The P2-like Phages and Their Parasite, P4

Bertani, L. Elizabeth; Six, Erich W.

doi:10.1007/978-1-4684-5490-1_2

Cited by 87 publications

(75 citation statements)

References 211 publications

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“…P2 is a temperate phage that can lysogenize many enterobacteria, including Escherichia coli (10). Bacteriophage P2 integrates into the host chromosome via a Campbell-like process, by site-specific recombination between a bacterial attB site and the attP site of circularized P2 DNA.…”

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

Haggård‐Ljungquist

1993

J Bacteriol

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Integration of the bacteriophage P2 genome into the Escherichia coli host chromosome occurs by site-specific recombination between the phage altP 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 (1HF) of E. coli were required to mediate integrative recombination in vitro between a supercoiled attP plasmid and a linear aUB 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 aUB 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 THF 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 A integration.P2 is a temperate phage that can lysogenize many enterobacteria, including Escherichia coli (10). Bacteriophage P2 integrates into the host chromosome via a Campbell-like process, by site-specific recombination between a bacterial attB site and the attP site of circularized P2 DNA. At least 10 different attB sites have been defined. In E. coli C, one site, locI, is preferred, and it must be occupied before any of the alternate sites are used. In E. coli K-12 no such preference is seen. We have recently shown that a cryptic P2 is already integrated into the K-12 locI-equivalent site (4). This could account for the strain variation in site preference. The DNA sequences of locI and three alternative attB sites, locTT, locIII, and locH, have been determined (4, 44). The conserved stretch of 27 bp in locI and attP is defined as the core sequence. The alternative sites show identity of 20 bp (locTT) and 17 bp (locIII and locH) to the attP core sequence.The only phage product known to be required for integration is that of the int gene (14,22). The int gene product is also involved in prophage excision and site-specific recombination between lytically multiplying phages. The DNA sequence of the int gene has been determined (44), and it codes for a polypeptide of 337 amino acids, with a molecular mass of 37.9 kDa. The P2 Int protein belongs to the integrase family of site-specific recombinases (3, 32). All members of this family of proteins carry out similar s...

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

Haggård‐Ljungquist

1993

J Bacteriol

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“…This, together with the fact that the element is flanked by 29-bp direct repeats that are different from the P4 attP and attB sequences, suggests that the cryptic prophage has its own site-specific integrase. Phage P4 is known as a satellite phage that parasitizes bacteriophage P2 (3). Recently, we have found that P2 phage can function as a helper to excise the cryptic prophage and to generate an infectious phage, named retronphage XR73, which strongly resembles phage P4 (26).…”

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Association of a retroelement with a P4-like cryptic prophage (retronphage phi R73) integrated into the selenocystyl tRNA gene of Escherichia coli

1991

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A new multicopy single-stranded DNA (msDNA-Ec73) was found in a clinical strain of Escherichia coli. consisting The recent discovery of reverse transcriptase (RT) in bacteria raises intriguing questions concerning its origin and functions (22,23,31,34). Although bacterial RTs are highly diverged from each other at the level of primary amino acid sequences (approximately 50o identity) and domain structure, they share conserved sequences with retroviral RTs, indicating that they are evolutionarily related (9,23,52). These bacterial retroelements are required for the synthesis of a peculiar satellite DNA called multicopy single-stranded DNA (msDNA). Bacterial RT genes are found in association with chromosomal regions that encode msDNA, and it has been proposed that this entire primitive retrosystem be termed a retron (49).msDNA consists of a single-stranded DNA ranging in size from 65 to 163 bases, which is branched out from an internal G residue of a short RNA by a 2',5' phosphodiester linkage (see references 24 and 30 for reviews). It is very stable in the cell because of extensive secondary structure in both the DNA and RNA moieties of the msDNA molecule as well as a DNA-RNA hybrid at their 3' ends. msDNA synthesis begins with the production of a long precursor RNA, which folds to form a stable secondary structure such that the folded precursor RNA serves not only as a primer for initiating msDNA synthesis but also as a template to form the branch linkage between the RNA and DNA components.

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“…박테리오파지 P4는 머리와 꼬리를 생성하는 유전자를 갖고 있지 않으므로, Escherichia coli 세포 내에 플라스미드 상태로 있다가 도움파지(helper phage)인 박테리오파지 P2가 존재할 때만 파지로 증식할 수 있는 위성파지(satellite phage)이다 (Bertani and Six, 1988). 박테리오파지 P4는 박테리오파지로 증식할 때 박테리오파지 P2의 머리와 꼬리 생성 유전자를 이 용하는데, 박테리오파지 P2의 유전체 보다 1/3 정도 작은 자신 의 유전체를 packaging하기에 알맞게 작은 머리 생성을 위해 머리 크기 결정 유전자인 sid (size determination)를 갖고 있다 (Shore et al, 1978).…”

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Characterization of the bacteriophage P4 sid<sup>+</sup> derivative overcoming P2sir-associated helper inefficiency through DNA conformational adaptation

Kim¹

2016

The Korean Journal of Microbiology

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A certain size of DNA (28-29 kb long) to be packaged into P2-size head and the mutation in sid gene of bacteriophage P4 are the major factors to overcome "P2 sir-associated helper inefficiency". To clarify whether the presence of sid mutation is essential to overcome "P2 sir-associated helper inefficiency" or not, we tested the P4 derivative, P4 delRI::kmr, which is sid + and whose genome size supposed to be 28.5 kb long in the case of being packaged into P2sir3-sized large head. As P4 delRI::kmr showed the low EOP with P2 sir3 lysogen, P4 delRI::kmr phage stock was prepared in P2 sir3 lysogen host to increase the EOP with P2 sir3 lysogen. Through this process, P4 delRI::kmr had been adapted for P2 sir3 lysogen. With a CsCl buoyant equilibrium density gradient experiment and gel electrophoresis of the isolated DNA, it was evident that the adaptation of P4 delRI::kmr for P2 sir3 lysogen was caused by the conformational change of DNA to be packaged into large head. The burst size determination experiments with P4 delRI::kmr phage stock adapted for P2 sir3 lysogen and normal P4 delRI::kmr phage stock showed that not the sid mutation but the size of DNA to be packaged (28-29 kb long) was essential to overcome "P2 sir-associated helper inefficiency".

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The P2-like Phages and Their Parasite, P4

Cited by 87 publications

References 211 publications

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

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

Association of a retroelement with a P4-like cryptic prophage (retronphage phi R73) integrated into the selenocystyl tRNA gene of Escherichia coli

Characterization of the bacteriophage P4 sid<sup>+</sup> derivative overcoming P2sir-associated helper inefficiency through DNA conformational adaptation

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