The RmInt1 group II intron has two different retrohoming pathways for mobility using predominantly the nascent lagging strand at DNA replication forks for priming

Abstract

Sinorhizobium meliloti RmInt1 is an efficient mobile group II intron that uses an unknown reverse transcriptase priming mechanism as the intron ribonucleoprotein complex can reverse splice into DNA target substrates but cannot carry out site‐specific second strand cleavage due to the lack of a C‐ terminal DNA endonuclease domain. We show here that, like other mobile group II introns, RmInt1 moves around by an efficient RNA‐based retrohoming mechanism. We found evidence of two distinct RmInt1 retrohoming pathways for mobility depending on the orientation of the target site relative to the direction of DNA replication. The preferred retrohoming pathway is consistent with reverse splicing of the intron RNA into single‐stranded DNA at a replication fork, using a nascent lagging DNA strand as the primer for reverse transcription. This strand bias is the opposite of that reported for mobility of the lactococcal Ll.ltrB intron in the absence of second strand cleavage. The mobility mechanism found here for RmInt1 may be used for dissemination by many bacterial group II introns encoding proteins lacking the DNA endonuclease domain.