Molecular recognition of tRNA(Pro) by Escherichia coli proline-tRNA synthetase

We have investigated the molecular recognition of tRNA(Pro) by Escherichia coli proline tRNA synthetase (ProRS) in vitro using semi-synthetic tRNAs and site-directed mutagenesis of full-length tRNA transcripts. These studies have led to an improved understanding of how this class II synthetase interacts with its tRNA substrate. The ability to efficiently aminoacylate a tRNA(Pro) molecule assembled by annealing together a shorter, chemically synthesized oligonucleotide and a 3/4 tRNA prepared enzymatically, has facilitated the identification of RNA structural features that are critical for aminoacylation by ProRS. This approach has been successful using either a 3'-3/4 tRNA annealed to a 5'-oligonucleotide or a 5'-3/4 tRNA annealed to a 3'-oligonucleotide. These studies show that ProRS appears to be particularly sensitive to mutations that result in structural changes in the core region of tRNA(Pro). Moreover, the so-called "variable pocket" nucleotides appear to be dispensable for aminoacylation. We have also identified a specific 2'-hydroxyl-base interaction between the ribose of U8 and the 2-amino group of G46 that makes a thermodynamically significant contribution to tRNA(Pro) aminoacylation by E. coli ProRS.