The Universally Conserved Nucleotides of the Small Subunit Ribosomal RNAs

Abstract

The ribosomal RNAs, along with their substrates the transfer RNAs, contain the most highly conserved nucleotides in all of biology. We have assembled a database containing the aligned sequences of the rRNAs from the small ribosomal subunit (the16S-like rRNAs) from organisms that span the entire phylogenetic spectrum, to identify the nucleotides that are universally conserved. In the 16S-like rRNA, which in its simplest (bacterial and archaeal) forms has around 1500 nucleotides, 80 are absolutely invariant, and another 65 have differences in only a single species out of the 1961 in our alignment. We examine the positions and detailed interactions of these 145 nucleotides in high-resolution structures of ribosome functional complexes. Nearly all of these nucleotides are exposed on the subunit interface surface of the small subunit, where the functional processes of the ribosome take place. However, only 42 of them have been directly implicated in specific ribosomal functions, such as contacting the tRNAs, mRNA and elongation factors. Another 43 invariant nucleotides appear to constrain the positions and orientations of those nucleotides that are directly involved in function. Yet others are parts of unusual non-canonical tertiary structures that may uniquely allow correct folding of the rRNA to form a functional ribosome. However, there remain 60 nucleotides whose universal conservation is unexplained, serving as a metric for the incompleteness of our understanding of ribosome structure and function.