Excision-deficient mutants of bacteriophage P2

In silico study of cox protein from P2 type enteric bacteriophages based on sequence, structure and dynamics to understand its functional integrity

Cox protein plays a critical role in deciding the lytic-lysogenic switch of P2 enteric phages. This phenomenon makes Cox protein one of the most important candidates in developing novel phage-based therapeutics against antibacterial resistant pathogens. The principle focus concerning protein and its decision making is a DNA binding event, which helps to regulate differential promoter expression. In the current study, we have attempted to understand the sequence, structural and dynamic features associated with Cox protein and its DNA binding. Unavailability of information was a big burden in further proceedings. We have done an extensive literature search to develop a database of Cox with relevant information. That information coupled with the methods of Sequence-based phylogenetic and conservation studies, Homology Modelling, Atomic-level Docking and Molecular Dynamics (MD) Simulation (50 ns each for 10 systems, i.e. total of 500 ns) were performed in the current study. Analysis of those extensive studies has provided us the required sequence to structure to dynamics to functional understanding. Our present study would indeed be very helpful in understanding the biochemical mechanism of Cox activation as well as designing potential phage therapeutics.

Bacteriophage P2

P2 is the original member of a highly successful family of temperate phages that are frequently found in the genomes of gram-negative bacteria. This article focuses on the organization of the P2 genome and reviews current knowledge about the function of each open reading frame.

Phylogenetic structure and evolution of regulatory genes and integrases of P2-like phages

The phylogenetic relationships and structural similarities of the proteins encoded within the regulatory region (containing the integrase gene and the lytic–lysogenic transcriptional switch genes) of P2-like phages were analyzed, and compared with the phylogenetic relationship of P2-like phages inferred from four structural genes. P2-like phages are thought to be one of the most genetically homogenous phage groups but the regulatory region nevertheless varies extensively between different phage genomes.

 

The analyses showed that there are many types of regulatory regions, but two types can be clearly distinguished; regions similar either to the phage P2 or to the phage 186 regulatory regions. These regions were also found to be most frequent among the sequenced P2-like phage or prophage genomes, and common in phages using Escherichia coli as a host. Both the phylogenetic and the structural analyses showed that these two regions are related. The integrases as well as the cox/apl genes show a common monophyletic origin but the immunity repressor genes, the type P2 C gene and the type 186 cI gene, are likely of different origin. There was no indication of recombination between the P2–186 types of regulatory genes but the comparison of the phylogenies of the regulatory region with the phylogeny based on four structural genes revealed recombinational events between the regulatory region and the structural genes.

Less common regulatory regions were phylogenetically heterogeneous and typically contained a fusion of genes from distantly related or unknown phages and P2-like genes.

Structural insight into DNA binding and oligomerization of the multifunctional Cox protein of bacteriophage P2

The Cox protein from bacteriophage P2 is a small multifunctional DNA-binding protein. It is involved in site-specific recombination leading to P2 prophage excision and functions as a transcriptional repressor of the P2 Pc promoter. Furthermore, it transcriptionally activates the unrelated, defective prophage P4 that depends on phage P2 late gene products for lytic growth. In this article, we have investigated the structural determinants to understand how P2 Cox performs these different functions. We have solved the structure of P2 Cox to 2.4 Å resolution. Interestingly, P2 Cox crystallized in a continuous oligomeric spiral with its DNA-binding helix and wing positioned outwards. The extended C-terminal part of P2 Cox is largely responsible for the oligomerization in the structure. The spacing between the repeating DNA-binding elements along the helical P2 Cox filament is consistent with DNA binding along the filament. Functional analyses of alanine mutants in P2 Cox argue for the importance of key residues for protein function. We here present the first structure from the Cox protein family and, together with previous biochemical observations, propose that P2 Cox achieves its various functions by specific binding of DNA while wrapping the DNA around its helical oligomer.

