The insertion element IS1 is a natural constituent of coliphage P1 DNA

Evolved Populations of Shigella flexneri Phage Sf6 Acquire Large Deletions, Altered Genomic Architecture, and Faster Life Cycles

Genomic architecture is the framework within which genes and regulatory elements evolve and where specific constructs may constrain or potentiate particular adaptations. One such construct is evident in phages that use a headful packaging strategy that results in progeny phage heads packaged with DNA until full rather than encapsidating a simple unit-length genome. Here, we investigate the evolution of the headful packaging phage Sf6 in response to barriers that impede efficient phage adsorption to the host cell. Ten replicate populations evolved faster Sf6 life cycles by parallel mutations found in a phage lysis gene and/or by large, 1.2- to 4.0-kb deletions that remove a mobile genetic IS911 element present in the ancestral phage genome. The fastest life cycles were found in phages that acquired both mutations. No mutations were found in genes encoding phage structural proteins, which were a priori expected from the experimental design that imposed a challenge for phage adsorption by using a Shigella flexneri host lacking receptors preferred by Sf6. We used DNA sequencing, molecular approaches, and physiological experiments on 82 clonal isolates taken from all 10 populations to reveal the genetic basis of the faster Sf6 life cycle. The majority of our isolates acquired deletions in the phage genome. Our results suggest that deletions are adaptive and can influence the duration of the phage life cycle while acting in conjunction with other lysis time-determining point mutations.

Bacteriophage recombineering in the lytic state using the lambda red recombinases

Bacteriophages, the historic model organisms facilitating the initiation of molecular biology, are still important candidates of numerous useful or promising biotechnological applications. Development of generally applicable, simple and rapid techniques for their genetic engineering is therefore a validated goal. In this article, we report the use of bacteriophage recombineering with electroporated DNA (BRED), for the first time in a coliphage. With the help of BRED, we removed a copy of mobile element IS1, shown to be active, from the genome of P1vir, a coliphage frequently used in genome engineering procedures. The engineered, IS-free coliphage, P1virdeltaIS, displayed normal plaque morphology, phage titre, burst size and capacity for generalized transduction. When performing head-to-head competition experiments, P1vir could not outperform P1virdeltaIS, further indicating that the specific copy of IS1 plays no direct role in lytic replication. Overall, P1virdeltaIS provides a genome engineering vehicle free of IS contamination, and BRED is likely to serve as a generally applicable tool for engineering bacteriophage genomes in a wide range of taxa.

Comparative genomic analysis of 60 Mycobacteriophage genomes: genome clustering, gene acquisition, and gene size

Mycobacteriophages are viruses that infect mycobacterial hosts. Expansion of a collection of sequenced phage genomes to a total of 60-all infecting a common bacterial host-provides further insight into their diversity and evolution. Of the 60 phage genomes, 55 can be grouped into nine clusters according to their nucleotide sequence similarities, 5 of which can be further divided into subclusters; 5 genomes do not cluster with other phages. The sequence diversity between genomes within a cluster varies greatly; for example, the 6 genomes in Cluster D share more than 97.5% average nucleotide similarity with one another. In contrast, similarity between the 2 genomes in Cluster I is barely detectable by diagonal plot analysis. In total, 6858 predicted open-reading frames have been grouped into 1523 phamilies (phams) of related sequences, 46% of which possess only a single member. Only 18.8% of the phams have sequence similarity to non-mycobacteriophage database entries, and fewer than 10% of all phams can be assigned functions based on database searching or synteny. Genome clustering facilitates the identification of genes that are in greatest genetic flux and are more likely to have been exchanged horizontally in relatively recent evolutionary time. Although mycobacteriophage genes exhibit a smaller average size than genes of their host (205 residues compared with 315), phage genes in higher flux average only 100 amino acids, suggesting that the primary units of genetic exchange correspond to single protein domains.

