Physical analysis of the genomes of hybrid phages between phage P1 and plasmid p15B

ATP-dependent restriction enzymes

The phenomenon of restriction and modification (R-M) was first observed in the course of studies on bacteriophages in the early 1950s. It was only in the 1960s that work of Arber and colleagues provided a molecular explanation for the host specificity. DNA restriction and modification enzymes are responsible for the host-specific barriers to interstrain and interspecies transfer of genetic information that have been observed in a variety of bacterial cell types. R-M systems comprise an endonuclease and a methyltransferase activity. They serve to protect bacterial cells against bacteriophage infection, because incoming foreign DNA is specifically cleaved by the restriction enzyme if it contains the recognition sequence of the endonuclease. The DNA is protected from cleavage by a specific methylation within the recognition sequence, which is introduced by the methyltransferase. Classic R-M systems are now divided into three types on the basis of enzyme complexity, cofactor requirements, and position of DNA cleavage, although new systems are being discovered that do not fit readily into this classification. This review concentrates on multisubunit, multifunctional ATP-dependent restriction enzymes. A growing number of these enzymes are being subjected to biochemical and genetic studies that, when combined with ongoing structural analyses, promise to provide detailed models for mechanisms of DNA recognition and catalysis. It is now clear that DNA cleavage by these enzymes involves highly unusual modes of interaction between the enzymes and their substrates. These unique features of mechanism pose exciting questions and in addition have led to the suggestion that these enzymes may have biological functions beyond that of restriction and modification. The purpose of this review is to describe the exciting developments in our understanding of how the ATP-dependent restriction enzymes recognize specific DNA sequences and cleave or modify DNA.

Accessory genes in the darA operon of bacteriophage P1 affect antirestriction function, generalized transduction, head morphogenesis, and host cell lysis

Bacteriophage P1 mutants with the 8.86-kb region between the invertible C-segment and the residential IS1 element deleted from their genome are still able to grow vegetatively and to lysogenize stably, but they show several phenotypic changes. These include the formation of minute plaques due to delayed cell lysis, the abundant production of small-headed particles, a lack of specific internal head proteins, sensitivity to type I host restriction systems, and altered properties to mediate generalized transduction. In the wild-type P1 genome, the accessory genes encoding the functions responsible for these characters are localized in the darA operon that is transcribed late during phage production. We determined the relevant DNA sequence that is located between the C-segment and the IS1 element and contains the cin gene for C-inversion and the accessory genes in the darA operon. The darA operon carries eight open reading frames that could encode polypeptides containing >100 amino acids. Genetic studies indicate that some of these open reading frames, in particular those residing in the 5' part of the darA operon, are responsible for the phenotypic traits identified. The study may contribute to a better comprehension of phage morphogenesis, of the mobilization of host DNA into phage particles mediating generalized transduction, of the defense against type I restriction systems, and of the control of host lysis.

Gene organization in the multiple DNA inversion region min of plasmid p15B of E.coli 15T-: assemblage of a variable gene

The bacteriophage P1-related plasmid p15B of E. coli 15T- contains a 3.5 kb long region which frequently undergoes complex rearrangements by DNA inversion. Site-specific recombination mediated by the Min DNA invertase occurs at six crossover sites and it eventually results in a population of 240 isomeric configurations of this region. We have determined 8.3-kb sequences of the invertible DNA and its flanking regions. The result explains how DNA inversion fuses variable 3' parts to a constant 5' part, thereby alternatively assembling one out of six different open reading frames (ORF). The resulting variable gene has a coding capacity of between 739 and 762 amino acids. A large portion of its constant part is composed of repeated sequences. The p15B sequences in front of the variable fusion gene encode a small ORF and a phage-specific late promoter and are highly homologous to P1 DNA. Adjacent to the DNA invertase gene min, we have found a truncated 5' region of a DNA invertase gene termed psi cin which is highly homologous to the phage P1 cin gene. Its recombinational enhancer segment is inactive, but it can be activated by the substitution of two nucleotides.

Sequence and deletion analysis of the recombination enhancement gene (ref) of bacteriophage P1: evidence for promoter-operator and attenuator-antiterminator control

