An alternative intron–exon pairing scheme implied by unexpected in vitro activities of group II intron RmInt1 from Sinorhizobium meliloti

Abstract RmInt1 is a mobile group II intron which interrupts IS Rm2011-2 , another mobile element from the bacterium Sinorhizobium meliloti . Ribozyme constructs derived from intron RmInt1 self-splice in vitro when incubated under permissive conditions, but the excised intron and ligated exons are largely replaced by unconventional products. These include a slightly shorter, 5′-end truncated 3′ exon, truncated variants of the linear and lariat forms of the intron-3′ exon reaction intermediate, as well as presumably circular molecules derived from the latter. Two factors explain the abundance of these products: (i) nucleotides 5–11 of the 3′ exon (IBS1*) provide a better match to the EBS1 5′-exon-binding site than the authentic IBS1 sequence in the 5′ exon; (ii) exon ligation is unusually inefficient, and especially so when the 5′ exon is truncated close to the second (IBS2) intron-binding site. We propose that reactions at the IBS1* site play a part in the regulation of the intron IS Rm2011-2 host in vivo.