Evolution of the ribosome at atomic resolution

Abstract

The origins and evolution of the ribosome, 3-4 billion years ago, remain imprinted in the biochemistry of extant life and in the structure of the ribosome. Processes of ribosomal RNA (rRNA) expansion can be "observed" by comparing 3D rRNA structures of bacteria (small), yeast (medium), and metazoans (large). rRNA size correlates well with species complexity. Differences in ribosomes across species reveal that rRNA expansion segments have been added to rRNAs without perturbing the preexisting core. Here we show that rRNA growth occurs by a limited number of processes that include inserting a branch helix onto a preexisting trunk helix and elongation of a helix. rRNA expansions can leave distinctive atomic resolution fingerprints, which we call "insertion fingerprints." Observation of insertion fingerprints in the ribosomal common core allows identification of probable ancestral expansion segments. Conceptually reversing these expansions allows extrapolation backward in time to generate models of primordial ribosomes. The approach presented here provides insight to the structure of pre-last universal common ancestor rRNAs and the subsequent expansions that shaped the peptidyl transferase center and the conserved core. We infer distinct phases of ribosomal evolution through which ribosomal particles evolve, acquiring coding and translocation, and extending and elaborating the exit tunnel.

Keywords: C value; RNA evolution; origin of life; phylogeny; translation.

Fig. 1.

Phylogram indicating the sizes of LSU rRNAs and the sizes of genomes. Circle radii are proportional to total length of LSU rRNAs. Circles are colored by C value, which is genome size measured in picograms. Two species here have anomalously high C values and are colored in black (Protopterus aethiopicus: C-value 133 pg, and Picea glauca: C-value 24 pg). The sizes of archaeal and bacterial LSU rRNAs are highly restrained, so they are represented by just one species each. The phylogram was computed using sTOL (37) and visualized with ITOL (38). Three species (P. aethiopicus, Adineta vaga, P. glauca) were manually added to the phylogram, because the genomes are not sufficiently annotated for sTOL analysis.

Fig. 2.

LSU rRNA secondary structures. (A) E. coli, (B) S. cerevisiae, and (C) H. sapiens. The color indicates the proximity in three dimensions to the site of peptidyl transfer. Blue is close to the site of peptidyl transfer and red is remote. In the secondary structures, the sites of expansion from E. coli to S. cerevisiae and from S. cerevisiae to H. sapiens are marked by arrows. Nucleotides that were not experimentally resolved in three dimensions are gray on the secondary structures.

Fig. 3.

The evolution of helix 25/ES 7 shows serial accretion of rRNA onto a frozen core. This image illustrates at the atomic level how helix 25 of the LSU rRNA grew from a small stem loop in the common core into a large rRNA domain in metazoans. Each accretion step adds to the previous rRNA core but leaves the core unaltered. Common ancestors, as defined in Fig. 1, are indicated. Pairs of structures are superimposed to illustrate the differences and to demonstrate how new rRNA accretes with preservation of the ancestral core rRNA. Each structure is experimentally determined by X-ray diffraction or Cryo-EM.

Fig. 4.

rRNA expansion elements in two and three dimensions. (A) Helix 52 is expanded by insertion. (B) Helix 38 is expanded by insertion. (C) Helix 101 is expanded by elongation. The secondary structure of the LSU common core rRNA, represented by that of E. coli (34), is a gray line at the center of the figure. Selected regions where the E. coli rRNA has been expanded to give the S. cerevisiae rRNA are enlarged. In the enlargements, the rRNA is blue for E. coli and red for S. cerevisiae, except that expansion elements of S. cerevisiae rRNA are green. These observed expansion processes, from blue rRNA to red/green rRNA, are symbolized by red arrows. Superimposed pre- and postexpanded rRNAs indicate trunk (old) and branch (new) elements. Insertion fingerprints, where trunk meets branch, are highlighted by gray circles. E. coli nucleotide numbers are provided, with S. cerevisiae numbering in parentheses.

Fig. 5.

Origins and evolution of the PTC. Trunk rRNA is shown before and after insertion of branch helix. (A) AES 1 (red) is expanded by insertion of AES 2 (teal). (B) AES 1 is expanded by insertion of AES 3 (blue). (C) AES 3 is expanded by insertion of AES 4 (green). (D) The secondary structure of AESs 1–5, which form the PTC and the exit pore (helices 74, 80, 89, 90, and 91–93). The ends of AES 2 are located in direct proximity to each other in three dimensions, indicated by a dashed line in the secondary structure. (E) AES 3 is expanded by insertion of AES 5 (gold). (F) The 3D structure of AESs 1–5, colored as in A–E. In each case, the before state was computationally modeled by removing the branch helix and sealing the trunk using energy minimization protocols. Positions of the P loop, the A loop, and the exit pore are marked. Enlarged and more detailed representations of the structures of AESs 1–5 are available in SI Appendix, Figs. S6–S9.

Fig. 6.

rRNA evolution mapped onto the LSU rRNA secondary structure. The common core is built up in six phases, by stepwise addition of ancestral expansion segments at sites marked by insertion fingerprints. (A) Each AES is individually colored and labeled by temporal number. AES colors are arbitrary, chosen to distinguish the expansions, such that no AES is the color of its neighbor. (B) Accretion of ancestral and eukaryotic expansion segments is distributed into eight phases, associated with ribosomal functions. Phase 1, rudimentary binding and catalysis (dark blue); phase 2, maturation of the PTC and exit pore (light blue); phase 3, early tunnel extension (green); phase 4, acquisition of the SSU interface (yellow); phase 5, acquisition of translocation function (orange); phase 6, late tunnel extension (red). Some AESs appear to be discontinuous on the secondary structure and so are labeled twice. A description of each AES and their partitioning into phases is given in SI Appendix, Table S3. The 3D structure of each phase is shown in SI Appendix, Fig. S11.