The tRNA Elbow in Structure, Recognition and Evolution

Abstract

Prominent in the L-shaped three-dimensional structure of tRNAs is the "elbow" where their two orthogonal helical stacks meet. It has a conserved structure arising from the interaction of the terminal loops of the D- and T-stem-loops, and presents to solution a flat face of a tertiary base pair between the D- and T-loops. In addition to the ribosome, which interacts with the elbow in all three of its tRNA binding sites, several cellular RNAs and many proteins are known to recognize the elbow. At least three classes of non-coding RNAs, namely 23S rRNA, ribonuclease P, and the T-box riboswitches, recognize the tRNA elbow employing an identical structural motif consisting of two interdigitated T-loops. In contrast, structural solutions to tRNA-elbow recognition by proteins are varied. Some enzymes responsible for post-transcriptional tRNA modification even disrupt the elbow structure in order to access their substrate nucleotides. The evolutionary origin of the elbow is mysterious, but, because it does not explicitly participate in the flow of genetic information, it has been proposed to be a late innovation. Regardless, it is biologically essential. Even some viruses that hijack the cellular machinery using tRNA decoys have convergently evolved near-perfect mimics of the tRNA elbow.

Keywords: RNA structure; T-loop; base stacking; convergent evolution; ribosome; tRNA elbow.

Figure 1

Structure of the tRNA elbow. (A) Schematic of the connectivity of tRNA. ASL, anticodon stem-loop. DSL, D-stem-loop. TSL, T-stem-loop. (B) Secondary structure of the yeast tRNA^Phe elbow. Non-canonical pairs between the D- and T-loops are depicted with Leontis-Westhof [29] symbols. Residue numbering reflects the tRNA convention. (C) Structure of the T-loop of yeast tRNA^Phe (PDB ID 1EHZ). Note the unstacked residue 56 corresponding to position 3 of the generalized T-loop, and the gap between residues 57 and 58, corresponding to positions 4 and 5 of the generalized T-loop. (D) Structure of the D-loop of yeast tRNA^Phe. Dihydrouridines are located at residues 16 and 17. (E) Interaction of D- and T-loops forms the elbow. Note inter-loop base pairs between residues 19 and 56, and intercalation of D-loop residue 18 into the T-loop. Structure figures were prepared with PyMol [30].

Figure 2

Interaction of the tRNA elbow with the ribosome. (A) Relative positions of the three classical state tRNAs from ribosome cocrystal structures. (PDB ID 4V6F). (B) Interaction of the tRNA elbow with helix 38 (the “A-site finger”). (PDB ID 4V6F) rRNA is in blue. (C) Interaction of the tRNA elbow with the L5 protein (cyan) in the P-site. (PDB ID 4V51). (D) Interaction of the tRNA elbow with the L1 stalk in the E-site. (PDB ID 4V4I). The two interdigitated T-loops of the L1 stalk are denoted T-Loop1 and T-Loop2 in the 5′ to 3′ direction.

Figure 3

Recognition of the tRNA elbow by the interdigitated T-loop motif. (A) The 5′ and 3′ interdigitated pentaloops of the ribosomal L1 stalk are colored red and cyan, respectively. The tRNA D- and T-loops are pale green and violet, respectively. (PDB ID 4V4I). (B) Structure of RNase P holoenzyme bound to pre-tRNA. (PDB ID 3Q1Q). (C) Structure of a glycine-specific T-box Stem I domain bound to its cognate tRNA^Gly. (PDB ID 4LCK). (D) Interdigitation of two head-to-tail pentanucleotide T-loops (red and cyan, respectively) forms a densely packed core structure. The five nucleotides that form each T-loop are numbered and the stacking gaps denoted by the rounded rectangles.

Figure 3

Recognition of the tRNA elbow by the interdigitated T-loop motif. (A) The 5′ and 3′ interdigitated pentaloops of the ribosomal L1 stalk are colored red and cyan, respectively. The tRNA D- and T-loops are pale green and violet, respectively. (PDB ID 4V4I). (B) Structure of RNase P holoenzyme bound to pre-tRNA. (PDB ID 3Q1Q). (C) Structure of a glycine-specific T-box Stem I domain bound to its cognate tRNA^Gly. (PDB ID 4LCK). (D) Interdigitation of two head-to-tail pentanucleotide T-loops (red and cyan, respectively) forms a densely packed core structure. The five nucleotides that form each T-loop are numbered and the stacking gaps denoted by the rounded rectangles.

Figure 4

Recognition of the tRNA elbow by tRNA-binding proteins. (A) Structure of LeuRS recognizing its cognate tRNA^Leu. (PDB ID 2V0G). (B) Structure of ValRS recognizing its cognate tRNA^Val. (PDB ID 1GAX). (C) Structure of bacterial amidotransferase GatCAB complexed with GluRS recognizing its cognate tRNA^Gln. (PDB ID 3AL0). (D) Structure of RNase Z recognizing pre-tRNA^Thr. (PDB ID 4GCW). (E) Structure of the dihydrouridine synthetase DusC bound to tRNA^Trp. (PDB ID 4YCP). (F) Model of pseudouridine synthase TruB bound to λ-form tRNA^Val based on its cocrystal structure in complex with a tRNA minihelix. (PDB ID 1K8W and 1J2B). (G) Structure of archaeosine transglycosylase ArcTGT bound to λ-form tRNA^Val (PDB ID 1J2B).