The ref gene of bacteriophage P1 stimulates recombination between two defective lacZ genes in the Escherichia coli chromosome (lac x lac recombination) and certain other RecA-dependent recombination processes. We determined the DNA sequence of the 5' portion of the ref gene and tested various regions for functionality by inserting DNA fragments lacking increasing amounts of 5' sequence into plasmid and lambda phage vectors and measuring the ability of the constructs to stimulate lac x lac recombination. The region found essential for Ref activity in the absence of external heterologous promoters encodes two presumptive promoters, pref-1 and pref-2, whose -10 regions fall in a nearly perfect 13-base-pair (bp) tandem repeat. The -10 region of the putative pref-1 is part of a phage P1 c1 repressor recognition sequence. The first two ATG codons in the ref reading frame are, respectively, 90 and 216 bp downstream from the putative promoter-operator region. Deletion analysis indicated that translation can initiate at either ATG (although neither is associated with a canonical ribosome-binding sequence) and that the 42 amino acids in between are not indispensable for Ref stimulation of lac x lac recombination. However, the shorter reading frame appears to encode a less active polypeptide. The 91-bp leader region between the putative promoter-operator and the first ATG contains 30 codons in frame with the ref structural sequence, but its frame can be shifted without affecting Ref activity. The leader region ends with an apparent rho-independent termination sequence (attenuator). Deletion of 18 bp of early leader sequence drastically reduced Ref activity, even when ref was driven by a heterologous promoter (plac). An 8-bp internal deletion in the putative attenuator sequence relieved this requirement for the early leader sequence. This latter observation, along with nucleotide complementarity between portions of the early leader and attenuator sequences, are consistent with preemption of attenuation by the early leader.

Amplification of drug resistance genes flanked by inversely repeated IS1 elements: involvement of IS1-promoted DNA rearrangements before amplification

Tn2653 contains one copy of the tet gene and two copies of the cat gene derived from plasmid pBR325 and is flanked by inverted repeats of IS1. Transposed onto the P1-15 prophage, it confers a chloramphenicol resistance phenotype to the Escherichia coli host. Because the prophage is perpetuated as a plasmid at about one copy per host chromosome, the host cell is still tetracycline sensitive even though P1-15 is carrying one copy of the tet gene. We isolated P1-15::Tn2653 mutants conferring a tetracycline resistance phenotype, in which the whole transposon and variable flanking P1-15 DNA segments were amplified. Amplification was most probably preceded by IS1-mediated DNA rearrangements which led to long direct repeats containing Tn2653 sequences and P1-15 DNA. Subsequent recombination events between these direct repeats led to amplification of a segment containing the tetracycline resistance gene in tandem arrays.

Expression and proteolytic processing of the darA antirestriction gene product of bacteriophage P1

The darA gene coding for one of the two bacteriophage P1 antirestriction functions is expressed late after infection or induction. The protein is made as a high-molecular-weight soluble precursor. This is proteolytically cleaved to the mature form, which is a structural component of the phage head. Defective mutants of the phage have been found in which the synthesis of gpdarA is normal but processing does not take place. These mutations all map to the same region of the P1 genome and we propose that they lie in the structural gene for the processing protease.

Two DNA antirestriction systems of bacteriophage P1, darA, and darB: characterization of darA- phages

Bacteriophage P1 is only weakly restricted when it infects cells carrying type I restriction and modification systems even though DNA purified from P1 phage particles is a good substrate for type I restriction enzymes in vitro. Here we show that this protection against restriction is due to the products of two phage genes which we call darA and darB (dar for defense against restriction). Each of the dar gene products provides protection against a different subset of type I restriction systems. The darA and darB gene products are found in the phage head and protect any DNA packaged into a phage head, including transduced chromosomal markers, from restriction. The proteins must, therefore, be injected into recipient cells along with the DNA. The proteins act strictly in cis. For example, upon double infection of restricting cells with dar+ and dar- P1 phages, the dar+ genomes are protected from restriction while the dar- genomes are efficiently restricted.

A cloned DNA fragment from bacteriophage P1 enhances IS2 insertion

A 1.75 kb DNA segment of the bacteriophage P1 genome is known to serve as a preferred target for IS2 insertions. The presence of this fragment in a plasmid expressing the galK gene dramatically increases the proportion of IS2 insertions among spontaneous galK- mutants. Subfragments from two different parts of the 1.75 kb segment independently stimulate IS2 insertion, while another subfragment does not. In the plasmids studied IS2 elements not only insert into the cloned P1 fragment but also into parts of the galK gene with similar probability and mostly in one orientation. Many insertion sites are unique but several specific sites within the preferred target are repeatedly used for IS2 integration. The experimental data are compatible with a proposed cooperative mechanism, according to which more than one attracting sequence on the same plasmid might significantly enhance the probability of a particular target region to attract IS2.

