The URF 5 gene of Chlamydomonas reinhardtii mitochondria: DNA sequence and mode of transcription.

A gene homologous to unassigned reading frame (URF) 5 of the mammalian mitochondrial genome has been identified in the mitochondrial DNA of the unicellular green alga, Chlamydomonas reinhardtii. The algal URF 5 gene is closely flanked by the gene for subunit I of cytochrome oxidase (COI) and by an unidentified gene (ORF x). The URF 5 and ORF x genes are transcribed in the same direction, but opposite to that of the COI gene. Transcript analysis reveals a 1.9-kb mRNA whose major 5' terminus maps to the putative URF 5 initiation codon and whose 3' end abuts the 5' end of the ORF x transcript. Characterization of other C. reinhardtii mitochondrial RNAs suggests a general pattern of abutting transcripts and mature mRNAs having little or no 5' leader sequence. While this is reminiscent of post-transcriptional processing in animal mitochondria, different mechanisms must be employed in the two systems, since tRNA sequences (which appear to function as transcript processing signals in animal mitochondria) do not generally flank protein coding sequences in the C. reinhardtii mitochondrial genome. Nevertheless, characteristic secondary structure motifs do occur within the 3'-terminal regions of C. reinhardtii mitochondrial mRNAs, and their location close to mRNA termini suggests that such motifs may play a role in directing the precise endonucleolytic cleavage of long primary transcripts.