Figure 5 The two halves of contemporary tRNA. The "top half" of tRNA is structurally and functionally independent and may be more ancient than the "bottom half" of the molecule.

tRNA is an independent structural domain that is recognized by RNase P (McClain et al., 1987; Yuan and Altman, 1994), Tu (Rasmussen et al., 1990), tRNA synthetases (McClain, 1993; Schimmel et al., 1993; Saks et al., 1994), and perhaps even ribosomal RNA (Noller et al., 1992). The importance of this domain in almost all macromolecular interactions involving tRNA suggests that it is ancient, as does its structural independence from the bottom half of the molecule. Second, the ability of the cell to distinguish each tRNA from all the others—solving what is usually referred to as the tRNA identity problem—depends to a surprising extent on the identity of specific nucleotides in the top half of the molecule (McClain, 1993; Schimmel et al., 1993; Saks et al., 1994), including the "discriminator base" just inboard from the CCA terminus (Crothers et al., 1972). This suggests that the identity of some tRNAs, and perhaps the specificity of the cognate aminoacyl-tRNA synthetases, was established before the bottom half of tRNA was incorporated into the molecule. Whether the bottom half of tRNA arose as an expansion loop within the top half or as an independent structural and functional domain that was subsequently incorporated into the top half is a question that future work may be able to resolve.