Evolution of a self-inducible cytolethal distending toxin type V-encoding bacteriophage from Escherichia coli O157:H7 to Shigella sonnei

Some cdt genes are located within the genome of inducible or cryptic bacteriophages, but there is little information about the mechanisms of cdt transfer because of the reduced number of inducible Cdt phages described. In this study, a new self-inducible Myoviridae Cdt phage (ΦAA91) was isolated from a nonclinical O157:H7 Shiga toxin-producing Escherichia coli strain and was used to lysogenize a cdt-negative strain of Shigella sonnei. We found that the phage induced from S. sonnei (ΦAA91-ss) was not identical to the original phage. ΦAA91-ss was used to infect a collection of 57 bacterial strains, was infectious in 59.6% of the strains, and was able to lysogenize 22.8% of them. The complete sequence of ΦAA91-ss showed a 33,628-bp genome with characteristics of a P2-like phage with the cdt operon located near the cosR site. We found an IS21 element composed of two open reading frames inserted within the cox gene of the phage, causing gene truncation. Truncation of cox does not affect lytic induction but could contribute to phage recombination and generation of lysogens. The IS21 element was not present in the ΦAA91 phage from E. coli, but it was incorporated into the phage genome after its transduction in Shigella. This study shows empirically the evolution of temperate bacteriophages carrying virulence genes after infecting a new host and the generation of a phage population with better lysogenic abilities that would ultimately lead to the emergence of new pathogenic strains.

Selected topics from classical bacterial genetics

Current cloning technology exploits many facts learned from classical bacterial genetics. This unit covers those that are critical to understanding the techniques described in this book. Topics include antibiotics, the LAC operon, the F factor, nonsense suppressors, genetic markers, genotype and phenotype, DNA restriction, modification and methylation and recombination.

Physical mapping of bacteriophage P2 mutations and their relation to the genetic map

Three new deletion mutants and an insertion mutant of E. coli bacteriophage P2, del2, vir79, del4 and sig5, were mapped by the electron microscope heteroduplex method. The deletions were found to cover 45.5-51.6%, 75.6-76.7% and 92.3-99.3% respectively of P2 DNA while sig5 represented a 3.7% insertion at 78.6% from the left end. The region covering 75.9-76.7% of P2 DNA is also deleted in the two previously characterized immunity insensitive variants of P2, vir22 and Hy dis. This region may identify the portion of the genome responsible for immunity. The physical and genetic maps of P2 were previously found to be colinear with respect to the two mutations vir22 and vir37. This relationship is confirmed by the position of del2.

The multifunctional bacteriophage P2 cox protein requires oligomerization for biological activity

The Cox protein of bacteriophage P2 is a multifunctional protein of 91 amino acids. It is directly involved in the site-specific recombination event leading to excision of P2 DNA out of the host chromosome. In this context, it functions as an architectural protein in the formation of the excisome. Cox is also a transcriptional repressor of the P2 Pc promoter, thereby ensuring lytic growth. Finally it promotes derepression of prophage P4, a nonrelated defective satellite phage, by activating the P4 P(LL) promoter that controls P4 DNA replication. In this case it binds upstream of the P(LL) promoter, which normally is activated by the P4 Delta protein. In this work we have analyzed the native form of the Cox protein in vivo, using a bacteriophage lambda cI-based oligomerization assay system, and in vitro, using gel filtration, cross-linking agents, and gel retardation assays. We found that P2 Cox has a strong oligomerization function in vivo as well as in vitro. The in vitro analysis indicates that its native form is a tetramer that can self-associate to octamers. Furthermore we show that oligomerization is necessary for the biological activity by characterizing different cox mutants and that oligomerization is mediated by the C-terminal region.

