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Chapter 7 : λ Integrase and the λ Int Family

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Abstract:

This chapter starts with Allan Campbell’s insightful proposal for the pathway by which the chromosome of bacteriophage λ is integrated into and excised from the chromosome of its host. The chapter discusses different levels of λ Int family complexity. There are presently four classes of integron integrases, IntI1 to -4, sharing approximately 50% identity. In contrast to the IntI1 integrase, which has not suggested any striking deviations from its cousins, the integron recombination targets, and , present several new variations on λ Int family themes. Recombination between sites with identical 7-bp spacer regions is not any more efficient than that for two sites differing at five positions. Recent evidence suggests that λ Int may have gone even further in evolving a dependence on arm binding. Whereas full Int binds very poorly to core-type DNA sites, C65 (lacking the N-terminal domain) binds very well. The amino acid and nucleotide residues responsible for distinction have been variously identified by genetic selections, construction of chimeric integrases (via recombination or site-directed mutagenesis), and alteration of core sites. Superimposing the crystal structure of the catalytic domain of vaccinia virus topoisomerase on the coordinates of the previously reported HP1 and Cre recombinase structures, it is apparent that the order and topology of the secondary and tertiary structural elements are strikingly similar. A unified topological mechanism of site-specific recombination by λ integrase family members has remained elusive until fairly recently, in contrast to the well-characterized mechanisms for several enzymes of the resolvase/invertase family.

Citation: Azaro M, Landy A. 2002. λ Integrase and the λ Int Family, p 118-148. In Craig N, Craigie R, Gellert M, Lambowitz A (ed), Mobile DNA II. ASM Press, Washington, DC. doi: 10.1128/9781555817954.ch7

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Gene Expression and Regulation
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Chromosomal DNA
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Type 1 Fimbriae
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DNA Synthesis
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Figures

Image of Figure 1.
Figure 1.

Integrative and excisive recombination pathways. The protein binding sites for arm-type Int (○), core-type Int (⇒), IHF (□), Xis (△), and Fis (◇) are indicated by filled symbols when that site is occupied by its cognate protein to make a competent recombination partner for integrative (⇓) or excisive (⇑) recombination. Required proteins (Int, IHF, and Xis) are in boldface type, and proteins that inhibit (Xis and IHF) or enhance (Fis) the indicated reactions are in italics. The Holliday junction intermediate (square brackets) results from the reciprocal single-strand swap of the 5′ ends liberated by Int cleavage. The three bases of swapped top strands are shown just prior to ligation and formation of the fourway junction. This is followed by conformational changes that allow cleavage, swapping, and ligation of the bottom strands, i.e., resolution of the Holliday junction to yield recombinant products.

Citation: Azaro M, Landy A. 2002. λ Integrase and the λ Int Family, p 118-148. In Craig N, Craigie R, Gellert M, Lambowitz A (ed), Mobile DNA II. ASM Press, Washington, DC. doi: 10.1128/9781555817954.ch7
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Image of Figure 2.
Figure 2.

Hierarchy of λ Int family attachment sites increasing in complexity from top to bottom. The sites of the heterobivalent recombinases (P2, P22, TnL5, HP1, and λ)are not ordered on the basis of organizational complexity. Nevertheless, their arrangement captures the variability in number, spacing, orientation, and nature of different DNA binding sites within each site. Each site map (except that for topoisomerase)is centered about its respective core region, which consists of the 6- to 8-bp overlap region (i.e., the locus of catalysis and strand exchange)and flanking inverted-repeat coretype protein binding sites (open arrowheads). Topoisomerase functions as a monomer, and therefore just one core site is indicated. Cre exemplifies the simplest recombinases in that it requires only a pair of inverted core sites (per partner). Although Flp, like Cre, needs only a single pair of inverted core sites (per partner), its biological sites contain a third core site adjacent to the functional pair. An inverted pair of core sites is sometimes sufficient for XerCDmediated recombination (e.g., at sites); however, for other substrates, such as XerCD requires participation of the accessory proteins ArgR and PepA (sites not shown). The remaining maps represent the sites of recombinases that are heterobivalent and also require accessory proteins. The intrinsically asymmetric integrase arm-type sites and excisive factor binding sites (Xis or cox sites)are indicated with black arrowheads and hatched arrows, respectively, while IHF binding sites are denoted with open boxes. The Xis site of L5 has not been mapped and is not indicated. The heterobivalent integrase site maps are ordered with the P arms to the left and the P′ arms to the right of the origin, except HP1, which has been reversed. The Tnmap depicts the structure of the circular transposon intermediate postexcision and preintegration. Note that the L5 is interchangeable with the D29 and likewise the HK022 is interchangeable with the λ

Citation: Azaro M, Landy A. 2002. λ Integrase and the λ Int Family, p 118-148. In Craig N, Craigie R, Gellert M, Lambowitz A (ed), Mobile DNA II. ASM Press, Washington, DC. doi: 10.1128/9781555817954.ch7
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Image of Figure 3.
Figure 3.