Sequence relations among the IncY plasmid p15B, P1, and P7 prophages

Electron microscopic analysis of heteroduplex molecules between the 94-kb plasmid p15B and the 92-kb phage P1 genome revealed nine regions of nonhomology, eight substitutions, and two neighboring insertions. Overall, the homologous segments correspond to 83% of the P1 genome and 81% of p15B. Heteroduplex molecules between p15B and the 99-kb phage P7 genome showed nonhomology in eight of the same nine regions; in addition, two new nonhomologous segments are present and P7 carries a 5-kb insertion representing Tn902. The DNA homology between those two genomes amounts to 79% of P7 DNA and 83% of p15B. Plasmid p15B contains two stem-loop structures. One of them has no equivalent structure on P1 and P7 DNA. The other substitutes the invertible C segments of P1 and P7 and their flanking sequences including cin, the gene for the site-specific recombinase mediating inversion.

An in vivo cointegrate of two plasmids from incompatibility group X

Formation of a recombinant plasmid designated pNH603 was observed when two plasmids from incompatibility group X, the multicopy plasmid pNH602 (a higher-copy-number deletion derivative of R6K) and the oligocopy plasmid R485, coexisted in a single Escherichia coli cell. According to its size and its restriction endonuclease cleavage pattern, plasmid pNH603 is a true cointegrate of pNH602 and R485. An insertion-sequence-like element coming from plasmid R485 is supposed to mediate the fusion of both replicons. The pNH603 copy number (1-2 per chromosome) indicates that the mechanism of replication of the low-copy-number plasmid is dominant in this cointegrate. No dissociation of pNH603 to parental plasmids was observed even in E. coli K-12 recA+ cells. On the other hand, deletion derivatives of four size classes originate from pNH603 in both recA+ and recA hosts. A miniplasmid designated pNH604, a representative of the most frequent 7 Mg/mol size class, was found, in a low number of copies per host chromosome.

A phage P1 function that stimulates homologous recombination of the Escherichia coli chromosome

Recombination between two different defective lacZ genes in the Escherichia coli chromosome (lac- X lac- recombination) was stimulated 2- to 8-fold by prophage P1, depending on the nature of the phage c1 repressor. The P1 BamHI restriction fragment B8 in a lambda-P1:B8 hybrid phage, stimulated lac- X lac- recombination 90-fold in the absence of P1 repressor. A gene necessary for recombination enhancement, designated ref, was localized to one end of B8. Ref expression from lambda-P1:B8 was repressed in trans by a P1 c+ prophage. Two P1 regulatory mutations, bof and lxc, derepressed prophage expression of ref and depressed a prophage function that complemented an E. coli mutant (ssb) deficient in the single-stranded DNA binding protein. Ref stimulation was dependent on preexisting E. coli recombination functions (RecA-RecBC and RecA-RecF). However, other (phage and plasmid) recombination processes involving these functions were not stimulated. ref::Tn5 phages plated and formed lysogens normally. Thus ref appears to be an integral, but not essential, phage gene that stimulates recombination of the host chromosome specifically.

Crossover sites cix for inversion of the invertible DNA segment C on the bacteriophage P7 genome

The bacteriophage P7 genome contains an invertible DNA segment called C which determines its host range. P7 C(+) phages produce plaques on Escherichia coli K12. The C segment consists of a 3-kb unique sequence and 0.62-kb inverted repeats of which one carries an internal 0.2-kb deletion. This deletion has been mapped within the right inverted repeat in the C(+) orientation. The crossover sites cix for inversion of the C segment do not map at the inside boundaries of the inverted repeats, as had been proposed. They are localized at the external ends of these repeats. Thus organization of the C segment in phage P7 is analogous to that in the related phage P1.

Transposable element IS1 intrinsically generates target duplications of variable length

Target duplication during transposition is one of the characteristics of mobile genetic elements. IS1, a resident insertion element of Escherichia coli K-12, was known to generate a 9-base-pair target duplication, while an IS1 variant, characterized by a nucleotide substitution in one of its terminal inverted repeats, was reported to duplicate 8 base pairs of its target during cointegration. We have constructed a series of transposons flanked by copies of either the normal or the variant IS1. The analysis of their transposition products revealed that transposons with normal termini as well as those with variant termini can intrinsically generate either 9- or 8-base-pair target duplications. We also observed that a normal IS1 from the host chromosome generated an 8-base-pair repeat. The possible relevance of the observation for the understanding of transposition processes and models to explain the variable length of target duplications are discussed.

IS30, a new insertion sequence of Escherichia coli K12

Three independent spontaneous mutations of prophage P1 affecting the ability of the phage to reproduce vegetatively are due to the insertion of a mobile genetic element, called IS30. The same sequence is also carried in the R plasmid NR 1-Basel, but not in the parental plasmid NR 1. Southern hybridisation study indicates that the Escherichia coli K 12 chromosome carries several copies of IS30 as a normal resident. IS30 is 1.2 kb long and contains unique restriction cleavage sites for BglII, ClaI, HindIII, NciI and HincII, and it is cleaved twice by the enzymes HpaII and TaqI. The ends of IS30 are formed by 26 bp long inverted repeats with 3 bases mismatched. Upon transposition IS30 generates a duplication of only 2 bp of the target. The following observations suggest a pronounced specificity in target selection by IS30. In transposition to the phage P1 genome a single integration site was used three times independently, and in both orientations. A short region of sequence homology has been identified between the P1 and NR 1-Basel insertion sites. IS30 has mediated cointegration as well as deletion. The entire IS30 sequences were duplicated in the cointegrates between a pBR322 derivative containing IS30 and the genome of phage P1-15, and several loci on the P1-15 genome served as fusion sites, some of which were used more than once.

