Structure and expression of Euglena gracilis nuclear rbcS genes encoding the small subunits of the ribulose 1,5-bisphosphate carboxylase/oxygenase: a novel splicing process for unusual intervening sequences?

In the protist Euglena gracilis, the small subunit of the chloroplast enzyme ribulose 1,5-bisphosphate carboxylase/oxygenase is encoded by nuclear rbcS genes and synthesized as a polyprotein precursor containing eight mature small subunit molecules. This large precursor is encoded by at least eight different nuclear genes as ascertained by transcript analysis. The structure of three rbcS genes was established and the coding sequences were found to be interrupted by many intervening sequences (IVS). Apart from the first 5' intron involved in trans-splicing, none of these IVSs obeys the GT-AG rule characteristic of introns in higher eukaryote genes. Surprisingly, these IVSs are located at identical positions within the three genes studied. Moreover, extensive sequence homologies were found between IVSs located in the same gene as well as in different genes. The sequences of these homologous IVSs differ only by inserted and/or deleted sequences. The striking conservation of the 5' and 3' regions of these IVSs is correlated to their potential secondary structures. These structures, which bring the IVS extremities together with the exon boundaries, could be involved in a novel splicing process. The second 5' IVS is shown to be excised before the addition of the spliced leader sequence to the pre-mRNA. Similarly, two 3' IVSs are excised before the polyadenylation step. These results suggest that IVS splicing is faster than eukaryotic genomic cis-splicing and involves components other than those of the classical spliceosomes.