Recombination between satellite phage P4 and its helper P2. I. In vivo and in vitro construction of P4: :P2 hybrid satellite phage

Plasmids containing cos ends inhibit the replication of phage phi CTX in Pseudomonas aeruginosa

In bacteriophage phi CTX, the cohesive end sequences cos, the integrase gene int, the attachment site attP (the target site for int) and the gene ctx encoding a pore-forming cytotoxin CTX, are clustered. Phi CTX can infect some Pseudomonas aeruginosa strains with a subsequent induction of CTX expression. The 41 and 477 bp fragments containing cos ends of phi CTX DNA were cloned into the high copy number plasmid pHA10. After pretransformation with the cos ends containing plasmids, plaque formation of phi CTX and cytotoxin production in phi CTX-infected Pseudomonas aeruginosa cells decreased by 100- and 10-fold respectively. Twelve hours after phi CTX infection proteins binding with cooperativity to cos sequence containing cleavable ends and the 10 bp flanking sequences were detected by gel electrophoretic mobility retardation of [32P]cos DNA. The results suggest that the cos binding proteins of phi CTX are involved in phi CTX replication.

Mechanisms of genome propagation and helper exploitation by satellite phage P4

Temperate coliphage P2 and satellite phage P4 have icosahedral capsids and contractile tails with side tail fibers. Because P4 requires all the capsid, tail, and lysis genes (late genes) of P2, the genomes of these phages are in constant communication during P4 development. The P4 genome (11,624 bp) and the P2 genome (33.8 kb) share homologous cos sites of 55 bp which are essential for generating 19-bp cohesive ends but are otherwise dissimilar. P4 turns on the expression of helper phage late genes by two mechanisms: derepression of P2 prophage and transactivation of P2 late-gene promoters. P4 also exploits the morphopoietic pathway of P2 by controlling the capsid size to fit its smaller genome. The P4 sid gene product is responsible for capsid size determination, and the P2 capsid gene product, gpN, is used to build both sizes. The P2 capsid contains 420 capsid protein subunits, and P4 contains 240 subunits. The size reduction appears to involve a major change of the whole hexamer complex. The P4 particles are less stable to heat inactivation, unless their capsids are coated with a P4-encoded decoration protein (the psu gene product). P4 uses a small RNA molecule as its immunity factor. Expression of P4 replication functions is prevented by premature transcription termination effected by this small RNA molecule, which contains a sequence that is complementary to a sequence in the transcript that it terminates.

The cos region of lactococcal bacteriophage phi LC3

The nucleotide sequence of the DNA regions flanking the cohesive end site of the temperate lactococcal bacteriophage phi LC3 was determined. Four pairs of sequence repeats of 8 to 13 base-pairs in length were revealed close to the cohesive ends. These repeats possibly represent signal sequences involved in phage DNA maturation and packaging. The start of an open reading frame was localized only 42 nucleotides from the left end of the phi LC3 phage double-stranded region, implying that transcription probably proceeds across the cos site. Compilation of the characteristics of the DNA termini of bacteriophages with complementary cohesive DNA ends suggests that phages of Gram-negative bacteria generally carry 5'-protruding single-strands whereas those of Gram-positive hosts carry 3'-protruding ends.

Characterization of phiLC3, a Lactococcus lactis subsp. cremoris temperature bacteriophage with cohesive single-stranded DNA ends

The temperate bacteriophage phiLC3, isolated from Lactococcus lactis subsp. cremoris, has an isometric head and a flexible tail containing 1 major protein and 8 minor proteins. Infection of a permissive L. lactis host strain yields a burst of about 50 phages per infected cell with a latent period of 60 min. A detailed restriction map of the phage chromosome was constructed by using 12 different restriction enzymes. The phage chromosome is a 33-kb linear double-stranded DNA molecule with unique cohesive ends and with a G + C content of 36.5%. Chemical sequencing of the DNA ends revealed 13-base 3' extended complementary single strands with a relatively high percentage of G + C. Pulsed-field gel electrophoretic analysis of DNA from a strain lysogenized with phiLC3 was used to localize the prophage to a 320-kb BamHI restriction endonuclease fragment from the host chromosomal DNA. This result indicates that lysogeny involves integration of the phage into the host chromosome. A spontaneous phiLC3 clear plaque mutant that was unable to give rise to lysogens was isolated.

Characterization of the cos sites of bacteriophages P2 and P4

A 641-bp cos-containing P2 DNA fragment was sequenced and compared to the P4 cos region. Alignment of the P2 and P4 cos regions shows a homologous region of 55 bp that has only three mismatches and contains a completely conserved region of dyad symmetry. A number of P4- and P2-derived cosmids were tested in an in vivo transduction assay in order to determine the minimal cos region required for packaging. These experiments show that the common region of 55 bp is sufficient for transduction with low frequency, but that a 125-bp cos-containing fragment contains all the information for transduction with optimal frequency.

Nonessential region of bacteriophage P4: DNA sequence, transcription, gene products, and functions

We sequenced the leftmost 2,640 base pairs of bacteriophage P4 DNA, thus completing the sequence of the 11,627-base-pair P4 genome. The newly sequenced region encodes three nonessential genes, which are called gop, beta, and cII (in order, from left to right). The gop gene product kills Escherichia coli when the beta protein is absent; the gop and beta genes are transcribed rightward from the same promoter. The cII gene is transcribed leftward to a rho-independent terminator. Mutation of this terminator creates a temperature-sensitive phenotype, presumably owing to a defect in expression of the beta gene.

