An archaeal homing endonuclease I- PogI cleaves at the insertion site of the neighboring intron, which has no nested open reading frame

Abstract

Homing endonucleases (HEs) of the LAGLIDADG family cleave intron/inteinless cognate DNA at, or near, the insertion site (IS) of their own intron/intein. Here, we describe a notable exception to this rule. Two introns, Pog.S1205 (length 32 bp) and Pog.S1213 (664 bp), whose ISs are 8 bp apart, exist within the 16S rRNA gene of the archaeon Pyrobaculum oguniense. Pog.S1213 harbors a nested open reading frame (ORF) encoding a 22 kDa monomeric protein, I- PogI, which contains two LAGLIDADG motifs and has optimal DNA cleavage activity at 90°C. Intriguingly, I- PogI cleaves the Pog.S1205-less substrate DNA in the presence or absence of Pog.S1213. The cleavage site (CS) of I- PogI does not coincide with the IS of Pog.S1213 but with that of Pog.S1205. Thus, I- PogI activity both promotes the homing of its own intron, Pog.S1213, and guarantees co-conversion of the ORF-less intron Pog.S1205.