Insertion of group II intron retroelements after intrinsic transcriptional terminators

Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, AB, Canada T2N 1N4

Edited by Alan M. Lambowitz, University of Texas, Austin, TX, and approved February 27, 2007 (received for review January 22, 2007)

Abstract

Mobile DNAs use many mechanisms to minimize damage to their hosts. Here we show that a subclass of group II introns avoids host damage by inserting directly after transcriptional terminator motifs in bacterial genomes (stem-loops followed by Ts). This property contrasts with the site-specific behavior of most group II introns, which insert into homing site sequences. Reconstituted ribonucleo protein particles of the Bacillus halodurans intron B.h.I1 are shown to reverse-splice into DNA targets in vitro but require the DNA to be single-stranded and fold into a stem-loop analogous to the RNA structure that forms during transcription termination. Recognition of this DNA stem-loop motif accounts for in vivo target specificity. Insertion after terminators is a previously unrecognized strategy for a selfish DNA because it prevents interruption of coding sequences and restricts expression of the mobile DNA after integration.

Footnotes

^†To whom correspondence should be addressed. E-mail: zimmerly{at}ucalgary.ca
Author contributions: A.R.R., W.S., and S.Z. designed research; A.R.R. and W.S. performed research; A.R.R. and S.Z. analyzed data; and A.R.R. and S.Z. wrote the paper.
↵*Present address: Department of Medicine, University of British Columbia, 2222 Health Sciences Mall, Vancouver, BC, Canada V6T 1Z3.
The authors declare no conflict of interest.
This article is a PNAS Direct Submission.
This article contains supporting information online at www.pnas.org/cgi/content/full/0700561104/DC1.
Abbreviations:

RNP,

ribonucleoprotein;

IEP,

intron-encoded protein;

RT,

reverse transcriptase;

IBS,

intron binding site;

EBS,

exon binding site.