Splicing of group II introns in spinach chloroplasts (in vivo): analysis of lariat formation.

To investigate the mechanism of chloroplast mRNA splicing in vivo, RNAs from four spinach chloroplast group II intron-containing genes were analyzed. For each of these genes, atpF, rpoC1, petD, and petB, Northern analysis of chloroplast RNAs detected putative lariat-intron/3' exon-splicing intermediates. Treatment of these RNAs with HeLa cell-debranching extract caused the putative splicing intermediates to disappear, thereby confirming their identities. The lariat-splicing intermediates were further examined by reverse transcriptase extension to determine the branch point location. The in vivo branch points of the atpF and petD introns were found to be eight bases upstream of their respective 3' intron/exon boundaries. In contrast, no splicing intermediates could be detected by primer-extension analysis of petB and rpoC1. This unexpected result served to demonstrate that the quantity of lariat-intron/3' exon-splicing intermediates present in the chloroplast RNA population is considerably less in the cases of rpoC1 and petB compared to atpF and petD. The steady-state level of any splicing intermediate is the result of a balance between the splicing kinetics of a particular RNA and the susceptibility of the splicing intermediate to degradation. We conclude that the balance between these two factors varies significantly for chloroplast introns, even for those, such as petB and petD, that are transcribed from the same promoter.