The specific interaction between aminoacyl-tRNAs and elongation factor Tu

Abstract

EF-Tu couples the hydrolysis of GTP with the accurate delivery of aminoacyl-tRNAs (aa-tRNAs) into the encoded ribosomal A site. The well-studied catalytic cycle of EF-Tu (Figure 1) can be subdivided into five phases: (1) the binding of EF-Tu•GTP to elongator aa-tRNAs; (2) the binding of the resulting ternary complex to the ribosomal A/T site where codon sampling occurs; (3) a conformational change of both the ribosome and the ternary complex with subsequent hydrolysis of GTP; (4) disruption of the ternary complex with release of phosphate, accommodation of the aa-tRNA into the A site, and release of EF-Tu•GDP from the ribosome; and (5) GDP-GTP exchange catalyzed by EF-Ts. Many of these phases have been dissected into several discrete steps using a variety of biochemical and biophysical methods (Pape et al., 1998; Gromadski et al., 2002; Blanchard et al., 2004). The mechanistic details of this EF-Tu-dependent decoding pathway are the focus of several articles in this volume. Here we discuss how the thermodynamic details of the interaction between EF-Tu and aa-tRNA differ for each tRNA species. We will summarize data showing that the sequence of three base pairs in the T stem of tRNA “tunes” its affinity for EF-Tu in a way that compensates for the variable contribution of the esterified amino acid to the overall binding affinity. This ensures that any correctly aminoacylated tRNA can initially bind to EF-Tu•GTP tightly enough for delivery to the ribosome but weakly enough that it can be released from EF-Tu•GDP during decoding. It appears that this sequence-specific tuning is highly conserved in bacteria and can largely explain the complex pattern of sequence conservation in the T stems of all bacterial tRNAs.