Domain structure and selected residues of λ Int. The heights of the boxes approximate the different affinities of the three domains for their respective DNA targets. The amino-terminal domain (residues 1 to 64) binds to arm-type sites and includes a single NEM-reactive cysteine (C25). The central CB domain (residues 65 to 169) binds to core-type sites and contains residues in close proximity to DNA, as determined by DNA-sensitive pyridoxal 5′-phosphate (PLP) reactivity with Lys 103, UV zero-length cross-linking to Ala 125-Ala 126, and photoactivated cross-linkingof 4-thio-T to Lys 141. The catalytic domain (residues 170 to 356) contains the most highly conserved λ Int family residues, includingthe catalytic pentad Arg212-Lys 235-His 308-Arg311-His 333 and the activesite nucleophile Tyr342.

Citation: Azaro M, Landy A. 2002. λ Integrase and the λ Int Family, p 118-148. In Craig N, Craigie R, Gellert M, Lambowitz A (ed), Mobile DNA II. ASM Press, Washington, DC. doi: 10.1128/9781555817954.ch7
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Image of Figure 4.
Figure 4.

Scheme of Holliday junction formation and resolution at the core sites of (COC′) and (BOB′) during integrative recombination. (a) The core sites are shown synapsed in antiparallel within a tetrameric arrangement of λ integrases. The 5′ terminus of the top strand from each partner substrate is indicated with an open square, and the top-strand and bottomstrand cleavage sites are represented with filled and open arrowheads, respectively. The integrases poised to cleave the top strands in (i.e., bound at C and B) are displayed with hatched ovals, while the integrases poised to cleave bottom strands in (i.e., bound at C′ and B′) are displayed with open ovals. The catalytically active Ints (i.e., at C and B) (accented with triple arrowheads) cleave the top strand of each partner (a), generating a transient enzyme-Tyr-3′-phosphodiester intermediate (not shown), and permit a reciprocal swap of 5′OH-terminated single-strand segments (each approximately 3 nucleotides long that, in turn, displace the covalently bound integrases and create a recombinant joint (black bar). The resulting Holliday junction (b) most closely resembles a top-strand crossed isomer. In this structure the integrases bound to C and B are still primed for cleavage and may reverse the first strand exchange event. The transition from panel b to panel c represents the isomerization of the tetramer-Holliday junction complex required to prime the integrases bound at C′ and B′ to cleave the bottom strands: the arms of the Holliday junction shift in a scissor-like fashion so that the top strands now subtend an obtuse angle while the bottom strands subtend an acute angle, and the branch point shifts approximately one position closer to the bottom strand cleavage sites. (d) The primed integrases execute the second pair of reciprocal swaps to generate the recombinant products (COB′) and (BOC′) by a step drawn here as primarily unidirectional.

Citation: Azaro M, Landy A. 2002. λ Integrase and the λ Int Family, p 118-148. In Craig N, Craigie R, Gellert M, Lambowitz A (ed), Mobile DNA II. ASM Press, Washington, DC. doi: 10.1128/9781555817954.ch7
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Image of Figure 5.
Figure 5.

Schematic representation of active-site catalytic residues from λ Int surroundingthe scissile phosphate of a substrate DNA. This model is based on, and representative of, a synthesis of structural and functional data derived from many systems (see text for details and references). For each λ Int residue there is also indicated the correspondingresidue from vaccinia virus topoisomerase (Topo), Cre, HP1, XerD, and Flp. The homologous residues of Topo and Cre are boxed and juxtaposed to their λ counterparts since they are referred to extensively in the text. The diagrammed positions approximate the relative disposition of each amino acid to the element with which it is expected to interact. Members of the canonical Arg-His-Argtriad are Arg 212, His 308, and Arg 311. Arg 212 is shown poised to make bidentate H bonds with the nonbridging oxygens of the scissile phosphate, while His 308 and Arg311 are both oriented to make only monovalent contacts. His 333 most likely interacts with a nonbridging oxygen and probably does not act as a general acid catalyst to assist in 5′OH release. The nucleophilic Tyr 342 is accented with triple arrowheads and is shown poised to execute an inline attack of the scissile phosphate to generate a covalent Tyr-3′-phosphate linkage and a freed 5′OH. Note that the Tyr may be shifted away from its target when the catalytic site is inactive. Lys 235 is a putative general acid catalyst and is shown prepared to donate a proton to the 5′ oxygen. The chirality of the nonbridging oxygens is indicated; note that R and S become R′ and S′ in the covalent complex.

Citation: Azaro M, Landy A. 2002. λ Integrase and the λ Int Family, p 118-148. In Craig N, Craigie R, Gellert M, Lambowitz A (ed), Mobile DNA II. ASM Press, Washington, DC. doi: 10.1128/9781555817954.ch7
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Image of Figure 6.
Figure 6.

Differential occupancy of H′ and P′1 sites of that characterize various recombination pathways. Occupied sites are indicated by filled symbols, while vacant sites are indicated by open symbols.

Citation: Azaro M, Landy A. 2002. λ Integrase and the λ Int Family, p 118-148. In Craig N, Craigie R, Gellert M, Lambowitz A (ed), Mobile DNA II. ASM Press, Washington, DC. doi: 10.1128/9781555817954.ch7
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