal synthesis of pre-early, early, and late proteins in bacteriophage BF23-infected cells has been studied by using five amber mutants defective in genes 1, 2, 10, 14, and 19. The synthesis of pre-early proteins is negatively regulated by the actions of gene 1, a pre-early gene. The switch from pre-early to early protein synthesis is mainly regulated by the second-step DNA transfer reaction, which is controlled by at least genes 1 and 2. Early proteins can be kinetically and genetically divided into two regulatory classes, designated Ea and Eb. The shutoff of Eb-early protein synthesis is associated with the turn-on of late protein synthesis. This step is controlled by genes 10, 14, and 19. Gene 10 also regulates negatively the synthesis of Ea-early proteins, indicating that this gene has a dual function in the regulation of early protein synthesis. The temporal synthesis of phage-encoded proteins is regulated mainly at the transcriptional level. Evidence is presented indicating that the host RNA polymerase is modified by the interaction with the gene products of genes 2, 10, and 14 (gp2, gp10, and gp14, respectively). gp2 interacts with the enzyme in the earlier stage of infection but is replaced by gp10 in the later stage. This exchange reaction depends on the presence of gp14 and gp19 and is related to the switch from Eb to late protein synthesis. Thus, the regulation of BF23 gene expression occurs in a coordinated manner throughout the development of this phage.

Cell-free transcription and translation of isolated restriction fragments localize bacteriophage T5 pre-early genes

In vitro transcription and translation of isolated restriction fragments containing all or part of the terminal redundancies of bacteriophage T5 localized virtually every pre-early gene to a small 6.3-kilobase BglI fragment. Among these genes were those encoding the A1 and A2 proteins, which are responsible for complete entry of the viral genome into its host, and the deoxynucleoside 5'-monophosphatase. A 3.9-kilobase BglI fragment containing the remainder of the pre-early region induced no proteins under these same conditions. Proteins induced by fragments including the right and left terminal redundancies were also compared and found to be identical. DNA immediately flanking the pre-early regions induced few proteins in vitro. Thus, this technique has allowed the overall gene organization of the pre-early region of T5 to be described.

Transcription regulatory elements in the late region of bacteriophage T5 DNA

Transcription promoters and terminators have been cloned from the late region of bacteriophage T5 DNA and their strengths determined in vivo in plasmid derivatives. DNA sequence analysis shows these transcription signals to be remarkable in that, in all four cases studied in detail, the promoters and terminators overlapped or were very close together.

Modification of RNA polymerase from Escherichia coli by pre-early gene products of bacteriophage T5

RNA polymerase from cells of Escherichia coli infected with T5 were recovered as a complex with two pre-early phage-coded polypeptides, the 60,000-dalton product of gene A1 and a previously reported 11,000-dalton polypeptide. This RNA polymerase complex had altered transcriptional specificity, in that it transcribed pre-early genes less efficiently than it did early genes.

Cloning of bacteriophage T5 DNA fragments. III. Expression in Escherichia coli mini-cells

Use has been made of the mini-cell system to study polypeptide synthesis from cloned EcoRI, HindIII and PstI fragments of T5 DNA. The correlation of certain gene products with known genes has been established, as well as the physical mapping of genes not yet identified genetically. In some cases, it has been possible to demonstrate the presence of T5 promoters on the cloned DNA fragments. The design of experiments to avoid certain artifacts inherent in the use of the mini-cell system is discussed.

Role of the T5 gene D15 nuclease in the generation of nicked bacteriophage T5 DNA

The processing of newly replicated concatameric T5 DNA into both single stranded DNA changed of unit length and single-stranded fragments of sizes comparable to those found in mature T5 virion DNA occurs in the absence of late T5 protein synthesis. The formation of unit-length, single-stranded DNA chains does not require the early T5 gene D15 nuclease: however, the subsequent formation of the single-stranded fragments does require that the D15 nuclease be functional. A reexamination of the properties of the purified D15 nuclease under a variety of conditions showed that, in addition to functioning as a 5' leads to 3' exonuclease, the enzyme can also introduce endonucleolytic scissions into mature T5 DNA in a reaction that requires duplex T5 DNA and preexisting, single-stranded interruptions.

Isolation and genetic characterizaion of Escherichia coli K-12 mutations affecting bacteriophage T5 restriction by the ColIb plasmid

A mutant derivative of Escherichia coli K-12 has been isolated which is permissive for bacteriophage T5 infection even when harboring a wild-type ColIb plasmid. The fully permissive phenotype was the result of two mutations that are located near the rpsL-rpsE region on the E. coli chromosome and are recessive to the wild-type alleles. These mutations had little or no effect on induction of colicin synthesis and did not affect the expression of antibiotic resistance by the resistance plasmids R64drd11 or R1drd19. Cells harboring the mutant alleles grew more slowly than isogenic wild-type derivatives in either minimal or complete media.