Bringing order to translation: the contributions of transfer RNA anticodon-domain modifications

Abstract

The biosynthesis of RNA includes its post-transcriptional modifications, and the crucial functions of these modifications have supported their conservation within all three kingdoms. For example, the modifications located within or adjacent to the anticodon of the transfer RNA (tRNA) enhance the accuracy of codon binding, maintain the translational reading frame and enable translocation of the tRNA from the A-site to the P-site of the ribosome. Although composed of different chemistries, the more than 70 known modifications of tRNA have in common their ability to reduce conformational dynamics, and to bring order to the internal loops and hairpin structures of RNA. The modified nucleosides of the anticodon domain of tRNA restrict its dynamics and shape its architecture; therefore, the need of the ribosome to constrain or remodel each tRNA to fit the decoding site is diminished. This concept reduces an entropic penalty for translation and provides a physicochemical basis for the conservation of RNA modifications in general.

Figure 1

Universal genetic code. The 64 codes are associated with the transfer RNA (tRNA) modifications that are important for decoding and/or translocation. Twofold degenerate amino-acid codes are highlighted in grey and fourfold degenerate codes are highlighted in tan. Amino acids with six codons are highlighted in blue. The threefold degenerate codons of Ile are highlighted in green, whereas the single codons of Met and Trp are highlighted in white. The three stop codons are highlighted in orange. Non-canonical codon use by some organisms and the mitochondrion is shown by using a small font for the amino acids (blue) or translational stop codons (red). The modified nucleoside abbreviations are defined in the text. Selenocysteine (Sec) and pyrrolysine (Pyl) codons are denoted in white. In the mitochondrion, tRNA^Met responds to AUG and AUA, which is not used as an Ile codon (Agris et al, 2007; Szymański & Barciszewski, 2007; Björk et al, 1987).

Figure 2

Modifications order the anticodon stem and loop domain of transfer RNA. (A) The secondary structure and tertiary folding of cytoplasmic transfer RNAs (tRNAs). The physical and functional domains of the tRNA structure are the amino-acid-accepting stem (AAS), and the stem and loop domains designated dihydrouridine (DSL), anticodon (ASL), variable (VL) and thymidine (TSL). tRNA can fold into its tertiary structure before modification. pre-tRNA will fold with the help of Mg²⁺ and the aid of the most conserved of the modifications (Helm, 2006; Nobles et al, 2001). These modifications occur outside of the anticodon domain. (B) Modification of the anticodon stem and loop domain (ASL) of tRNA and its effect on dynamics. The ASL (left) is unmodified and disordered. Extensive modifications at wobble position 34 and purine 37 restrain the dynamics of the anticodon loop, and direct its conformation towards that of the canonical structure shown on the right.

Figure 3

Anticodon recognition and transfer RNA accommodation on the ribosome. (A) The complex of aminoacylated transfer RNA (tRNA) bound to elongation factor/GTP enters the A-site (left). The anticodon of the tRNA makes contact with the messenger RNA (mRNA) codon; however, the tRNA with a disordered anticodon stem and loop domain (ASL) cannot contact the codon correctly and is rejected by the ribosome (right). An aminoacyl-tRNA having successfully received the growing peptide now occupies the P-site, while the tRNA from which it received the nascent protein occupies the ribosome's exit or E-site. (B) Accommodation of aminoacyl-tRNA in the A-site. A complex of aminoacylated tRNA with elongation factor and GTP enters the A-site (left). Modifications have restricted the dynamics and shaped the architecture of the ASL of the tRNA. With recognition that the tRNA has the correct anticodon, the 16S ribosomal RNA (rRNA) nucleosides A1492, A1493 and G530 hydrogen bond to the backbones of the mRNA and the anticodon. The small ribosomal subunit and the tRNA undergo conformational changes. The conformation of the tRNA above the ASL changes, but the architecture of the ASL and its interaction with the codon remain unchanged (right). GTP is hydrolysed and the elongation factor-GDP leaves the ribosome.

Paul F. Agris