Characterization and splicing in vivo of a Sinorhizobium meliloti group II intron associated with particular insertion sequences of the IS630-Tc1/IS3 retroposon superfamily.

By sequence analysis of Sinorhizobium meliloti strain GR4 plasmid pRmeGR4b, we have identified a group II intron named RmInt1 inserted within the insertion sequence ISRm2011-2 of the IS630-Tc1/IS3 retroposon superfamily. Like some other group II introns, RmInt1 possesses, in addition to the structurally conserved ribozyme core, an open reading frame (ORF) with homology to reverse transcriptases. Using a T7 expression system in Escherichia coli, we show that the intron is active in splicing in vivo and that splicing efficiency requires the intron-encoded ORF, which suggests that the putative intron encoded protein has a maturase function. DNA hybridization studies indicate that intron RmInt1 is widespread within S. meliloti native populations and appears to be mostly located within this IS element. Nevertheless, some S. meliloti strains harbour one copy of RmInt1 at a different location. DNA sequence analysis of the 5' exon of one of these heterologous intron insertion sites revealed the presence of a putative IS element closely related to insertion sequence ISRm2011-2. The intron-binding sites (IBS1 and IBS2 motifs) are conserved, although a transition of a G-->A in the IBS1 has occurred. Our results demonstrate an association of intron RmInt1 with particular insertion sequences of the IS630-Tc1/IS3 retroposon superfamily that may have ensured the spread and maintenance of this group II intron in S. meliloti.