Commentary: History of the ribosome and the origin of translation - PubMed (original) (raw)

Figure 1

Fact checking the insertion fingerprint (IF) evidence of ribosomal evolution. (A) Given a model of branch-to-trunk outward growth of rRNA molecules by insertion of a branch helix (B) into a junction (node) between two trunk helices (T) that are coaxially stacked, the unfolding molecular structure resembles a rooted phylogenetic tree. Tree branches are helical stem structures and nodes (splits) of trees are junctions of rRNA. Character state change from T to B in the derived branch of the tree is made explicit using a standard cladistic notation. (B) Trees describing the evolution of rRNA molecules show how structures (branches of trees) grow by insertions, leaving behind IFs (nodes illustrated with circles). Only coaxially stacked helices and its tree branch correlates are shown. Evidence of inward growth homoplasies (black nodes describing IF “reversals”) indicate other possible molecular origins (see B,C), which challenge the validity of both the generative evolutionary algorithm and the resulting trees. The star indicates the approximate location of the base of the molecules, with their 5′ and 3′ termini. The arrow indicates the direction of time. Some junctions are labeled with the names of IFs with incorrect branch-to-trunk assignments and notable subtending helices that play functional and structural roles. (C) Example of an inward growth IF claimed to represent an insertion of branch h33-h34 onto trunk h32 of the 16S rRNA molecule (see aes10/11 in Table S2 of Petrov et al., 2015). The atomic structural model shows instead that coaxially stacked h33-h34 helices (colored red) actually make the trunk of this typical “family B” three-way junction. A radial view reveals the coaxially stacked helical structures, which hold functionally important pivot points. The IF (labeled B17) is visible in the molecular side view. The inset describes a network interaction diagram of the same junction in a different structure, again showing the h33-h34 stacked helices (redrawn from Lescoute and Westhof, 2006). Any claim that the coaxially stacked h33-h34 is a branch that “caps” an older h32 trunk is ad hoc, erases the original IF signature, and introduces a serious ambiguity (see Figure 10C and discussion in Caetano-Anollés and Caetano-Anollés, 2015a), which defeats the entire algorithmic implementation. (D) Road blocks to outward growth create multiple ribosomal origins. An examination of rRNA junctions (Caetano-Anollés and Caetano-Anollés, 2015a,b) shows 17 homoplasious IFs (inward growth IFs labeled B1–B17) that create 19 possible structural origins (numbered and colored substructures) in large and small subunit rRNA. The table describes helices in trunks and branches of IF regions. In particular, inward growth IF B11 effectively splits the origin of the PTC in two, and together with B9 and B10 cannot leave IF signatures (see Figure 9 in Caetano-Anollés and Caetano-Anollés, 2015a). B2, B3, B5, B8, and B16 affect inferences related to subunit co-evolution. B6 splits domain III in its two subdomains (Lanier et al., 2016), which correspond to substructures 8 and 9. Substructure 15 (in gray) contains the proposed central core (domain A) of 16S rRNA, which bares structural similarity to the anticodon stem of tRNAVal but little resemblance to its central tRNA junction (Gulen et al., 2016). Similarities are incompatible with the Petrov et al. (2015) chronology.