Bacteriophage P2 and P4 morphogenesis: structure and function of the connector

The connector, the structure located between the bacteriophage capsid and tail, is interesting from several points of view. The connector is in many cases involved in the initiation of the capsid assembly process, functions as a gate for DNA transport in and out of the capsid, and is, as implied by the name, the structure connecting a tail to the capsid. Occupying a position on a 5-fold axis in the capsid and connected to a coaxial 6-fold tail, it mediates a symmetry mismatch between the two. To understand how the connector is capable of all these interactions its structure needs to be worked out. We have focused on the bacteriophage P2/P4 connector, and here we report an image reconstruction based on 2D crystalline layers of connector protein expressed from a plasmid in the absence of other phage proteins. The overall design of the connector complies well with that of other phage connectors, being a toroid structure having a conspicuous central channel. Our data suggests a 12-fold symmetry, i.e., 12 protrusions emerge from the more compact central part of the structure. However, rotational analysis of single particles suggests that there are both 12- and 13-mers present in the crude sample. The connectors used in this image reconstruction work differ from connectors in virions by having retained the amino-terminal 26 amino acids normally cleaved off during the morphogenetic process. We have used different late gene mutants to demonstrate that this processing occurs during DNA packaging, since only mutants in gene P, coding for the large terminase subunit, accumulate uncleaved connector protein. The suggestion that the cleavage might be intimately involved in the DNA packaging process is substantiated by the fact that the fragment cleaved off is highly basic and is homologous to known DNA binding sequences.

The Cox protein is a modulator of directionality in bacteriophage P2 site-specific recombination

The P2 Cox protein is known to repress the Pc promoter, which controls the expression of the P2 immunity repressor C. It has also been shown that Cox can activate the late promoter PLL of the unrelated phage P4. By this process, a P2 phage infecting a P4 lysogen is capable of inducing replication of the P4 genome, an example of viral transactivation. In this report, we present evidence that Cox is also directly involved in both prophage excision and phage integration. While purified Cox, in addition to P2 Int and Escherichia coli integration host factor, was required for attR x attL (excisive) recombination in vitro, it was inhibitory to attP x attB (integrative) recombination. The same amounts of Int and integration host factor which mediated optimal excisive recombination in vitro also mediated optimal integrative recombination. We quantified and compared the relative efficiencies of attB, attR, and attL in recombination with attP and discuss the functional implications of the results. DNase I protection experiments revealed an extended 70-bp Cox-protected region on the right arm of attP, centered at about +60 bp from the center of the core sequence. Gel shift assays suggest that there are two Cox binding sites within this region. Together, these data support the theory that in vivo, P2 can exert control over the direction of recombination by either expressing Int alone or Int and Cox together.

The Cro-like Apl repressor of coliphage 186 is required for prophage excision and binds near the phage attachment site

The Apl protein of the temperature coliphage 186 represses transcription of the immunity repressor gene and down-regulates lytic transcription. It is shown here that an apl- mutant is competent for lytic development and establishes lysogeny normally but is defective in excision of the prophage. The Apl protein binds between the lytic and lysogenic promoters and also near the phage attachment site, suggesting that its role in excision is direct. Apl thus appears to act as an excisionase as well as a repressor. The pattern of Apl-induced DNase I enhancements indicates that the DNA is bent by Apl. Potential Apl recognition sequences are identified; these sequences are directly repeated several times across each binding region and are spaced 10 or 11 bases apart, suggesting that Apl binds to one face of the DNA helix.

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.

Characterization of the binding sites of two proteins involved in the bacteriophage P2 site-specific recombination system

Integration of the bacteriophage P2 genome into the Escherichia coli host chromosome occurs by site-specific recombination between the phage attP and E. coli attB sites. The phage-encoded 38-kDa protein, integrase, is known to be necessary for both phage integration as well as excision. In order to begin the molecular characterization of this recombination event, we have cloned the int gene and overproduced and partially purified the Int protein and an N-terminal truncated form of Int. Both the wild-type Int protein and the integration host factor (IHF) of E. coli were required to mediate integrative recombination in vitro between a supercoiled attP plasmid and a linear attB substrate. Footprint experiments revealed one Int-protected region on both of the attP arms, each containing direct repeats of the consensus sequence TGTGGACA. The common core sequences at attP and attB were also protected by Int from nuclease digestion, and these contained a different consensus sequence, AA T/A T/A C/A T/G CCC, arranged as inverted repeats at each core. A single IHF-protected site was located on the P (left) arm, placed between the core- and P arm-binding site for Int. Cooperative binding by Int and IHF to the attP region was demonstrated with band-shift assays and footprinting studies. Our data support the existence of two DNA-binding domains on Int, having unrelated sequence specificities. We propose that P2 Int, IHF, attP, and attB assemble in a higher-order complex, or intasome, prior to site-specific integrative recombination analogous to that formed during lambda integration.

