Characterization of fragmented mitochondrial ribosomal RNAs of the colorless green alga Polytomella parva

We have identified previously in mitochondrial DNA of the colorless, chlorophycean, green algal taxon, Polytomella parva, potential coding regions for four small subunit (SSU) and eight large subunit (LSU) rRNA fragments. In this study with P.parva, we isolated RNA from a mitochondrial-enriched preparation, characterized the 12 mitochondrial rRNA transcripts by either northern blot analysis or chemical sequencing and performed secondary structure modeling of the SSU and LSU rRNA sequences. The results show the following features about the mitochondrial SSU and LSU rRNAs of P.parva: (i) they are considerably shorter than their homologs from other green algae, although the main domains typical of conventional rRNAs are conserved; (ii) the rRNA fragmentation pattern is most similar to that of Chlamydomonas reinhardtii among green algae that have been characterized; (iii) three nucleotides are missing from the normally highly conserved GTPase center of the LSU rRNA; and (iv) post-transcriptional modification of the 3′-terminal region of the SSU rRNA is unusual in that it has the 'eubacterial' 3-methyluridine (corresponding to m³U at Escherichia coli 16S rRNA position 1498) but lacks the more highly conserved modifications at two adjacent A residues (corresponding to N⁶,N⁶-dimethyladenosine at E.coli 16S rRNA positions 1518 and 1519). This is the first report of the characterization by direct sequencing of fragmented mitochondrial rRNAs from a green alga.