The GC content of LSU rRNA evolves across topological and functional regions of the ribosome in all three domains of life

•LSU ribosomal RNA is the ribozyme that catalyzes translation.•Variation in its GC content was measured across regions of the ribosome, in many Bacteria, Eukaryota, Archaea.•GC variation across taxa increases, smoothly, from the deep to the superficial regions.•This reflects the in-out pattern of increasing variation of all the nucleotides (A, C, G, T).•This GC mapping will help to improve models used for phylogenetic-tree reconstruction.

Large-subunit rRNA is the ribozyme that catalyzes protein synthesis by translation, and many of its features vary along a deep-to-superficial gradient. By measuring the G + C proportions in this rRNA in all three domains of life (60 bacteria, 379 eukaryote, and 23 archaean sequences), we tested whether the proportion of GC nucleotides varies along this in-out gradient. The rRNA regions used were several zones identified by Bokov and Steinberg (2009) as being arranged from deep to superficial within the LSU. To the Bokov–Steinberg zones, we added the most superficial zone of all, the divergent domains (expansion segments), which are greatly enlarged in eukaryotes. Regression lines constructed from the hundreds of species of organisms revealed the expected in-out gradient, showing that species with high %GC (or high %AT) in their rRNA distribute more of these abundant nucleotides into the peripheral zones. This could be explained by the evolutionary rates of replacement of all nucleotides (A, C, G, T), because these latter rates are fastest at the periphery and slowest near the conserved core. As an overall explanation, we propose that when extrinsic factors (whole-genome nucleotide composition, or environmental temperature) demand the percentage of GC in the rRNA of a species be high or low, then the deep-lying zones are buffered against GC variation because they are the slowest to evolve. The deep, conserved zones are also the most involved in translation, hinting that stabilizing selection there prevents a high GC variability that would diminish LSU rRNA’s core functions. We found only a few domain-specific trends in rRNA-GC distribution, which relate to many Archaea living at high temperatures or to the highly complex genes and adaptations of Eukaryota. Use of rRNA sequences in molecular phylogenetic studies, for reconstructing the relationships of organisms across the tree of life, requires accurate models of how rRNA evolves. The demonstration that GC distributes in regular patterns across rRNA regions can improve these tree-reconstruction models in the future and should yield phylogenies of greater accuracy.

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