Ribosomal RNAs in both prokaryotes and eukaryotes feature numerous repeats of three or more nucleotides with the same nucleobase (homoiterons). In prokaryotes these repeats are much more frequent in thermophile compared to mesophile or psychrophile species, and have similar frequency in both large RNAs. These features point to use of prokaryotic homoiterons in stabilization of both ribosomal subunits. The two large RNAs of eukaryotic cytoplasmic ribosomes have expanded to a different degree across the evolutionary ladder. The big RNA of the larger subunit (60S LSU) evolved expansion segments of up to 2400 nucleotides, and the smaller subunit (40S SSU) RNA acquired expansion segments of not more than 700 nucleotides. In the examined eukaryotes abundance of rRNA homoiterons generally follows size and nucleotide bias of the expansion segments, and increases with GC content and especially with phylogenetic rank. Both the nucleotide bias and frequency of homoiterons are much larger in metazoan and angiosperm LSU compared to the respective SSU RNAs. This is especially pronounced in the tetrapod vertebrates and seems to culminate in the hominid mammals. The stability of secondary structure in polyribonucleotides would significantly connect to GC content, and should also relate to G and C homoiteron content. RNA modeling points to considerable presence of homoiteron-rich double-stranded segments especially in vertebrate LSU RNAs, and homoiterons with four or more nucleotides in the vertebrate and angiosperm LSU RNAs are largely confined to the expansion segments. These features could mainly relate to protein export function and attachment of LSU to endoplasmic reticulum and other subcellular networks.
Keywords: ES, an expansion segment; LSU, large cytoplasmic ribosome subunit (50S in prokaryotes and archaea, 60S in eukaryotes); PCN, homoionic motifs with ⩾3% and ⩾50% ionic residues, found especially in Polynucleotide-binding proteins, Carrier proteins and Nuclear localization signals; RNA expansion segment; RNA nucleotide bias; RNA nucleotide repeat; SSU, small cytoplasmic ribosome subunit (30S in prokaryotes and archaea, 40S in eukaryotes); XN or NX, [X = a number] a nucleotide unit with same nucleobases (homoiteron), such as 4U or U4 for UUUU; aa, amino acid residues; mRNP, messenger ribonucleoprotein; ncRNA, non-coding RNA; nt, nucleotides; u, nucleotide unit.