Requirements for DNA hairpin formation by RAG1/2

Abstract

The rearrangement of antigen receptor genes is initiated by doublestrand breaks catalyzed by the RAG1/2 complex at the junctions of recombination signal sequences and coding segments. As with some ''cut-and-paste'' transposases, such as Tn5 and Hermes, a DNA hairpin is formed at one end of the break via a nicked intermediate. By using abasic DNA substrates, we show that different base positions are important for the two steps of cleavage. Removal of one base in the coding flank enhances hairpin formation, bypassing a requirement for a paired complex of two signal sequences. Rescue by abasic substrates is consistent with a base-flip mechanism seen in the crystal structure of the Tn5 postcleavage complex and may mimic the DNA changes on paired complex formation. We have searched for a tryptophan residue in RAG1 that would be the functional equivalent of W298 in Tn5, which stabilizes the DNA interaction by stacking the flipped base on the indole ring. A W956A mutation in RAG1 had an inhibitory effect on both nicking and hairpin stages that could be rescued by abasic substrates. W956 is therefore a likely candidate for interacting with this base during hairpin formation.immunoglobulin gene ͉ recombination ͉ transposase I n many vertebrates, the vast antigen-binding repertoire of immunoglobulins and T cell receptors is created by combinatorial V(D)J recombination using an array of variable (V), diversity (D), and joining (J) gene segments in B and T cell genomic DNA (1). A complex of the RAG1 and RAG2 gene products is responsible for initiating DNA cleavage and probably for mediating the recruitment of nonhomologous end-joining factors to process and join the broken V, (D), and J segments.The sites of DNA cleavage are directed by recombination signal sequences (RSSs) that flank each coding segment. The two types of RSSs (denoted 12RSS and 23RSS) consist of conserved heptamer and nonamer motifs separated by a spacer of 12 or 23 nonconserved base pairs. Normally, DNA cleavage occurs when the RAG complex recognizes and pairs a 12RSS and a 23RSS, thus ensuring the correct recombination of a V to a J or of a V to a D and of a D to a J segment (termed the ''12/23 rule'') (2). Ordered assembly usually begins with RAG1/2 binding to the 12RSS, followed by capture of free 23RSS (3, 4). Changes in the sensitivity of a 12RSS to chemical modification occur upon RAG1/2 binding, consistent with some unwinding at the heptamer-coding border (5, 6). Double-strand breaks at the coding-RSS border are produced by a nick 5Ј of the heptamer; nucleophilic attack on the opposing strand by the 3Ј hydroxyl group at the nick then creates a hairpin by a transesterification reaction (7). The resulting double-strand break consists of a hairpin on the coding flank and a blunt-ended signal sequence. In the presence of Mg 2ϩ , the complete reaction takes place only in the presence of an RSS pair (coupled cleavage) (8, 9). The mechanism of DNA cleavage has been characterized in vitro, mainly with truncated RAG proteins that retain activity but are mor...

RAG-Heptamer Interaction in the Synaptic Complex Is a Crucial Biochemical Checkpoint for the 12/23 Recombination Rule

“…S7). These results may suggest that the nicking in a single RSS complex relaxes the 7-mer region and that the subsequent 12/23 synapsis formation facilitates the base unstacking in the coding region, leading to hairpin formation (52).…”

“…Region-RAG proteins have been suggested to induce DNA distortion near the cleavage site in both coding and 7-mer sequences (4,5,(51)(52)(53)(54)(55)(56). Because the hairpin tip is unpaired and unstacked, a similar distortion is expected to occur in the coding region before the hairpin forms.…”

“…It is possible that the coding base adjacent to the scissile phosphate is not only unpaired but also flipped out of the helix during hairpin formation (52). Such a flipped-out base is observed in the hairpin-like structure of the Tn5 transposon (58).…”

“…Distortion of the Coding Region DNA and Hairpin FormationAn abasic nucleotide, when incorporated 3Ј to the scissile phosphate, is more stimulatory to the hairpin formation than mismatched bases (52,55). It is possible that the coding base adjacent to the scissile phosphate is not only unpaired but also flipped out of the helix during hairpin formation (52).…”

“…To bring the scissile phosphate to the active site, the coding DNA must be unpaired and unstacked. Stabilization of flipped-out bases by the Trp 893 and/or Trp 956 residue(s) of RAG1 may also be important in this process (52,61).…”