tRNA evolution from the proto-tRNA minihelix world

Abstract

Multiple models have been advanced for the evolution of cloverleaf tRNA. Here, the conserved archaeal tRNA core (75-nt) is posited to have evolved from ligation of three proto-tRNA minihelices (31-nt) and two-symmetrical 9-nt deletions within joined acceptor stems (93 - 18 = 75-nt). The primary evidence for this conclusion is that the 5-nt stem 7-nt anticodon loop and the 5-nt stem 7-nt T loop are structurally homologous and related by coding sequence. We posit that the D loop was generated from a third minihelix (31-nt) in which the stem and loop became rearranged after 9-nt acceptor stem deletions and cloverleaf folding. The most 3´-5-nt segment of the D loop and the 5-nt V loop are apparent remnants of the joined acceptor stems (14 - 9 = 5-nt). Before refolding in the tRNA cloverleaf, we posit that the 3'-5-nt segment of the D loop and the 5-nt V loop were paired, and, in the tRNA cloverleaf, frequent pairing of positions 29 (D loop) and 47 (V loop) remains (numbered on a 75-nt tRNA cloverleaf core). Amazingly, after >3.5 billion years of evolutionary pressure on the tRNA cloverleaf structure, a model can be constructed that convincingly describes the genesis of 75/75-nt conserved archaeal tRNA core positions. Judging from the tRNA structure, cloverleaf tRNA appears to represent at least a second-generation scheme (and possibly a third-generation scheme) that replaced a robust 31-nt minihelix protein-coding system, evidence for which is preserved in the cloverleaf structure. Understanding tRNA evolution provides insights into ribosome and rRNA evolution.

Keywords: D loop; T loop; V loop; acceptor stems; anticodon loop; proto-tRNA minihelices; rRNA evolution; ribosome evolution; tRNA evolution; tRNA microhelices; tRNA structure.

Figure 1.

A model for tRNA evolution. (A) A Sulfolobus solfataricus typical tRNA structure (similar to a consensus sequence). The numbering system is based on a 75-nt tRNA core. (B) The model. 3-31-nt minihelices are ligated. A symmetrical 9-nt deletion occurs within two-ligated acceptor stems. Green: 7-nt acceptor stems; blue: 5-nt relics of acceptor stems after deletions; red + yellow: 17-nt microhelices; yellow: anticodons; no highlight: 9-nt symmetrical deletions.

Figure 2.

The T loop and the Ac loop are homologs. (A) The tRNA cloverleaf includes two related microhelices: the T loop and Ac loop (red). (B) An overlay of the 17-nt anticodon loop (7-nt) and stem (2 × 5-nt) (red) and the 17-nt T loop (7-nt) and stem (2 × 5-nt) (blue) shows remarkable structural similarity. Because of a 3-nt deletion in the D loop, numbering from within the D loop for S. cerevisiae tRNA^PHE is reduced by 3-nt compared to the model for 75-nt tRNA evolution (see Fig. 1). In the sequence, yellow shading indicates DNA-coding identity and green shading similarity. The anticodon is bold and underlined. Five indicates 5-methyl-cytosine. P is pseudo-uridine. One and Y are adenosine derivatives. O is a uracil or a guanosine derivative. Blue circles in (B) indicate anticodon positions.

Figure 3.

A logo comparison of archaeal tRNAs is shown. The left panel represents 500 archaeal tRNAs. The right panel represents 104/500 total archaeal tRNAs selected for having no deletions in the D loop (104 tRNAs). The numbering is based on the 75-nt tRNA model (Fig. 1).

Figure 4.

Logo comparisons of archaeal and bacterial tRNA^GLY with GCC anticodons.

Figure 5.

Logo comparisons of archaeal Sulfolobus tRNAs (139 tRNAs from three Sulfolobus species).

Figure 6.

Fitting the model to the structure of the tRNA cloverleaf. (A) Cloverleaf tRNA numbered according to the 75-nt model. Coloring is as in Fig. 1B, except the D loop microhelix is colored orange instead of red to emphasize that this segment of the D loop is a refolded 17-nt microhelix. 7-nt acceptor stems (As) are green (1–7 and 69–75). The 3′-CCA end is green. 5-nt acceptor stem relics (D loop (25–29); V loop (47–51)) are blue. 17-nt microhelices are red and yellow (Ac loop (30–46); T loop (52–68)) or orange and yellow (D loop (8–24)). Anticodon derived sequences are yellow. (B) A 17-nt microhelix. (C) A 31-nt minihelix with a 3´-CCA.

Figure 7.

A mechanism to generate complex RNAs such as cloverleaf tRNA and proto-rRNAs via replication of 31-nt minihelices (MH). MH1 and MH1´ are complements.

Figure 8.

A proposed model for mRNA-encoded translation in the 31-nt proto-tRNA minihelix world. A similar model, with expected lower fidelity (no acceptor stems), could be constructed based on amino-acylated 17-nt microhelices with 3´-CCA ends.