The discovery of the mitochondrial DNA from the chlorophycean green alga Chlamydamonas reinhardtii that encodes discontinuous rRNA genes split into 12 modules, led to a suggestion that the primordial ribosome might have consisted of a complex of individual small RNAs contributing specific functional elements 13. Previously published mitoribosomal structures mostly contained subunits consisting of a single or two rRNA fragments 1, 2, 3, 4, 8, 9, 10, 11, 12. This diversification is partially driven by the continuous reduction of the mitochondrial genome, resulting in the generally reduced size of mitoribosomal RNAs 7, 8. In mitochondria, the rRNA and the associated protein architecture has diverged considerably relative to their bacterial ancestors, which allowed an acquisition of accessory functions 1, 2, 3, 4, 5, 6.

Both subunits are composed of a catalytic rRNA core and scaffolding proteins. Ribosomes consist of the small subunit (SSU) that selects aminoacyl-tRNAs cognate to mRNA codons, and the large subunit (LSU) that contains the peptidyl transferase centre and polypeptide exit tunnel. Finally, in the exit tunnel, mL128 constricts the tunnel width of the vestibular area, and mL105, a homolog of a membrane targeting component mediates contacts with an inner membrane bound insertase. Together, the structural analysis provides insight into the evolution of the ribosomal machinery in mitochondria. On the protein level, eleven peripherally associated HEAT-repeat proteins are involved in the binding of 3′ rRNA termini, and the structure features a prominent pseudo-trimer of one of them (mL116). Through comparison to other ribosomes with fragmented rRNAs, we observe that the pattern is shared across large evolutionary distances, and between cellular compartments, indicating an evolutionary convergence and supporting the concept of a primordial fragmented ribosome. The mt-5S rRNA is stabilised by mL40 that is also found in mitoribosomes lacking the 5S, which suggests an evolutionary pathway.

We found that the rRNA contains a non-canonical reduced form of the 5S, as well as a permutation of the LSU domain I. Here, we report a 2.9 Å resolution structure of the mitoribosome from the alga Polytomella magna harbouring a reduced rRNA split into 13 fragments. Mitoribosomes of green algae display a great structural divergence from their tracheophyte relatives, with fragmentation of both rRNA and proteins as a defining feature.

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