The catalytic group-I introns of the psbA gene of Chlamydomonas reinhardtii: core structures, ORFs and evolutionary implications

The sequences and predicted secondary structures of the four catalytic grou p-I introns in the psbA gene of Chlamydomonas reinhardtii, Cr.psbA-1-Cr.psb A-4, have been determined. Cr.psbA-4 and Cr.psbA-4 are subgroup-IA1 introns and have similar secondary structures, except at the 3' end where Cr.psbA- 1 contains a large inverted-repeat domain. Cr.psbA-4 is closely related to intron 1 of the Chlamydomonas moewusii psbA gene, with which it shares the same location, high nucleotide identity in the core, and an identically pla ced ORF that shows 58% amino-acid identity. Cr.psbA-2 is a subgroup-IA3 int ron, and shows similarities to the Chlamydomonas eugametos rRNA intron, Ce. LSU-1. Cr.psbA-3 is a subgroup-IA2 intron, and is remarkably similar to the T4 phage intron, sunY. Interestingly, a degenerate version of Cr.psbA-3 is located in the intergenic region between the chloroplast petA and petD gen es. All four introns contain ORFs, which potentially code for basic protein s of 11-38 kDa. The ORFs in introns 2 and 3 contain variants of the GIY-YIG motif; however, the Cr.psbA-2 ORF is free-standing, whereas the Cr.psbA-3 ORF is contiguous and in-frame with the upstream exon. The CI.psbA-4 ORF co ntains an H-N-H motif, and possibly a GIY-YIG motif. These data indicate th at the C. reinhardtii psbA introns have multiple origins, and illustrate so me of the evolutionary DNA dynamics associated with group-I introns in Chla mydomonas.