Field of Science

RNA is so passé. Mitochondrial ribosomes ditch rRNA in favour of protein

Mitochondria are the energy-producing organelles of eukaryotes that evolved from a endosymbiotic bacterial ancestor, probably before the divergence of all known eukaryotes. They retain a minimal genome, which in humans amounts to just 37 genes: 13 for components of respiratory complexes and 24 for translation (22 transfer (t) RNAs and 2 ribosomal (r) RNAs).

Translation is pretty bizarre in mitochondria, and very different among different eukaryotic lineages in terms of mRNA features and involvement of protein factors. Vasya has covered some peculiarities of mitochondrial information processing in his blog posts here, here and here. I want to touch upon another part of it: rRNA reduction and replacement with protein.

The mammalian mitochondrial ribosome is bigger than that of its bacterial counterpart, however it contains less RNA, with the remainder of its mass being made up of ribosomal proteins (RBPs) that are encoded in the nucleus and post-translationally targeted to mitochondria. The extra RBPs that have evolved to replace the RNA tend to have no recognisable homologues in prokaryotic or eukaryotic cytoplasmic proteomes, and are evolving faster than cytoplasmic RBPs (O'Brien, 2002). 

Nematode ribosomes are even more striking in their rRNA loss, as you can see from the figure below, and are even more protein-rich (Watanabe, 2010; Zhao et al., 2005).

Figure and caption from WATANABE, K. (2010): Three-dimensional models for large mt ribosomal RNA (gray) from mammalian (middle) and C. elegans (right) mitochondria, based on the crystal structure of a bacterial 50S subunit108) (left). The outline shows an edge line of the crystal structure of the 50S subunit from the crown view. Some functional rRNA domains are colored: red, P loop; blue, A loop; green, S/R loop; light blue, L2 binding helix (H66). The topological orientation of the ribosomal protein is based on the model for the mammalian mt ribosome.

So why is this happening? Maybe this replacement of RNA with protein is a part of the ongoing transition from the RNA world into the protein world. But why is this replacement so pronounced in mitochondria? I wonder whether instead, it might be linked to RNA stability within the unique mitochondrial environment. Only very few mRNAs are present in mitochondria. For most of the proteins required there, the mRNA and proteins are made elsewhere in the cell and only then targeted to mitochondria. Perhaps mitochondrial chemistry isn't RNA-friendly, and it's beneficial for the cell to cut it down wherever possible and replace with more stable protein. I'm intrigued, but really not sure about this, and couldn't find any references to back up the idea, so I'd be grateful for any comments or links to references that any readers may have!

O'Brien TW (2002). Evolution of a protein-rich mitochondrial ribosome: implications for human genetic disease. Gene, 286 (1), 73-9 PMID: 11943462

WATANABE, K. (2010). Unique features of animal mitochondrial translation systems Proceedings of the Japan Academy, Series B, 86 (1), 11-39 DOI: 10.2183/pjab.86.11

Zhao F, Ohtsuki T, Yamada K, Yoshinari S, Kita K, Watanabe Y, & Watanabe K (2005). Isolation and physiochemical properties of protein-rich nematode mitochondrial ribosomes. Biochemistry, 44 (25), 9232-7 PMID: 15966747


  1. Aubrey de Grey has a description in his book Ending Aging (chapters 5 and 6) of why DNA in mitochondria suffer more damage than in the nucleus.

  2. Thanks for the tip! DNA damage might just explain it. Mitochondria can import some RNAs, but possibly the ribosomal RNA is just too big and structured. So instead of gene transfer to the nucleus (which is the solution for other components of the translational machinery), coding sequence reduction and replacement with protein is the best means means of avoiding damage as much as possible.

  3. I like the stability argument; obv OXPHOS is a major source of ROS. I wonder if Nick Lane has given this any consideration in his writings (ref his mito book in 1995 et al. writings). I'm about to look into some of your references, thanks for posting them.

    Another possibility might be that the regulation of transcription/translation within the mitos require more protein-protein contact between signaling/regulatory peptides, etc., and so additional protein within the ribosome may be better handled on the stage of co-evolution. Great topic.


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