Genes encoding a subunit of respiratory NADH dehydrogenase (ND1) and a reverse transcriptase-like protein (RTL) are linked to ribosomal RNA gene pieces in Chlamydomonas reinhardtii mitochondrial DNA.

Abstract

Two long and uninterrupted reading frames, specifying the ND1 and RTL genes, are embedded within fragmented rRNA genes in the 15.8‐kb mitochondrial genome of Chlamydomonas reinhardtii, a unicellular green alga. The ND1 gene encodes a subunit of respiratory NADH dehydrogenase, a standard mitochondrial gene, while the RTL gene is related to the reverse transcriptase‐like part of some optional introns and plasmids in fungal mitochondria. The universal genetic code is used in both the ND1 and RTL genes; however, the latter is distinguished from the other protein coding genes of C. reinhardtii mtDNA by several characteristics which suggest that RTL may be a more recently acquired gene. Flanking each of the protein coding genes, whose mRNAs are of similar abundance, are some of the ‘scrambled’ rRNA gene pieces that are a unique feature of C. reinhardtii mtDNA. These sub‐genic modules give rise to high‐abundance, small‐sized pieces of rRNA, which are not spliced in this genetic system. Judging by the observed juxtaposition of transcripts as they hybridize to the genome, the mature rRNA and mRNA species from this region appear to be generated by precise endonucleolytic cleavages of a long RNA precursor. We suggest a model, involving reverse transcription of rRNAs and insertion of the resulting cDNAs into the mitochondrial genome, that might account for the pattern of dispersed rRNA gene pieces in C. reinhardtii mitochondrial DNA.

Mitochondrial Genome Sequence Evolution in Chlamydomonas

“…Interestingly, rtl has not been identified in other completely sequenced (Denovan-Wright et al 1998;Kroymann and Zetsche 1998;Kü ck et al 2000;Nedelcu et al 2000) and nearly completely sequenced (Fan and Lee 2002) chlorophycean mitochondrial genomes. Nevertheless, there is evidence that rtl is transcribed in C. reinhardtii (Boer and Gray 1988b), and as observed in this study, there are no frameshifting changes in the C. reinhardtii and C. incerta rtl sequences, in spite of the presence of seven additional codons at two different locations in the 59-end of the C. incerta sequence relative to the C. reinhardtii homolog and of numerous point substitution differences. These results suggest that rtl is not a pseudogene.…”

“…The rRNA genes are broken into several pieces (four for the SSU and eight for the LSU) interspersed with one another and with protein-and tRNA-coding regions (Boer and Gray 1988a). The nonstandard gene in C. reinhardtii mtDNA has been described as a reverse transcriptase-like (rtl) coding sequence (Boer and Gray 1988b) whose function and evolutionary origin remain uncertain.…”

Systems Analysis of the Response of Photosynthesis, Metabolism, and Growth to an Increase in Irradiance in the Photosynthetic Model OrganismChlamydomonas reinhardtii

“…Nine of the 137 chloroplast or mitochondrial transcripts (6.6%) changed significantly (P < 0.05, Wilcoxon rank sum test corrected for multiple hypotheses testing by the Benjamini-Hochberg correction procedure; Supplemental Data Set 1). Two transcripts involved in chlorophyll biosynthesis (chlB and chlN, subunits of the dark operative protochlorophyllide oxidoreductase) (Bröcker et al, 2010), rbcL, and a mitochondrial rRNA species (rrnL-2a) were all expressed at a lower level in higher light, whereas three transcripts, the chloroplastidial orf271 and orf140 (both derived from the WENDY transposon; Fan et al, 1995) and the mitochondrial reverse transcriptase-like (Boer and Gray, 1988) transcript, increased. The three transcripts that increased in abundance are of transposon origin and have unknown functions.…”

The Complete Mitochondrial DNA Sequence of Scenedesmus obliquus Reflects an Intermediate Stage in the Evolution of the Green Algal Mitochondrial Genome

“…No intronic ORF has been identified in either the Scenedesmus or Pedinomonas rnl group II introns, although an ORF coding for a potential reverse transcriptase is present in the P. littoralis counterpart (Fontaine et al 1995). It is noteworthy that a RT-like gene (rtl) is located between two rnl coding regions in the mitochondrial genome of C. reinhardtii (Boer and Gray 1988c); the sequence and secondary structure of its flanking regions suggest that this rtl might be the remnant of an intronic ORF harbored by a group II intron inserted 55 bp upstream of the insertion site of the Scenedesmus rnl_d group II intron (Nedelcu and Lee 1998c). …”