Genetic analysis of the immunity region of phage-plasmid P4

In the prophage P4, expression of the early genes is prevented by premature termination of transcription from the constitutive promoter PLE. In order to identify the region coding for the immunity determinant, we cloned several fragments of P4 DNA and tested their ability to confer immunity to P4 superinfection. A 357 bp long fragment (P4 8418-8774) is sufficient to confer immunity to an infecting P4 phage and to complement the immunity-defective P4 cl405 mutant, both in the presence and in the absence of the helper phage P2. The immunity region covers PLE and the cl locus. We were unable to obtain evidence of translation of the region, thus we suggest that P4 immunity is not elicited by a protein but by a transcript (or transcripts) encoded by the region downstream of the promoter PLE. The promoter PLE appears to be necessary for the expression of P4 immunity: fragments in which the PLE region is deleted did not complement P4 cl405 for lysogenization, although they still interfered with P4 growth. Two complementary sequences downstream of PLE (seqA and seqB) at the 5' and 3' ends of the immunity region play an essential role in the control of P4 immunity.

Bacteriophage P2 and P4 morphogenesis: protein processing and capsid size determination

An interesting feature of the bacteriophage P2-P4 system is the switch in size between a large P2 (60 nm) and a small P4 (45 nm) capsid. We have investigated whether the protein processing reactions cleaving the primary translation product gpN to several capsid proteins (h1, h2, and N*) are involved in this switch. Using antibodies specific against gpN and its derivatives we have identified all the structural components of mature P2 and P4 particles that are derived from gpN. Our estimate of the relative amounts of gpN derivatives suggests that the previously identified minor capsid proteins h1 and h2 can only be essential structural components of the P4, and not the P2, capsid. Nevertheless, the relative amounts are similar in vivo during a P2 and a P4 infection. This indicates that the switch in head size is not caused by the presence of elevated amounts of h1 and h2 during P4 morphogenesis. We have also identified the sites where gpN is cleaved to its derivatives h1, h2, and N*, ascertaining that the cleavage sites are the same in P2 and P4. Our results indicate that the processing reactions are not directly involved in the head size determination mechanism.

Control of bacteriophage P2 gene expression: analysis of transcription of the ogr gene

The bacteriophage P2 ogr gene encodes an 8.3-kDa protein that is a positive effector of P2 late gene transcription. The ogr gene is preceded by a promoter sequence (Pogr) resembling a normal Escherichia coli promoter and is located just downstream of a late transcription unit. We analyzed the kinetics and regulation of ogr gene transcription by using an ogr-specific antisense RNA probe in an S1 mapping assay. During a normal P2 infection, ogr gene transcription starts from Pogr at an intermediate time between the onset of early and late transcription. At late times after infection the ogr gene is cotranscribed with the late FETUD operon; the ogr gene product thus positively regulates its own synthesis from the P2 late promoter PF. Expression of the P2 late genes also requires P2 DNA replication. Complementation experiments and transcriptional analysis show that a nonreplicating P2 phage expresses the ogr gene from Pogr but is unable to transcribe the late genes. A P2 ogr-defective phage makes an increased level of ogr mRNA, consistent with autogenous control from Pogr. Transcription of the ogr gene in the prophage of a P2 heteroimmune lysogen is stimulated after infection with P2, suggesting that Pogr is under indirect immunity control and is activated by a yet-unidentified P2 early gene product during infection.

