Further physical characterization of deletion and substitution mutants affecting the control of lysogeny in bacteriophage P2

Control of prophage integration and excision in bacteriophage P2: nucleotide sequences of the int gene and att sites

Integration of bacteriophage P2 into the Escherichia coli host genome involves recombination between two specific attachment sites, attP and attB, one on the phage and the other on the host genome, respectively. The reaction is controlled by the product of the phage int gene, a basic polypeptide of about 37 kDa [Ljungquist and Bertani, Mol. Gen. Genet. 192 (1983) 87-94]. The int gene appears to be expressed differently by an infecting phage, as opposed to a prophage [Bertani, Proc. Natl. Acad. Sci. USA 65 (1970) 331-336]. A 1200-bp region of P2 DNA containing the int gene and attP, the prophage hybrid ends attL and attR, and one bacterial attachment site, the preferred site locI from E. coli strain C, have all been sequenced. An open reading frame coding for a polypeptide of 337 amino acids corresponds to the int gene. The gene has no obvious promoter sequence preceding it. The int gene transcript seems to continue past the attP site downstream from it, suggesting a possible explanation for the previously observed difference in integration and excision. A comparison of the four attachment sites reveals a common 'core' sequence of 27 bp: 5'-AAAAAATAAGCCCGTGTAAGGGAGATT-3'. The P2 nip1 mutation, which increases prophage excision [Calendar et al., Virology 47 (1972) 68-75], was found to lie within the int gene itself. The P2 saf variant, which has altered site preference [Six, Virology 29 (1966) 106-125], has a bp substitution within the core sequence. Three deletion/substitution mutants, vir22, vir94 and del3, also have altered core sequences.

Directed mutagenesis of the bacteriophage P2 ogr gene defines an essential function

The ogr gene of bacteriophage P2 codes for a basic protein of 72 amino acids which is thought to be essential for activation of P2 late gene transcription. However, conditionally lethal mutations in the ogr gene have never been isolated. We have constructed a P2 ogr deletion mutant by in vitro techniques. This deletion phage, P2-del15, grows in a host which provides the ogr gene product in trans from a plasmid but fails to grow in hosts lacking the ogr plasmid. This demonstrates that the ogr gene is essential for P2 lytic growth. The deletion in P2del15 has removed about half of the carboxy-terminal part of the ogr gene. The transcript from this deletion mutant can be distinguished from the wild-type transcript by S1 nuclease protection. The analysis of such transcripts suggests that the ogr gene product may negatively regulate its own transcription.

Control of gene expression in the P2-related temperate coliphages. IV. Concerning the late control gene and control of its transcription

In this paper we have sequenced four amber mutants and thereby confirmed the gene D (CP65) and gene B (CP67) assignments made in the accompanying paper (Kalionis et al., 1986). We have also studied, by gel electrophoresis, the transcription patterns of gene B in vivo. In a lysogen, gene B is present on a short transcript under autogenous (negative) control. Upon prophage induction, this transcript is amplified, but later in the cycle gene B is present on a larger transcript that originates in the late region. We have detected two copies of an inverted repeat in the promoter region of the B gene that we predict is recognized by the B protein. One arm of this repeat is associated with three of four P2 late promoters, downstream from the start point of transcription. The repeat is not present in the promoter region of P2 ogr. We describe the considerable homology in amino acid sequence seen with the late control proteins 186 gpB, P4 gp delta and P2 gpOgr, and present a working model for control of late gene transcription.

Regulation of bacteriophage P2 late-gene expression: the ogr gene

The ogr gene product of bacteriophage P2 is a positive regulatory factor required for P2 late-gene transcription. We have determined the nucleotide sequence of the ogr gene, which encodes a basic polypeptide of 72 amino acids. P2 growth is blocked by a host mutation, rpoA109, in the alpha subunit of DNA-dependent RNA polymerase. The ogr52 mutation, which allows P2 to grow in an rpoA109 strain, was shown to be a single nucleotide change, in the codon for residue 42, that changes tyrosine to cysteine. The predicted amino acid sequence of the Ogr protein does not show similarity to DNA-binding proteins that are known to affect promoter recognition, to sigma factors, or to other characterized transcriptional regulatory proteins. We have inserted the ogr gene into a plasmid under control of the leftward promoter and operator of bacteriophage lambda. Thermal induction of ogr gene expression in this plasmid results in overproduction of a small protein that has been shown by complementation to possess Ogr function.

Immunity repressor of bacteriophage P2. Identification and DNA-binding activity

The product of gene C of the temperate bacteriophage P2, the immunity repressor, can be detected as a unique band eluting from phosphocellulose columns at 0.12 M-potassium phosphate when differentially labelled with a radioactive amino acid: the band is absent when phages that either have lost gene C through deletion or carry a suppressor-sensitive mutation in the gene are used. The repressor in its monomeric form is about 11,000 in molecular weight. At near physiological salt concentrations, the form predominantly recovered is the dimer. In filter-binding assays, the partially purified repressor binds wild-type P2 DNA strongly. It does not bind DNA of P2 vir94, a deletion that removes all the genetic elements involved in the regulation of lysogeny; it also does not bind, or binds inefficiently, DNA of P2 vir3, a mutation in the operator that controls the early replicative functions of P2. At the concentrations employed, the dimer is the active form in binding. The P2 repressor clearly differs in several features from the well-studied immunity repressor of bacteriophage lambda.

Properties and products of the cloned int gene of bacteriophage P2

Fragments of DNA of the temperate phage P2, generated by treatment with the restriction enzyme PstI, have been cloned into the plasmid pBR322. One such fragment, which has its endpoints within phage genes T and C, carries the structural P2 int gene as well as its promoter and the phage att site. When introduced into a suitable bacterial host, the cloned fragment mediates the integration and excision of int- mutants of P2 and recombination within the phage att site in mixed infection. All these activities are independent of the orientation of the fragment within the plasmid. When introduced into minicells, the fragment produces, in addition to the products of genes D and U, a protein of 35-37,000 daltons identified as the int protein. A study of the map location of two amber int mutants, together with the sizes of the polypeptides they produce, indicates that the P2 int gene is transcribed from right to left on the P2 map, i.e. starting near gene C and proceeding toward att.

Cloning of the immunity repressor determinant of bacteriophage P2 in the pBR322 plasmid

Through in vitro recombination of DNA restriction fragments, we have constructed a plasmid, which expressed in vivo the immunity repressor gene (C) of bacteriophage P2. A bacterial strain carrying such a plasmid showed a high level of P2 specific immunity. It was lysogenized normally by an infecting P2, but the frequency of spontaneous phage production was reduced about 10(4) fold as compared to a normal P2 lysogen. Satellite phage P4, known to derepress P2 lysogens, was unable to derepress the plasmid-carrying lysogenic strain so to allow growth of coinfecting P2. Phage P4 multiplied on the plasmid-carrying, P2-lysogenic strain, but due to a prolonged latent period failed to form plaques on this strain.

A restriction endonuclease cleavage map of bacteriophage P2

A restriction endonuclease cleavage map of phage P2 was constructed. The enzymes used and, within parenthesis, the number of their cleavage sites on the P2 lg cc DNA molecule were: AvaI(3), BalI(1), BAMI(3), BglII(3), HaeIII (more than 40; only three were mapped), HindIII(0), HpaI(10), KpnI(3), PstI(3), SalI(2) and SmaI(2). The EcoRI cleavage sites (3), as determined earlier, were used as reference points for this study. The DNAs of a variety of P2 mutants carrying chromosomal aberrations (dell, del2, del3, del6, vir22, vir37(2), vir79 and vir94) were also similarly examined.