Scrambled ribosomal RNA gene pieces in chlamydomonas reinhardtii mitochondrial DNA

We describe here a bizarre organization of the single large subunit (LSU) and small subunit (SSU) rRNA genes in the mitochondrial DNA of Chlamydomonas reinhardtii. Each gene is discontinuous, with gene pieces encoding specific rRNA domains (“modules”) interspersed with one another and with intact protein coding and tRNA genes throughout a 6 kbp region. Transcript mapping experiments reveal the presence of abundant small rRNAs whose sizes approximate the sizes of the modules encoding them. Evidently, rRNA splicing does not occur in this system; instead, secondary structure modeling supports the view that the SSU and LSU rRNAs each functions as a noncovalent network of small RNAs, rather than as a single covalently continuous molecule. We propose that such a modular pattern may reflect the structure of the primordial ribosome.