Genetic analysis of the DNA recognition sequence of the P2 Cox protein

The Cox protein of temperate Escherichia coli phage P2 is involved in three important biological processes: (i) excision of the integrated prophage genome (G. Lindahl and M. Sunshine, Virology 49:180-187, 1972), (ii) transcriptional repression of the P2 Pc promoter, which controls the expression of the immunity repressor C and the integrase (S. Saha, E. Haggård-Ljungquist, and K. Nordström, EMBO J. 6:3191-3199, 1987), and (iii) transcriptional activation of the late PII promoter of the unrelated satellite phage P4 (S. Saha, E. Haggård-Ljungquist, and K. Nordström, Proc. Natl. Acad. Sci. USA 86:3973-3977, 1989). A comparison of the DNA regions protected by Cox from DNaseI degradation has revealed a presumptive Cox recognition sequence (Saha et al., Proc. Natl. Acad. Sci. USA). The binding region of Cox in the P2 Pc promoter contains three presumptive recognition sequences, "Cox boxes," located in tandem. P2 vir3 and P2 vir24 are virulent deletion mutants unable to plate on Cox-producing strains, most likely because the deletions locate the new early promoters too close to the Cox-binding region (Saha et al., EMBO J.). In this report, spontaneous P2 vir3 and vir24 mutants, no longer sensitive to repression by the Cox protein, have been isolated. These mutants plate with equal efficiency on strains with or without a Cox-producing plasmid, and they have been named cor for cox resistance. Three types are recognized; the four P2 vir3 cor mutants have a 1-base deletion in the first Cox box, while the P2 vir24 cor mutants were of two types; four have a base substitution in the first Cox box, and one has a base substitution in the second Cox box. The effect of the Cox protein on the mutated P2 vir3 and vir24 promoters was analyzed in vivo by using fusions to a promoterless cat (chloramphenicol acetyltransferase) gene. The activities of the P2 vir3 and vir24 early promoters, as opposed to the wild-type early Pe promoter, are drastically reduced by the Cox protein, and the cor mutation renders them as resistant to Cox as the wild-type Pe promoter. Thus, at least the first two Cox boxes are essential for binding of the Cox protein.

Direct and general selection for lysogens of Escherichia coli by phage lambda recombinant clones

We report a simple in vivo technique for introducing an antibiotic resistance marker into phage lambda. This technique could be used for direct selection of lysogens harboring recombinant phages from the Kohara lambda bank (a collection of ordered lambda clones carrying Escherichia coli DNA segments). The two-step method uses homologous recombination and lambda DNA packaging to replace the nonessential lambda DNA lying between the lysis genes and the right cohesive (cos) end with the neomycin phosphotransferase (npt) gene from Tn903. This occurs during lytic growth of the phage on a plasmid-containing host strain. Neomycin-resistant (npt+) recombinant phages are then selected from the lysates containing the progeny phage by transduction of a polA1 lambda lysogenic host strain to neomycin resistance. We have tested this method with two different Kohara lambda phage clones; in both cases, neomycin resistance cotransduced with the auxotrophic marker carried by the lambda clone, indicating complete genetic linkage. Linkage was verified by restriction mapping of purified DNA from a recombinant phage clone. We also demonstrate that insertion of the npt+ recombinant phages into the lambda prophage can be readily distinguished from insertion into bacterial chromosomal sequences.

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.

Activation of prophage P4 by the P2 Cox protein and the sites of action of the Cox protein on the two phage genomes

Phage P2 induces the unrelated prophage P4. In this paper we show that this is due to the activation of the P4 late promoter PII by the P2 Cox protein. This is in contrast to the effects of Cox on P2, for which it is known from previous work that it acts as a repressor of the promoter Pc, which is responsible for expression of the immunity repressor C. The activator role of Cox was revealed by its effect on replication of P4 DNA and on the formation of chloramphenicol acetyltransferase when a promoterless cat gene was inserted downstream of the P4 PII promoter. DNase I protection studies revealed that the Cox protein binds to the repressor promoter Pc of phage P2 and to the promoter PII of phage P4. In the latter case the Cox protein binds upstream of the -35 region, in analogy to several other activators of promoters. A weak binding was found in the promoters Pe of phage P2 and Ple of phage P4. The Cox protein is a case of viral transactivation of the replication genes of one phage by a control protein of the other. However, the effects of the Cox protein are totally different in the two phages, repressive in one case and activating in the other.

