Fig. 5. Microsporidian ribosomes use small molecules as ribosomal building blocks to compensate for the rRNA and protein reduction.

a The cryo-EM map indicates the presence of the extra-ribosomal nucleotide bound to the E. cuniculi ribosome. In the E. cuniculi ribosome this nucleotide occupies the same space as the 25 S rRNA nucleotide A3186 (S. cerevisiae numbering) in most other eukaryotic ribosomes. b In the E. cuniculi ribosome structure, this nucleotide is being sandwiched between ribosomal proteins uL9 and eL20, stabilizing contacts between these two proteins. c–d Analyses of eL20 sequence conservation in microsporidian species. A phylogenetic tree of microsporidian species (c) and a multiple sequence alignment of protein eL20 (d) illustrate that the nucleotide-binding residues F170 and K172 are conserved in most canonical microsporidia (aside from S. lophii), except for the early-branched microsporidia, in which the rRNA expansion ES39L is preserved. e The plot shows that the nucleotide-binding residues F170 and K172 are only found in eL20 from microsporidian parasites with highly reduced genomes and not in other eukaryotes. Overall, these data indicate that microsporidian ribosomes have evolved a nucleotide-binding site that appears to bind AMP molecules and use them to stabilize protein–protein interactions in the ribosome structure. The high degree of conservation of this binding site among microsporidia and its absence in other eukaryotes indicates that this site may provide a selective advantage for microsporidia survival. Therefore, the nucleotide-binding pocket in microsporidian ribosomes appears not to be a vestigial feature or the ultimate form of rRNA degeneration, as previously suggested³², but a useful evolutionary innovation that allows microsporidian ribosomes to directly bind small molecules, utilizing them as molecular building blocks for ribosome assembly. This finding makes microsporidian ribosomes the only known ribosomes that use single nucleotides as a structural building block. f A hypothetic evolutionary path of the nucleotide-binding acquisition.