A nicked group II intron and trans-splicing in liverwort, Marchantia polymorpha, chloroplasts.

The chloroplast gene rps12 for ribosomal protein S12 in a liverwort, Marchantia polymorpha, is split into three exons by two introns, one of which (intron 1) is discontinuous. Exon 1 of rps12 for the N-terminal portion of the S12 protein is far from exons 2 and 3 for the C-terminal portion on the opposite DNA strand. S1-nuclease protection analysis and Northern hybridization with RNA isolated from the liverwort chloroplasts showed that: (i) the exons 1 and 2-3 of the rps12 gene with the neighboring genes were transcribed separately, (ii) the trans-splicing of intron 1 occurred after the processing of two primary transcripts to two pre-mRNAs, and (iii) there was no particular order for the splicing of intron 1 (trans) and intron 2 (cis) in the rps12 gene. We propose a bimolecular interaction model for trans-splicing by assuming that intermolecular base pairings between two pre-mRNAs result in the formation of the structure typical of group II introns except for disruption in the loop III region. This structure could be constructed in intron 1 of tobacco rps12 gene.