Attachment sites for bacteriophage P2 on the Escherichia coli chromosome: DNA sequences, localization on the physical map, and detection of a P2-like remnant in E. coli K-12 derivatives

Barreiro, Virginia; Haggård‐Ljungquist, Elisabeth

doi:10.1128/jb.174.12.4086-4093.1992

Cited by 36 publications

(35 citation statements)

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“…Many phage att sites overlap tRNAs (for review, see Campbell 1992), and ssrA, encoding the tmRNA, has a 3Ј structure like a tRNA and overlaps the att site of a cryptic prophage (Kirby et al 1994). In this work, we found that the 3Ј end and terminator of #14 overlaps the previously mapped phage P2 att site (Barreiro and Haggard-Ljungquist 1992). #14 sRNA does not obviously resemble a tRNA, suggesting that the overlap between phage att sites and RNA genes extends beyond tRNAs and related molecules and may be common to additional sRNAs.…”

Section: Evaluation Of Selection Criteriamentioning

confidence: 49%

Identification of novel small RNAs using comparative genomics and microarrays

Wassarman¹,

Repoila²,

Rosenow³

et al. 2001

Genes Dev.

642

614

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A burgeoning list of small RNAs with a variety of regulatory functions has been identified in both prokaryotic and eukaryotic cells. However, it remains difficult to identify small RNAs by sequence inspection. We used the high conservation of small RNAs among closely related bacterial species, as well as analysis of transcripts detected by high-density oligonucleotide probe arrays, to predict the presence of novel small RNA genes in the intergenic regions of the Escherichia coli genome. The existence of 23 distinct new RNA species was confirmed by Northern analysis. Of these, six are predicted to encode short ORFs, whereas 17 are likely to be novel functional small RNAs. We discovered that many of these small RNAs interact with the RNA-binding protein Hfq, pointing to a global role of the Hfq protein in facilitating small RNA function. The approaches used here should allow identification of small RNAs in other organisms.

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Section: Evaluation Of Selection Criteriamentioning

confidence: 49%

Identification of novel small RNAs using comparative genomics and microarrays

Wassarman¹,

Repoila²,

Rosenow³

et al. 2001

Genes Dev.

642

614

View full text Add to dashboard Cite

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“…In E. coli C, P2 inserts preferentially within a 27-bp identity segment (locI) and less frequently at secondary sites that are similar but not identical to locl (5,50). In E. coli K-12, locI is occupied by a defective prophage, and infecting P2 inserts only at secondary sites.…”

Section: Secondary Sitesmentioning

confidence: 99%

Chromosomal insertion sites for phages and plasmids

1992

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“…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.…”

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confidence: 99%

“…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.…”

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confidence: 99%

“…4 and 5). We used the DNA fragments PCR 4 and PCR S (top strand), 5' end labelled at the 71.8R or 72.OR end (Table 2), or the fragments PCR 6, -7, and -8 (bottom strand), 5' end labelled at 72.4L, 72.5L, or 73.0L, as no other binding sites could be detected outside the region from -120 bp to + 120 bp around the attP core sequence. Three regions of protection by wt Int could be discerned, one centered at the common core sequence, a second centered at =-62 on the P arm, and a third centered at =+110 on the P' arm (Fig.…”

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confidence: 99%

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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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Attachment sites for bacteriophage P2 on the Escherichia coli chromosome: DNA sequences, localization on the physical map, and detection of a P2-like remnant in E. coli K-12 derivatives

Cited by 36 publications

References 36 publications

Identification of novel small RNAs using comparative genomics and microarrays

Identification of novel small RNAs using comparative genomics and microarrays

Chromosomal insertion sites for phages and plasmids

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

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