Functional interactions by transfer RNAs in the ribosome

Abstract

Recent X-ray crystal structures of the ribosome have revolutionized the field by providing a much-needed structural framework to understand ribosome function. Indeed, the crystal structures rationalize much of the genetic and biochemical data that have been meticulously gathered over 50 years. Here, we focus on the interactions between tRNAs and the ribosome and describe some of the insights that the structures provide about the mechanism of translation. Both high-resolution structures and functional studies are essential for fully appreciating the complex process of protein synthesis.

Figure 1. Schematic illustration of the major steps in protein synthesis

In the initiation step of protein synthesis the 30S subunit (yellow) binds mRNA, initiator tRNA (purple stem-loop), IF1 (magenta), IF2 (cyan) and IF3 (dark green) before binding the 50S subunit (salmon). During the elongation cycle the 70S ribosome binds EF-Tu•GTP-tRNA ternary complex (pink and green stem-loop) and catalyze peptide bond formation. The mRNA-tRNAs are translocated by EF-G (blue). In the termination step, RF1 (light green) or RF2 recognize the stop codons and catalyze the release of the newly completed polypeptide (colored circles). RF1 and RF2 are removed from the ribosome by RF3 (purple). In the recycling step, the ribosome is dissociated into 30S and 50S subunits by the action of RRF (orange), EF-G and IF3 (see text for more details).

Figure 2. Interactions of P site tRNA with the ribosome

(A) Overview of the P site tRNA (magenta) interacting with bases in 16S rRNA (yellow), 23S rRNA (salmon) and proteins S9, S13, L5, L16, and L27 (orange tubes). Specific bases in the rRNAs are shown in cyan color and the mRNA is colored black. (B) Interactions between the anticodon arm of P site tRNA and the 30S subunit. (C) Interactions between the 3’ CCA end of P site tRNA and the 50S subunit.

Figure 3. Interactions of A site tRNA with the ribosome

(A) Overview of the A site tRNA (green) interacting with bases in 16S rRNA (yellow), 23S rRNA (salmon) and proteins S12, S13, L16, and L27 (orange tubes). Specific bases in the rRNAs are shown in red color and the mRNA is colored black. (B) Interactions between the anticodon arm of A site tRNA and the 30S subunit. (C) Interactions between the 3’ CCA end of A site tRNA and the 50S subunit.

Figure 4. Interactions of E site tRNA with the ribosome

(A) Overview of the E site tRNA (blue) interacting with bases in 16S rRNA (yellow), 23S rRNA (salmon) and proteins S7, S11, L1, L28, and L33 (orange tubes). Specific bases in the rRNAs are shown in violet color and the mRNA is colored black. (B) Interactions between the anticodon arm of E site tRNA and the 30S subunit. (C) Interactions between the 3’ CCA end of E site tRNA and the 50S subunit.