DNA sequences of bacteriophage P2 early genes cox and B and their regulatory sites

Part of the early operon of the temperate phage P2 of Escherichia coli, including genes cox (involved in prophage excision) and B (required for phage specific DNA synthesis), was sequenced. The results are consistent with an early promoter spanning the repressor binding sites, a leader sequence of about 80 bases which overlaps the leader sequence of the repressor gene for about 30 bases, and coordinate transcription of genes cox and B with a termination signal after the B gene. In addition, the data provide amino acid sequences for the Cox and B proteins of 91 and 166 residues, respectively and reveal a hitherto undetected coding sequence between genes cox and B that has the potential to produce a very basic polypeptide of 56 residues. Slight structural similarities between the P2 Cox protein and the analogous Xis protein of phage lambda were noted and the P2 B gene product was compared with proteins that interact with the DnaB protein of E. coli.

Selection of lambda Spi- transducing phages using the P2 old gene cloned onto a plasmid

The old gene product of the P2 prophage interferes with plaque formation by lambda wild type phage but allows lambda phages whose red and gam genes have been deleted to form small, visible plaques (the lambda Spi- phenotype). The old gene product also kills Escherichia coli recB or recC mutants. We have cloned the old gene into the high-copy-number plasmid pBR322, where it prevents plaque formation by both lambda Spi+ and lambda Spi- phages. We transferred a DNA fragment that carries the old gene to the low-copy-number plasmid pSC101 and found that lambda Spi- phages can be selected on strains that carry this plasmid. The plasmid-borne old gene kills E. coli recB mutants, providing a selection for old- mutants.

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.

DNA sequences of the repressor gene and operator region of bacteriophage P2

The nucleotide sequence of the repressor gene C of the temperate phage P2 has been determined. It codes for a nonbasic polypeptide, 99 amino acids long. Twelve repressor-defective mutants have been mapped. All but one are located within the presumed coding part of the gene. There is a strong promoter sequence and an 8-base-pair inverted repeat preceding the gene. The P2 repressor protein shows structural similarity to other DNA-binding proteins. The operator region for the early replication functions was located by sequencing the DNA of three virulent mutants. The sequence indicates that there are two repressor-binding sites. In addition, one of the sites shows sequence homology with part of the operator region of the biotin operon of Escherichia coli.

Lambda replacement vectors carrying polylinker sequences

To simplify the construction and screening of genomic libraries, we have made a new family of lambda replacement vectors (EMBL1, EMBL2, EMBL3, EMBL4) and derivatives containing amber mutations (EMBL3 Sam, EMBL3 AamBam, EMBL3 AamSam). These vectors have a large capacity and polylinker sequences flanking the middle fragment. The polylinkers allow a choice of cloning enzymes and, especially useful in the case of cloning of Sau3A partial digests, the excision of the entire insert by flanking SalI (EMBL3) or EcoRI (EMBL4) sites. Phages with inserts can be selected either biochemically (particularly EMBL3) or genetically by their Spi- phenotype. Amber derivatives of the EMBL3 vector allow the application of genetic screening procedures based on selection for the products of homologous recombination events, and for the selective cloning of DNA sequences linked to supF genes.

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.

In vitro activation of bacteriophage P2 late gene expression by extracts from phage P4-infected cells

We have used a cell-free, DNA-dependent protein-synthesizing system to study the stimulation of phage P2 late gene expression by satellite phage P4. An activity is present in extracts prepared from P4-infected cells, which, when added to the in vitro system with P2 DNA template, stimulates the synthesis of a number of P2 proteins. These stimulated proteins include the major P2 capsid protein (N gene product) and a major component of the P2 phage tail (FII gene product). Extracts prepared from P4-infected cells are also able to stimulate the synthesis from P4 DNA of two low-molecular-weight proteins (18,500 and 17,000 Mr). The stimulating activity has no effect on the synthesis of proteins from lambda plac5 template. Extracts prepared from cells infected with P4 alpha amber mutants lack this stimulating activity.