Genome of bacteriophage P1

P1 is a bacteriophage of Escherichia coli and other enteric bacteria. It lysogenizes its hosts as a circular, low-copy-number plasmid. We have determined the complete nucleotide sequences of two strains of a P1 thermoinducible mutant, P1 c1-100. The P1 genome (93,601 bp) contains at least 117 genes, of which almost two-thirds had not been sequenced previously and 49 have no homologs in other organisms. Protein-coding genes occupy 92% of the genome and are organized in 45 operons, of which four are decisive for the choice between lysis and lysogeny. Four others ensure plasmid maintenance. The majority of the remaining 37 operons are involved in lytic development. Seventeen operons are transcribed from sigma(70) promoters directly controlled by the master phage repressor C1. Late operons are transcribed from promoters recognized by the E. coli RNA polymerase holoenzyme in the presence of the Lpa protein, the product of a C1-controlled P1 gene. Three species of P1-encoded tRNAs provide differential controls of translation, and a P1-encoded DNA methyltransferase with putative bifunctionality influences transcription, replication, and DNA packaging. The genome is particularly rich in Chi recombinogenic sites. The base content and distribution in P1 DNA indicate that replication of P1 from its plasmid origin had more impact on the base compositional asymmetries of the P1 genome than replication from the lytic origin of replication.

IS elements as constituents of bacterial genomes

We provide here an overview of our present understanding of the distribution of different insertion sequences (ISs) within bacterial genomes (both chromosomes and plasmids). This is at present fragmentary and a significant effort is needed in the analysis of the increasing number of genomes whose sequence has been determined. We also consider some of the properties of ISs which are important in their role of assembling, reassorting, and transmitting groups of genes.

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.

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.

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.

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.

Regulatory regions of ColE1 that are involved in determination of plasmid copy number

The copy number of plasmid ColE1 has been known to increase when the Hae II-C segment downstream from the replication origin is deleted. The presence of the 306-base-pair (bp) Hpa II region in the segment is sufficient for reduction of the copy number. Plasmids harboring the region express a trans-acting function that is responsible for the copy number reduction and synthesize a unique protein. A protein specified by the region is purified to near homogeneity and identified as the 63-amino-acid protein encoded by the Hpa II segment. The region, which includes segments 19-25 bp and 53-311 bp downstream from the start site of the primer RNA, is involved in determination of sensitivity to the inhibitory function. In vivo transcription of the galK gene, which is directed by the primer promoter in a segment inserted in front of the structural gene, is inhibited by a plasmid carrying the Hpa II region. The inhibition is strong when the promoter segment contains up to 135 bp downstream from the primer RNA start site, whereas it is weak when only the region up to 52 bp downstream is present.

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

The genomes of three plaque-forming recombinant phages between phage P1 and plasmid p15B were characterized by restriction cleavage analysis and electron microscopic heteroduplex studies. The structure of all three P1-15 hybrid genomes differs from that of P1 DNA in the res mod region coding for restriction and modification systems EcoP15 and EcoP1, respectively. P1-15 hybrid 2 shows an additional major difference to P1 around the site of the residential IS1 element of P1 and it does not carry an IS1 in its genome.

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.

The origin of replication of plasmid p15A and comparative studies on the nucleotide sequences around the origin of related plasmids

Replication of Escherichia coli plasmid p15A was examined by use of a cell extract or a mixture of three purified E. coli enzymes: RNA polymerase; RNAase H; and DNA polymerase I. In each system, replication initiates at any of three consecutive nucleotides located at a unique site. Primer transcription starts 508 bp upstream of the replication origin. The region between 294 and 524 bp upstream of the origin determines the incompatibility property. This region specifies an RNA (RNA I) of about 105 nucleotides that is involved in regulation of primer formation. We compare the nucleotide sequences around the origins of related plasmids p15A, ColE1, pBR322, RSF1030 and CloDF13, and discuss the significance of possible RNA secondary structures in primer formation.

