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Cunt Brunette Cuntbrunette O %EF%BF%BD%EF%BF%BD%EF%BF%BD%EF%BF%BD%CF%B5%EF%BF%BD%EF%BF%BD Szh 1 Cunt Brunette Sequences in attB that affect the ability of C integrase to synapse and to activate DNA cleavage--《核酸研究医学期刊》--医学期刊频道--首席医学网

Cunt Brunette Cuntbrunette O %EF%BF%BD%EF%BF%BD%EF%BF%BD%EF%BF%BD%CF%B5%EF%BF%BD%EF%BF%BD Szh 1 Cunt Brunette

【摘要】  Phage integrases are required for recombination of the phage genome with the host chromosome either to establish or exit from the lysogenic state. C31 integrase is a member of the serine recombinase family of site-specific recombinases. In the absence of any accessory factors integrase is unidirectional, catalysing the integration reaction between the phage and host attachment sites, attP x attB to generate the hybrid sites, attL and attR. The basis for this directionality is due to selective synapsis of attP and attB sites. Here we show that mutations in attB can block the integration reaction at different stages. Mutations at positions distal to the crossover site inhibit recombination by destabilizing the synapse with attP without significantly affecting DNA-binding affinity. These data are consistent with the proposal that integrase adopts a specific conformation on binding to attB that permits synapsis with attP. Other attB mutants with changes close to the crossover site are able to form a stable synapse but cleavage of the substrates is prevented. These mutants indicate that there is a post-synaptic DNA recognition event that results in activation of DNA cleavage.

【关键词】  sequences integrase activate cleavage

INTRODUCTION

C31 integrase and several of its relatives are being widely used for precise engineering of complex genomes (1¨C8) and are emerging as promising new tools for gene therapy (9¨C15). In addition to being highly portable C31 integrase is, unlike other recombinases used for genome manipulation such as Cre and Flp, unidirectional (7,16,17). In nature phage integrases are required for recombination of the phage genome with the host chromosome either to establish or exit from the lysogenic state. For integration the host-encoded attB site undergoes a conservative and reciprocal recombination with the phage attP site to form the hybrid product sites, attL and attR. During induction into the lytic cycle, the phage genome excises and this reaction normally requires integrase and an accessory protein Xis (18,19). Phage-encoded integrases can belong to the tyrosine or the serine recombinase families (20). Both families of proteins act by binding to their cognate substrates and bringing the DNAs together in a synapse. Recombination is initiated by cleaving DNA strands, which undergo strand exchange to form recombinant products and these are then released (21). While the mechanism of phage integrase, a tyrosine recombinase, is well understood (18,22,23), the mechanism of action of integrases such as C31 integrase that belong to the serine recombinase family, is less clear.

All serine recombinases have a conserved catalytic domain required for DNA cleavage and rejoining (20,24). The resolvase/invertases also have a small (60 amino acids; aa) C-terminal DNA-binding domain (25). The serine integrases, some transposases and the staphylococcal cassette recombinases (Ccr proteins; required for the movement of methicillin resistance gene in MRSA) are so-called large serine recombinases as they have extensive C-terminal domains (300¨C500 aa in length; 20). Sequence alignments of these large serine recombinases indicate that they are an extremely diverse family. Experiments with C31 integrase, mycobacteriophage Bxb1 integrase and TnpX transposase suggest that the recombination mechanism used by the large serine recombinases resembles that of the well-studied resolvase/invertases (17,24,26¨C33). DNA cleavage occurs at a 2 bp crossover sequence to form a staggered break and a transient covalent phosphoserine bond between the recessed 5' ends and the recombinase is formed (17,27). Strand exchange most likely occurs by rotation of two recombinase subunits bound to half sites relative to the other two subunits (34¨C37). Rejoining of the products is dependent on the complementarity of the DNA sequence at the staggered breaks; if there is a mismatch at this sequence, joining of the products is severely inhibited but iteration of strand exchange results in changes in the topology of the substrates (17,28,38).