Recombinant P4 bacteriophages propagate as viable lytic phages or as autonomous plasmids in Klebsiella pneumoniae

We demonstrate the use of bacteriophage P4 as a molecular cloning vector in Klebsiella pneumoniae. A hybrid P4 phage, constructed in vitro, that contains a K. pneumoniae hisDG DNA fragment can be propagated either as a lytic viable specialized transducing phage or as an autonomous, self-replicating plasmid. Hybrid P4 genomes existing as plasmids can be readily converted into non-defective P4-hybrid phage particles by superinfection with helper phage P2. Infection of a K. pneumoniae hisD non-P2 lysogen with P4-hisD hybrid phage results in approximately 90% of the infected cells becoming stably transduced to HisD+. Because P4 interferes with P2 growth, high titre stocks of P4 hybrid phages are relatively free (less than or equal to 10(-6) of P2 contamination. The hisG gene product was detected in ultraviolet light irradiated host cells infected by the P4-hisDG hybrid phage. A mutant of P4 (P4sid1) that directs the packaging of P4 DNA into P2 sized capsids should permit the construction of hybrid phages carrying 26 kilobase inserts.

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

A deletion of phage P2, del6 (L.E. Bertani, 1980), thought to remove the structural gene int, and a deletion/substitution, vir94, thought to remove genes int, C and cox, were mapped by electron microscopy, using the heteroduplex technique. Four independent deletion/substitution mutations, all affecting the regulatory region of P2, were compared in all possible combinations with the same technique: two showed sequence homology in their substitution DNA. The results confirm the model proposed for the origin of these mutants, analogous to that for the origin of transducing variants in phage lambda, but suggest in first approximation that the exchange between the P2 DNA and the chromosome of the host bacterium may occur at several different bacterial sites. A map of the regulatory region of P2, based on all data available from the study of deletions and insertions, is presented.

X-ray sensitivity of Escherichia coli lysogenic for bacteriophage P2

Strains of Escherichia coli C or K lysogenic for the non-inducible phage P2 show a lower survival following X-ray irradiation as compared to nonlysogenic strains. This difference in X-ray sensitivity is not accompanied by a significant difference in X-ray induced mutability. The capacity of X-irradiated P2 lysogens to multiply any of a number of unirradiated infecting phages is severely impaired. These effects of X-ray treatment can be most simply explained as a consequence of the fact that protein and RNA syntheses are strongly inhibited in P2 lysogens after X-irradiation. All the above events specifically occurring in X-rayed P2 lysogens are dependent on the P2 gene old.

Interaction of P2 bacteriophage with the dnaB gene of Escherichia coli

The dnaB gene product of Escherischia coli is required for multiplication of temperate phage P2. At 37 C in dnaB-ts mutnats, P2 will not plaque and gives a very small burst of progeny. P2 mutants have been isolated which can grow well enough to plaque under these conditions. This type of phage mutant is cis dominant, and one such mutant (P2rlb1) has been mapped near the left end of the early gene B and to the right of the cox4 (excision) mutation. The rlb1 mutation does not lie at the replication origin, but may affect transcription in the early region, which includes the replication origin. It may also represent a site on the P2 DNA which interacts with the dnaB gene product.

Deletions in bacteriophage P2. Circularity of the genetic map and its orientation relative to the DNA denaturation map

Several types of viable chromosomal deletions of bacteriophage P2 were isolated. One type gives the immunity insensitive phenotype and may extend to the genes for the immunity repressor (C) and for integrative recombination (int). Two other types delete genes (old and fun) known to be active in the lysogenic state. For such deletion mutants the relationship between particle density and DNA length was established. The deletions were located in respect to previously mapped genes and the results were compared with electron microscopical studies (by Inman and collaborators) of the P2 chromosome. It is concluded that the best representation of the genetic map of P2 is circular. The cohesive ends of the linear P2 DNA molecule are most likely formed between genes old and Q. Except for the neighborhood of gene old, the previously published, linear genetic map of P2 (Lindahl) is colinear with the melting map of the P2 chromosome (Inman). Preliminary evidence for some specific recombination event often accompanying integrative recombination between phage chromosomes is presented.

A transcribing activity induced by satellite phage P4

Satellite bacteriophage P4 induces a new transcribing enzyme that synthesizes polyriboguanylic acid in the presence of the poly(dG).poly(dC) homopolymer pair. This transcribing activity was partially purified and shown to be distinct from the host RNA polymerase. Analysis of conditional lethal mutants suggests that this new enzyme is necessary for replication of phage DNA.