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.

Bacteriophage P4 DNA replication. Nucleotide sequence of the P4 replication gene and the cis replication region

A 3100 base piece of DNA from the 11,500 base genome of bacteriophage P4 was analyzed for its nucleotide sequence. This segment of DNA contains two open reading frames of 106 and 777 amino acid residues; the latter of which is the coding sequence for the Mr 84,841 alpha protein, which is necessary for P4 DNA replication and is thought to act as a P4-specific DNA primase. A region of about 300 base-pairs localized just beyond the alpha gene and about 4500 bases from the origin of replication (ori), was defined as the locus for P4's cis replication region (crr). This region is required for replication both in vivo and in vitro, and consists of two directly repeated sequences of 120 base-pairs that match one another at 98 positions. These directly repeated sequences are separated by 60 base-pairs, which are not necessary for replication. Each repeat in crr contains three copies of the octamer TGTTCACC that is found six times in ori. Either of the 120 base-pair repeat sequences in crr is sufficient for replication, and the entire crr can function in an inverted orientation. crr is also active at a distance of 1800 bases from the P4 origin of replication.

Bacteriophage P4 DNA replication. Location of the P4 origin

An electron microscopic examination of replicating bacteriophage P4 DNA molecules has revealed theta-type structures that replicate bidirectionally from a single origin. Many replicating P4 DNA molecules also contain long (2000 bases) single-strand DNA regions at the growing fork that are deployed in a trans configuration, which supports the concept of continuous leading strand and discontinuous lagging strand syntheses. The position of the P4 origin was localized by the use of a plasmid complementation test for replication in vivo, as well as by labeling of DNA replicating in vitro in the presence of a chain-terminating inhibitor. During this study we discovered a second site on the P4 genome which is essential for replication, and we have named it crr (cis region required for replication). The site is located at least 3300 bases from the origin but appears to be required for the initiation of DNA replication in vivo as well as in vitro.

The replication of bacteriophage P4 DNA in vitro. Partial purification of the P4 alpha gene product

A soluble enzyme system has been prepared from a phage P4-infected Escherichia coli strain that supports the replication of exogenous, supercoiled P4 DNA. This DNA synthesis in vitro depends upon the four deoxyribonucleotides and ATP, but is enhanced about four- to fivefold by the presence of other ribonucleotides. E. coli DNA polymerase III holoenzyme, the E. coli single-strand DNA binding protein, and the partially purified P4 alpha gene product are required for replication in vitro. Rifamycin does not inhibit P4 replication in vitro. Since the P4 alpha gene codes for a rifamycin-resistant RNA polymerase (Barrett et al., 1983), and since P4 DNA replication is independent of the host primase (Bowden et al., 1975), we believe the alpha gene product is functioning as a P4-specific DNA primase.

Plasmid mode of propagation of the genetic element P4

The satellite bacteriophage P4, in the presence of a helper phage, can enter either the lytic or the lysogenic cycle. In the absence of the helper, P4 can integrate in the bacterial chromosome. In addition, the partially immunity-insensitive mutant P4 vir1 can be maintained as a plasmid. We have found that in the absence of the helper, P4 wt also can be maintained as a plasmid, and that both P4 wt and P4 vir1 have two options for their intracellular propagation: a repressed-integrated or a derepressed-high copy number plasmid mode of maintenance. In the repressed mode, the P4 wt genome is only found integrated into the bacterial chromosome, while the P4 vir1 is found also as a low copy number plasmid coexisting with the integrated P4 vir1 genome. The clones carrying P4 in the derepressed-high copy number plasmid state are obtained at low frequency (0.3%) upon infection with P4 wt, while the vir1 mutation increases this frequency about 300-fold. Such clones can be distinguished easily because of their typical colony morphology (rosettes), due to the presence of filamentous cells. Filamentation of the bacterial host suggests that the presence of derepressed P4 genomes in high copy number interferes with the normal cell division mechanism. The derepressed clones are rather stable, but may revert spontaneously to the repressed state. Spontaneous transition from the repressed to the derepressed state was not observed; however, it can be induced by P2 or P4 vir1 superinfection of P4 wt and P4 vir1 lysogens or by growing the P4 vir1 lysogens up to the late exponential phase. The ability of P4 to choose either of two stable states and the potential to shift between these two modes of propagation indicate that the synthesis of the immunity repressor is regulated.

Circular genetic map of satellite bacteriophage P4

A genetic map of satellite bacteriophage P4 has been constructed by means of standard multifactor crosses. The genetic map appears to be a circular permutation of the mature DNA physical map. In addition, a set of markers appear to be linked both to the left and to the right of the same gene alpha. These facts suggest that the P4 genetic map is circular. Since terminal redundancy and/or cyclic permutation are not known to be present in P4 mature DNA, the circularity of P4 genetic map may reflect the physical circularity of the molecules involved in the recombination process. The low frequency of recombination and the strong negative interference observed are in agreement with the above hypothesis.