Sequences in attB that affect the ability of C integrase to synapse and to activate DNA cleavage

作者：Milind Gupta, Rob Till2 and Margaret C. M. Smith    作者单位：1Institute of Medical Sciences, University of Aberdeen, Foresterhill, Aberdeen AB25 2ZD and 2Institute of Genetics, Queens Medical Centre, University of Nottingham, Nottingham NG7 2UH, UKTo whom correspondence should be addressed. Tel: 01224 555739; Fax: 01224 555844; Email: Maggie.smith@abdn.ac.uk

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【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.

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