Divergence from the resolvase paradigm by the serine integrases occurs in the nature of substrate recognition and the formation of the synapse. The pairs of recombination sites used by the serine integrases have different sequences; for example, the C31 attP and attB sites share 39% sequence identity . The recombination sites are generally short, 50 bp (10,17,29,40). The minimal sites for C31 integrase have been defined as a 39 bp attP site and a 34 bp attB site (10). Under in vitro conditions C31 integrase converts 80% of attB and attP to products in the absence of accessory proteins and there are no restrictions on the topology of the substrates (16,27,28). Moreover, in these in vitro reactions, C31 integrase is catalytically inert on all other combinations of substrates including attL and attR (28). Hatfull and colleagues have shown that Bxb1 integrase has similar properties and they have gone on to show that Bxb1 integrase binds to its substrates as a dimer (17,26). The synapse is therefore likely to contain a tetramer of integrase subunits (26).

Figure 1. C31 attB and attP sites. (A) The double-stranded DNA sequences of the S. coelicolor attB site (green) and the attP site (blue) are shown. The crossover dinucleotides are shown in black. The colons connecting the two sequences indicate the positions of sequence identity between the aligned attB and attP sites. The grey shading indicates the positions where sequence conservation can be detected between the attB or attP sites and their pseudo-sites from Streptomyces or Mycobacteria (pseudo-attB sites) or from human or mouse cell lines (pseudo-attP sites) (9,41¨C43). (B) Summary of mutation scanning in attB. The attB site is shown as a single-strand sequence where each base acts as point on the x-axis of a histogram. The y-axis shows the fold reduction in product made when mutations are introduced in attB. The positions are annotated according to the numbering shown. The activities of attB sites with double mutations at symmetrical positions (eg ¨C/+1, ¨C/+2, etc.) are shown in pink and the activities of mutants with single mutations are shown in black. The data for the summary graph were calculated from the estimated absolute activities shown in Table 1, Figure 2 and Supplementary Data, Figure S1. Beneath the attB sequence, three of the S. coelicolor pseudo-attB sites are shown for comparison with the wild-type attB. The four sites have been aligned and are shaded according to whether there is 100% identity (black background and white text) or 75% identity (grey background) between the sites.

Figure 2. Recombination activities of attB mutant sites. Recombination activities are shown for the wild-type attB site (A), mutant sites at position 2 (B), 6 (C), 12 (D), 15 (E), 16 (F) 18 (G). Panel H shows the activities of partially symmetrized attB sites that contain the right sequence between +12 and +18 changed to the same sequence as on the left (¨C12 to ¨C18), 2L (+12 to +18) or vice versa, 2R (¨C12 to ¨C18). Recombination assays were performed using the standard plasmid assay containing the plasmid indicated in each panel and pRT702 encoding attP. The concentrations of integrase used for each set of six reactions in panels A to C and E, F and H was 0, 441, 110, 55, 27 and 14 nM. The concentrations of integrase used for each set of six reactions in panels D and G was 0, 351, 87, 43, 21 and 10 nM.

Table 1. List of mutant attB sites and their activity compared to the wild-type attB

A major focus in our lab has been to understand why C31 integrase can only recombine attB and attP in vitro. We have shown previously that integrase cannot synapse pairs of recombination sites other than attP with attB indicating that the formation of the synapse is the major block to excision in vitro (27). We and others have proposed that integrase adopts specific conformations when bound to attP and attB sites that enable the formation of a synapse, but when bound to attL and attR disable or destabilize the synapse (26,27,29). In this model, the interactions between integrase and attP and attB are central to the formation of the synaptic interface. Some clues as to the preferred sequences of attP and attB have been obtained previously through studies that have characterized the substrates used by integrase when one of the cognate sites is not present (9,41,42). Pseudo-attB sites in the bacterial host, Streptomyces coelicolor and other actinomycetes show a strong preference for certain bases . Similarly, pseudo-attP sites have been characterized in mammalian genomes and these also show base specific preferences (Figure 1). Many of the bases that are conserved in the pseudo-attP and pseudo-attB sites are also conserved between attP and attB (Figure 1).

