Complex group-I introns in nuclear SSU rDNA of red and green algae: evidence of homing-endonuclease pseudogenes in the Bangiophyceae

The green alga Scenedesmus pupukensis and the red alga Porphyra spiralis co ntain large group-IC1 introns in their nuclear small subunit ribosomal RNA genes due to the presence of open reading frames at the 5' end of the intro ns. The putative 555 amino-acid Scenedesmus-encoded protein harbors a seque nce motif resembling the bacterial S9 ribosomal proteins. The Porphyra intr on self-splices in vitro, and generates both ligated exons and a full-lengt h intron RNA circle. The Porphyra intron has an unusual structural organiza tion by encoding a potential 149 amino-acid homing-endonuclease-like protei n on the complementary strand. A comparison between related group-I introns in the Bangiophyceae revealed homing-endonuclease-like pseudogenes due to frame-shifts and deletions in Porphyra and Bangia. The Scenedesmus and Porp hyra introns provide new insights into the evolution and possible novel fun ctions of nuclear group-I intron proteins.