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, 4 (4), a003681

Evolution of Protein Synthesis From an RNA World

Affiliations

Evolution of Protein Synthesis From an RNA World

Harry F Noller. Cold Spring Harb Perspect Biol.

Abstract

Because of the molecular complexity of the ribosome and protein synthesis, it is a challenge to imagine how translation could have evolved from a primitive RNA World. Two specific suggestions are made here to help to address this, involving separate evolution of the peptidyl transferase and decoding functions. First, it is proposed that translation originally arose not to synthesize functional proteins, but to provide simple (perhaps random) peptides that bound to RNA, increasing its available structure space, and therefore its functional capabilities. Second, it is proposed that the decoding site of the ribosome evolved from a mechanism for duplication of RNA. This process involved homodimeric "duplicator RNAs," resembling the anticodon arms of tRNAs, which directed ligation of trinucleotides in response to an RNA template.

Figures

Figure 1.
Figure 1.
Cross-section of the crystal structure of the T. thermophilus 70S ribosome (Yusupov et al. 2001), with the 30S subunit on the left and the 50S subunit on the right. The locations of the peptidyl-tRNA (orange) at the subunit interface, the mRNA (green-yellow-red) wrapping around the neck of the 30S subunit, and a modeled α-helical nascent polypeptide chain (green) in the polypeptide exit tunnel are indicated. The 16S rRNA is shown in cyan, 23S rRNA in grey, 5S rRNA in grey-blue, 30S subunit proteins in dark blue, and 50S subunit proteins in magenta.
Figure 2.
Figure 2.
Interface and solvent views of the 30S and 50S subunits, as observed in the 70S ribosome crystal structure (Yusupov et al. 2001), showing the positions of the A-, P- and E-site tRNAs (yellow, orange, and red, respectively). Top, interface views of the 50S (left) and 30S (right) subunits, showing the relative absence of proteins surrounding the functional sites. Bottom, corresponding solvent surfaces of the subunits.
Figure 3.
Figure 3.
Steric minor-groove calibration of Watson-Crick codon-anticodon pairing by three conserved bases of 16S rRNA. (left) Contacts between G530, A1492, and A1493 of 16S rRNA and the codon-anticodon base pairs in the 30S A site (Ogle et al. 2001). (right) Type I and type II A-minor interactions (Nissen et al. 2001).
Figure 4.
Figure 4.
Duplicator RNA. (left) A schematic cartoon representing the structure of a duplicator RNA (dRNA) monomer, showing its two identity elements: A self-complementary tetramer tail and a degenerate anticodon triplet. There are 16 possible dRNAs. (right) A dRNA homodimer, formed by base pairing of its self-complementary tail. The wavy line indicates that other details of the structure between the anticodon and tail are not intended to be explicit.
Figure 5.
Figure 5.
Indirect templating of RNA duplication mediated by dRNA homodimers. One dRNA dimer (left) is bound to the last triplet (GAN) in the product RNA, stabilized by a structure resembling the 30S ribosomal P site (blue box). A second dRNA dimer (right), bound to the next (CCN) triplet in the template by pairing with one of its GGN anticodons, binds the incoming substrate CCN trimer via base pairing with its other GGN anticodon. Discrimination of correct pairing with the incoming substrate trimer is promoted by A-minor interactions by a structure resembling the 30S ribosomal A site (red box). Binding of the upper anticodon triplets to the template RNA also uses structures resembling the 30S A and P sites (not shown).
Figure 6.
Figure 6.
Influence of the HIV Tat peptide on the folding of TAR RNA (Puglisi et al. 1992). (A) Secondary structure of TAR RNA; (B) NMR structure of the free TAR RNA; (C) NMR structure of the TAR RNA bound to a nine-amino acid peptide from Tat protein or bound to a single argininamide (shown). The argininamide is shown in orange and the three-nucleotide bulge loop in dark blue.

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