Bacteriophage P1 carries two related sets of genes determining its host range in the invertible C segment of its genome

The bacteriophage P1 genome carries an invertible C segment consisting of 3-kb unique sequences flanked by 0.6-kb inverted repeats. Host range mutations of P1 have been mapped in the C segment region. P1 derivatives carrying insertions and deletions in the left half of the C segment in one of two orientations termed C(+) do not affect the plaque-forming ability on Escherichia coli K12 and E coli C, whereas those having insertions in the right half of the C segment fail to form plaques on these hosts. An E. coli C mutant which allows the latter insertion mutants with the C segment in the C(-) configuration to form plaques has been isolated. Not only P1 C(-) but also P1 C(+) phages gave plaques on this E. coli C mutant. The results are consistent with the notion that the C segment of P1 carries two sets of genes for host specificity, and that C inversion alters the P1 host range through activation of one set of the genes. Furthermore, extended host range mutants can be isolated by point mutation in either set of the P1 genes. C inversion is a slow process, but it occurs on the phage genome upon its vegetative growth as well as on the prophage in the lysogenic state. The 3-kb invertible G segment of the phage Mu genome is known to be homologous with the central 3-kb part of the C segment of P1 and to carry also two sets of genes for Mu host specificity. While only Mu G(-) grows on E. coli C, both Mu G(+) and Mu G(-) phages form plaques on the E. coli C mutant sensitive to P1 C(-). In the discussion the gene organization of the P1 C segment is compared with that of the Mu G segment.

DNA restriction--modification genes of phage P1 and plasmid p15B. Structure and in vitro transcription

The EcoP1 and EcoP15 DNA restriction-modification systems are coded by the related P1 prophage and p15B plasmid. We have examined the organization of the genes for these systems using P1 itself, "P1-P15" hybrid phages expressing the EcoP15 restriction specificity of p15B and cloned restriction fragments derived from these phage DNAs. The results of transposon mutagenesis, restriction cleavage analysis. DNA heteroduplex analysis and in vitro transcription mapping allow the following conclusions to be drawn concerning the structural genes. (1) All of the genetic information necessary to specify either system is contained within a contiguous DNA segment of 5 x 10(3) bases which encodes two genes. One of them, necessary for both restriction and modification, we call mod and the other, required only for restriction (together with mod), we call res. (2) The res gene is about 2.8 x 10(3) bases long and at the heteroduplex level is largely identical for P1 and P15: it shows a small region of partial nonhomology and some restriction cleavage site differences. The mod gene is about 2.2 x 10(3) bases long and contains a 1.2 x 10(3) base long region of non-homology between P1 and P15 toward the N-terminus of the gene. The rest of the gene at this level of analysis is identical for the two systems. (3) Each of the genes is transcribed in vitro from its own promoter. It is possible that the res gene is also transcribed by readthrough from the mod promoter.

Sequence of the site-specific recombinase gene cin and of its substrates serving in the inversion of the C segment of bacteriophage P1

Inversion of the 4.2-kb C segment flanked by 0.6-kb inverted repeats on the bacteriophage P1 genome is mediated by the P1-encoded site-specific cin recombinase. The cin gene lies adjacent to the C segment and the C inversion cross-over sites cixL and cixR are at the external ends of the inverted repeats. We have sequenced the DNA containing the cin gene and these cix sites. The cin structural gene consists of 561 nucleotides and terminates at the inverted repeat end where the cixL site is located. Only two nucleotides in the cixL region differ from those in the cixR and they are within the cin TAA stop codon. The cin promoter was localized by transposon mutagenesis within a 0.1-kb segment, which contains probable promoter sequences overlapping with a 'pseudo-cix' sequence cixPp. In a particular mutant, integration of an IS1-flanked transposon into the cin control region promoted weak expression of the cin gene. The cin and cix sequences show homology with corresponding, functionally related sequences for H inversion in Salmonella and with cross-over sites for G inversion in phage Mu. Based on a comparison of the DNA sequences and of the gene organizations, a possible evolutionary relationship between these three inversion systems and the possible significance of the cixPp sequence in the cin promoter are discussed.