Rescuing an essential enzyme-RNA complex with a non-essential appended domain

Abstract

Certain protein-RNA complexes, such as synthetase-tRNA complexes, are essential for cell survival. These complexes are formed with a precise molecular fit along the interface of the reacting partners, and mutational analyses have shown that amino acid or nucleotide substitutions at the interface can be used to disrupt functional or repair non-functional complexes. In contrast, we demonstrate here a feature of a eukaryote system that rescues a disrupted complex without directly re-engineering the interface. The monomeric yeast Saccharomyces cerevisiae glutaminyl-tRNA synthetase, like several other class I eukaryote tRNA synthetases, has an active-site-containing 'body' that is closely homologous to its Escherichia coli relative, but is tagged at its N-terminus with a novel and dispensable appended domain whose role has been obscure. Because of differences between the yeast and E. coli glutamine tRNAs that presumably perturb the enzyme-tRNA interface, E. coli glutaminyl-tRNA synthetase does not charge yeast tRNA. However, linking the novel appended domain of the yeast to the E. coli enzyme enabled the E. coli protein to function as a yeast enzyme, in vitro and in vivo. The appended domain appears to contribute an RNA interaction that compensates for weak or poor complex formation. In eukaryotes, extra appended domains occur frequently in these proteins. These domains may be essential when there are conditions that would otherwise weaken or disrupt formation of a critical RNA-protein complex. They may also be adapted for other, specialized RNA-related functions in specific instances.