Inverted duplication in the genome of the temperate Streptomyces phage SH3

The DNA of the temperate Streptomyces phage SH3 contains 100 base-pair long inverted repeats separated by a 940 base-pair long segment of DNA as revealed by electronmicroscopic analysis of snapback structures formed after rapid intrastrand reannealing of denatured DNA. The inverted repeat structure was found preferentially at map unit 22 of the circular physical map, in rare cases also in other positions, suggesting a movable character of this genetic element.

Incompatibility of plasmids containing the replication origin of the Escherichia coli chromosome

Plasmids containing the replication origin of the Escherichia coli chromosome (oriC plasmids) are unstable in certain recA strains of E. coli. However, they can be maintained more stably in other recA strains. This stable maintenance has allowed us to study the incompatibility properties of oriC plasmids. We have found that two oriC plasmids are incompatible: they cannot be stably coinherited in individual dividing cells. An oriC plasmid is excluded from growing bacteria at a much faster rate in the presence of a hybrid plasmid made from an oriC plasmid and a high-copy-number vector plasmid than in the presence of another oriC plasmid. By inserting various segments around the oriC region into high-copy-number vectors, we have shown that two different regions in the vicinity of the oriC region determine incompatibility. One region, which we named incA, includes the region essential for autonomous replication of the oriC plasmid. The other, incB, is adjacent to incA but is not required for autonomous replication.

A site-specific, conservative recombination system carried by bacteriophage P1. Mapping the recombinase gene cin and the cross-over sites cix for the inversion of the C segment

The bacteriophage P1 genome carries an invertible C segment consisting of 3-kb unique sequences flanked by 0.6-kb inverted repeats. With insertion and deletion mutants of P1 derivatives the site-specific recombinase gene cin for C inversion) has been mapped adjacent to the C segment and the cix sites (for C inversion cross-over) have been located at the outside ends of the inverted repeats. Inversion of the C segment functions as a biological switch and controls expression of the gene(s) responsible for phage infectivity carried on the C segment. The cin gene product can promote recombination between a 'quasi- cix ' site on plasmid pBR322 and a cix site on P1 DNA. The junctions formed on the resulting co-integrate can also serve as cix sites. This observation implies a potential evolutionary process to bring genes under the control of a biological switch acting by DNA inversion.

Cointegrates between bacteriophage P1 DNA and plasmid pBR322 derivatives suggest molecular mechanisms for P1-mediated transduction of small plasmids

We characterized cointegrates formed in an Escherichia coli rec+ strain between bacteriophage P1 genomes and small plasmids related to pBR322. The partners were, on the one hand, either phage P1 DNA, which carries one copy of IS1, or phage P1-15 DNA, a derivative which lacks the IS1, and, on the other hand, plasmids containing either a split IS1 or no. In the presence of IS1 sequences on both partners, cointegrates were usually formed by reciprocal recombination between SI1 sequences. Cointegrates between P1 and a plasmid carrying no IS1 sequence were formed by transpositional cointegration mediated by IS1 of P1. Cointegrates between P1-15 and small plasmid containing a split IS1 were formed by one of three ways: (a) acquisition of an IS1 by P1-15 followed by reciprocal recombination between IS1 sequences, (b) transpositional cointegration mediated by the split IS1 element, Tn2657, or (c) involvement of the invertible segment carried on P1-15 DNA. Most cointegrates segregated into the small plasmids and phage P1 derivatives. A comparison of the phenomenon studied and of their frequencies allowed us to conclude that cointegrate formation is a molecular mechanism involved in the transduction of plasmids smaller than those packageable into P1 virions, although it does not seem to be the only process used.

pUR222, a vector for cloning and rapid chemical sequencing of DNA

A multipurpose plasmid, pUR222, was constructed. It contains six unique cloning sites (PstI, SalI, AccI, HindII, BamHI and EcoRI) in a small region of its lac Z-gene part. Insertion of foreign DNA into the plasmid can be easily detected. Bacteria harbouring recombinant plasmids generally give rise to white colonies, while those containing only vector DNA form blue colonies on indicator plates. Plasmid DNA purified by a rapid method (Birnboim, H.C. and Doly, J. (1979) Nucl. Acids. Res. 7, 1513-1523) can be used for chemical sequencing of the cloned insert DNA. Labeled fragments need not be isolated after cutting with the proper restriction enzymes and are treated directly according to the sequencing protocol of Maxam and Gilbert.

