The phylogenetically conserved doublet tertiary interaction in domain III of the large subunit rRNA is crucial for ribosomal protein binding.

Previous phylogenetic analysis of rRNA sequences for covariant base changes has identified approximately 20 potential tertiary interactions. One of these is present in domain III of the large subunit rRNA and consists of two adjacent Watson-Crick base pairs that, in Saccharomyces cerevisiae 26S rRNA, connect positions 1523 and 1524 to positions 1611 and 1612. This interaction would strongly affect the structure of an evolutionarily highly conserved region that acts as the binding site for the early-assembling ribosomal proteins L25 and EL23 of S. cerevisiae and Escherichia coli, respectively. To assess the functional importance of this tertiary interaction, we determined the ability of synthetically prepared S. cerevisiae ribosomal protein L25 to associate in vitro with synthetic 26S rRNA fragments containing sequence variations at positions 1523 and 1524 and/or positions 1611 and 1612. Mutations that prevent the formation of both base pairs abolished L25 binding completely, whereas the introduction of compensatory mutations fully restored protein binding. Disruption of only the U1524.A1611 pair reduced L25 binding to approximately 30% of the value shown by the wild-type 26S rRNA fragment, whereas disruption of the G1523.C1612 base pair resulted in almost complete loss of protein binding. These results strongly support the existence and functional importance of the proposed doublet tertiary interaction in domain III of the large subunit rRNA.