A 3′ splice site-binding sequence in the catalytic core of a group I intron

Abstract

RIBOZYMES use specific RNA–RNA interactions for substrate binding and active-site formation. Self-splicing group I introns have ˜70 nucleotides constituting the core, a region containing sequences and structures indispensable for catalytic function^1–3. The catalytic core must interact with the substrates used for the two steps of the self-splicing reaction, that is, guanosine, the 5′-splice-site helix (P1) and the 3′ splice site. Mutational evidence suggests that core sequences near segment J6/7 that joins the base-paired stems P6 and P7, and the bulged base of P7(5′), participate in binding guanosine substrate^4–5, but nothing is known about the interactions between the core, the 5′-splice-site helix and the 3′ splice site. On the basis of comparative sequence data, it has been suggested that two specific bases in the catalytic core of group I introns might form a binding sequence for the 3′ splice site⁶. Here we present genetic evidence that such a binding site exists in the core of the Tetrahymena large subunit ribosomal RNA intron. We demonstrate that this pairing, termed P9.0, is functionally important in the exon ligation step of self-splicing, but is not itself responsible for 3′-splice-site selection.