Characterization of P1argF derivatives from Escherichia coli K12 transduction. I. IS1 elements flank the argF gene segment

Specialized transducing derivatives of the temperate bacteriophage P1 (P1std) are selected by transduction into recipients with deletions in the corresponding genes (Stodolsky 1973). When Escherichia coli K12 strains are used as donors in such transduction experiments, P1argF derivatives can be selected. The argF gene is unique to these strains (Glansdorff et al. 1967). Under these experimental conditions P1argF are formed with frequencies 10,000 times greater than other P1std. The majority of the P1argF derivatives that have been analyzed are indistinguishable by cleavage analyses. One such derivative, P1argF5 has been characterized in detail. Heteroduplex analysis against P1, P7, and P1CmO identified an 11 kb insertion of DNA precisely at the naturally occurring IS1 locus of P1. Cleavage analysis with EcoRI, BamHI and PstI confirmed this finding. To further define the argF insertion, a P1Cm13argF derivative was constructed having the IS1 sequences of Cm13 and argF in opposite orientation. Intrastrand annealing of P1Cm13argF5 DNA established that the argF segment is flanked by directly repeated IS1 sequences. The IS1-argF-IS1 segment is designated Tn2901. The assignment of the map position of the argF gene within the 11 kb insert of P1argF5 is discussed. The evolutionary significance of this finding and a model for P1argF formation is also presented.

IS4 is still found at its chromosomal site after transposition to galT

IS4-DNA has been hybridized to separated DNA fragments of E. coli K12 strain M28 and to three mutants caused by transposition of IS4 to galT. The parental strain shows one band hybridizing to IS4 representing one copy of IS4 in the chromosome. The mutants have this copy retained and show in addition a second band corresponding to the IS4 copy in galT. The experiments support the hypothesis that transposition of IS4 is accompanied by replication of the element.

Electron microscopic observation of new transposable elements inserted into P22 phage genome from R plasmids

By using phage P22spl, a deletion mutant of phage P22, the structures of two new transposons on P22 genomes were studied by the electron microscopic heteroduplex method. One of these was the Cm (chloramphenicol) transposon derived from an R plasmid, NR1, and the other the Km (kanamycin) transposon frin obr502. the heteroduplex between P22 phage DNAs with and without the Cm transposon revealed that the Cm transposon was similar in structure to the Tn9 element, a well-known Cm transposon derived from the R plasmid pMS14. On the other hand, the Km transposon of pNR502 was quite different in structure from other Km transposons reported previously. This transposon consists of a 6.8 kilobase (kb) segment of DNA, in which a short inverted repeat is contained. The heteroduplex experiments showed that a 4.5 kb segment of DNA was deleted from the P22 genome in the P22spl genome. Because of a shorter unit length of the genome, phage P22spl is considered to be useful of assaying various kinds of transposable elements.

Genetic evidence for absence of transposition functions from the internal part of Tn981 a relative of Tn9

Inverse transposition of the DNA of pBR322 was found to be mediated by the small transposon Tn981 a relative of Tn9 flanked by direct repeats of IS1. Since the resulting structure IS1::pBR322::IS1 (Tn983) is transposed in a second step in the absence of Tn981, it is concluded that all the functions necessary for transposition of IS1 flanked transposons are coded for by IS1 itself or the E. coli chromosome, respectively.

