A programmable seeker RNA guides target selection by IS1111and IS110type insertion sequences

Abstract

SUMMARYIS1111and IS110insertion sequence (IS) family members encode an unusual DEDD transposase type and exhibit specific target site selection. The IS1111group include identifiable subterminal inverted repeats (sTIR) not found in the IS110type [1]. IS in both families include a noncoding region (NCR) of significant length and, as each individual IS or group of closely related IS selects a different site, we had previously proposed that an NCR-derived RNA was involved in target selection [2]. Here, we found that the NCR is usually downstream of the transposase gene in IS1111family IS and upstream in the IS110type. Four IS1111and one IS110family members that target different sequences were used to demonstrate that the NCR determines a short seeker RNA (seekRNA) that co-purified with the transposase. The seekRNA was essential for transposition of the IS or a cargo flanked by IS ends from and to the preferred target. Short sequences matching both top and bottom strands of the target were identified in the seekRNA but their order in IS1111and IS110family IS was reversed. Reprogramming the seekRNA and donor flank to target a different site was demonstrated, indicating future biotechnological potential for these systems.