Unique tRNA introns of an enslaved algal cell

Nucleomorphs are remnant nuclei of eukaryotic, secondary endosymbionts exclusively found in cryptophytes and chlorarachniophytes. The nucleomorph of the cryptophyte Guillardia theta codes for 36 transfer RNA (tRNA) genes, 15 of them predicted to contain introns and 1 pseudo-tRNA. Some of the predicted intervening sequences are manifested at positions not known in Eukarya, even tRNAs with more than one intron were suggested. By isolating reverse transcriptase-polymerase chain reaction products of the spliced tRNAs we verify the processing of all predicted intron-harboring tRNAs and demonstrate the splicing of the smallest introns (3 nt) investigated so far. However, the spliced intervening sequences are in some cases shifted in respect to the predicted ones. Moreover, we show that introns, if inserted into the B-box of tRNA genes in the nucleomorph of cryptophytes, mimic promoter regions and do not abolish transcription by RNA polymerase III. Consequently, internal nucleomorph-encoded tRNA promoter regions are in some cases dissected from the sequence of the mature tRNAs. By reanalyzing tRNA introns of a recently sequenced red algae we furthermore show that splicing of introns at unusual positions may be introduced in cryptophytes by its secondary endosymbiont. However, in contrast to the rest of the symbiont genome, introns are not minimized in quantity but are instead scattered along the tRNA genes.