Does the insertion element IS1 transpose preferentially into A+T-rich DNA segments?

IS1-mediated insertion and deletion formation occur preferentially into A+T-rich regions of DNA of bacteriophate P1 and of the r-determinant of the R plasmid NR1. The significance of this correlation is discussed in view of other published data.

Nucleotide sequence analysis of the chloramphenicol resistance transposon Tn9

The transposable genetic element Tn9 consists of two direct repeats of the insertion sequence IS1 flanking a region of 1,102 base pairs which determines chloramphenicol resistance. Transposition of Tn9 leads to the duplication of a 9-base pair sequence which preexists at the site of insertion. One copy of this sequence is found at each end of the inserted element. The chloramphenicol resistance determined by Tn9, and by various other R plasmids, is due to the synthesis of the enzyme chloramphenicol acetyl transferase (CAT). This enzyme catalyses the formation of acetylated derivatives of chloramphenicol which are inactive as inhibitors of protein synthesis. By using the chain termination technique of DNA sequencing, we have now determined the nucleotide sequence of the 1,102 base pair region between the directly repeated IS1 sequence in the bacterial transposon Tn9 (encoding chloramphenicol resistance). The amino acid sequence of CAT predicted from the nucleotide sequence is identical to that determined by Shaw and coworkers. An analysis of the sequence suggests that the internal 1,102 base pair region is not directly involved in transposition.

Some properties of the chloramphenicol resistance transposon Tn9

We have isolated variants of the plasmid RTF which have received the transposon Tn9 from bacteriophage P1Cm. We have shown by the formation of heteroduplex molecules between one RTF:Tn9 derivative and R100.1 that Tn9 is homologous to the r-determinant region of R100.1 which carries the determinants for chloramphenicol resistance. This suggests that Tn9 was derived from an r-det like structure by deletion, possibly mediated by one of the flanking IS1 elements. In spite of the similarity in structure between Tn9 and r-det however, we have demonstrated two distinct differences in the behavior of these two elements: 1) Tn9 but not r-det, is able to amplify, by a recA dependent mechanism, when cells harboring RTF::Tn9 are grown in the presence of chloramphenicol, and 2) Tn9, unlike r-det, does not form extrachromosomal circular molecules when RTF::Tn9 is tegrated into the bacterial chromosome.

Amplification of chloramphenicol resistance transposons carried by phage P1Cm in Escherichia coli

We have characterized a number of P1Cm phages which contain the resistance genes to chloramphenicol and fusidic acid as IS1-flanked Cm transposons. Restriction cleavage and electron microscopic analysis showed that these Cm transposons were carried as monomers (M) or tandem dimers (D). Lysogens of P1Cm (D) are more resistant to chloramphenicol than those of its P1Cm (M) presumably as a result of an increased gene dosage. Amplification of the Cm transposons to tandem multimers was frequently observed in P1Cm (D) lysogens grown in the presence of high concentrations of chloramphenicol or fusidic acid and was also detected in P1Cm (M) lysogens. The degree of amplification varied in different clones which suggests that cells containing spontaneously amplified Cm transposons were selected by high doses of the antibiotics. The dimeric as well as the amplified Cm transposons carried in P1Cm lysogens grown in the absence of chloramphenicol displayed considerable stability. Mechanisms for the amplification of the IS1-flanked transposons are discussed.

Multiple physical differences in the genome structure of functionally related bacteriophages P1 and P7

Comparative restriction cleavage analysis of the genomes of bacteriophage P7, of several recombinant phages between P7 and P1, and of bacteriophage P1 allowed to draw PstI, Bg/II, BamHI and HindIII cleavage maps of all genomes studied. The data obtained complement Yun and Vapnek's (1977) conclusions with regard to areas of major nonhomology based on electron microscopical heteroduplex analysis and they identify several additional minor differences between P1 and P7. The use of hybrid phage strains allowed to locate the genes for particular functions on the physical genome map.