A new RNA–DNA interaction required for integration of group II intron retrotransposons into DNA targets

Mobile group II introns are site-specific retrotransposable elements abundant in bacterial and organellar genomes. They are composed of a large and highly structured ribozyme and an intron-encoded reverse transcriptase that binds tightly to its intron to yield a ribonucleoprotein (RNP) particle. During the first stage of the mobility pathway, the intron RNA catalyses its own insertion directly into the DNA target site. Recognition of the proper target rests primarily on multiple base-pairing interactions between the intron RNA and the target DNA, while the protein makes contacts with only a few target positions by yet-unidentified mechanisms. Using a combination of comparative sequence analyses and in vivo mobility assays we demonstrate the existence of a new base-pairing interaction named EBS2a–IBS2a between the intron RNA and its DNA target site. This pairing adopts a Watson–Crick geometry and is essential for intron mobility, most probably by driving unwinding of the DNA duplex. Importantly, formation of EBS2a–IBS2a also requires the reverse transcriptase enzyme which stabilizes the pairing in a non-sequence-specific manner. In addition to bringing to light a new structural device that allows subgroup IIB1 and IIB2 introns to invade their targets with high efficiency and specificity our work has important implications for the biotechnological applications of group II introns in bacterial gene targeting.