To examine the integrase¨CattB interaction in more detail, the minimal attB site was subjected to mutagenesis and the activities of the mutants assayed in recombination and binding assays. Recombination defective attB mutants that could still bind to integrase with affinities not dissimilar to the wild-type attB site were found to be blocked either at synapsis or at DNA cleavage. The most likely explanation is that there are two separate recognition events that occur between integrase and the attB site. The first event results in a protein¨Cprotein interface that enables synapsis and the second post-synapsis event results in activation of DNA cleavage.

MATERIALS AND METHODS

Bacterial strains and plasmids

Escherichia coli strains DH5 and DS941 were used as general cloning hosts and were grown in LB or 2xYT (44). E. coli transformation, plasmid preparations and DNA manipulation were performed as described previously (44).

Plasmids pRT600 and pRT700 were constructed previously by insertion of annealed oligonucleotides RM1/RM2 containing attB (51 bp) and RM3/RM4 attP (50 bp) sites inserted into pGEM7 cut with EcoRI and Csp45I (29). For this work, the attP site from pRT700 was excised with BamHI and EcoRI and inserted into BamHI and EcoRI cut pSP72 to form pRT702. Plasmids containing mutant attB sites at all positions except for ¨C/+3, ¨C/+8 and ¨C/+12 were constructed as for pRT600; annealed oligonucleotides (see Supplementary Data, Table S1) were inserted into pGEM7 cut with EcoRI and Csp45I. Plasmids containing mutations at ¨C/+3, ¨C/+8 and ¨C/+12 were constructed differently; PCR amplification using primers containing a randomized base at positions 3, 8 or 12 (Supplementary Data, Table S2) resulted in fragments that could be inserted into pGEM7 and these were then sequenced to determine the nature of the mutations. To create the double mutants with mutations at symmetrical positions, fragments containing the two single mutations were spliced together using the unique StyI site in the centre of the attB site. All the plasmids containing the mutant attB sites were subjected to confirmation by sequencing.

Recombination assays

Standard recombination assays between two attachment sites located on two separate plasmids were performed as described previously. Plasmids (100 ng each) containing attB (or the mutant attBs) and attP were mixed with 18 µl of recombination buffer (10 mM Tris pH 7.5, 1 mM EDTA pH 8, 100 mM NaCl, 5 mM DTT, 5 mM spermidine, 4.5% glycerol and 0.5 mg/ml bovine serum albumin) and C31 integrase was added to the recombination reaction to final concentrations 0, 441, 110, 55, 27 or 14 nM unless otherwise stated. Reactions were incubated at 30¡ãC for 1 h unless otherwise stated and terminated by incubation at 65¡ãC for 10 min. After addition of an equal volume of 2x restriction buffer (20 mM Tris-HCl pH 7.9, 100 mM NaCl, 20 mM MgCl2, 2 mM DTT) the plasmids were treated with HindIII restriction endonuclease (37¡ãC for 2 h) and the fragments were separated by electrophoresis through 0.8% agarose gels in 1x TBE buffer (100 V). HindIII linearizes the substrates containing attB (or mutant attBs) and attP to give DNA molecules of 3035 and 2491 bp, respectively. The recombination product is a cointegrate of the two substrate plasmids and is cut by HindIII into two fragments; 5435 bp containing attL and 91 bp containing attR. Only the attL fragment is detected routinely after electrophoresis.

Recombination reactions were also performed using a plasmid encoding the attP site, pRT702, and annealed oligonucleotides containing the attB sequence or its mutant derivatives (the ¡®oligo-plasmid¡¯ assay; see Table S2 in the Supplementary Data for the sequences of the oligos) (17). pRT702 (100 ng) was mixed with 4.5 ng of annealed oligonucleotides encoding a mutant attB site and 18 µl of recombination buffer. C31 integrase (1 µl) was added to give final concentrations as described above (i.e. 0, 441, 110, 55, 27 and 14 nM) and the reactions were incubated at 30¡ãC for 1 h. The recombination reactions were terminated by heat inactivating the samples at 65¡ãC for 10 min and the products of recombination were analysed on 0.8% agarose gels in 1x TBE buffer (100 V). The products of recombination were identified as linear DNAs (2546 bp).

DNA binding and radioactive recombination assays

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