Ancestral Interactions of Ribosomal RNA and Ribosomal Proteins

Abstract

We have proposed that the ancient ribosome increased in size during early evolution by addition of small folding-competent RNAs. In this Accretion Model, small RNAs and peptides were subsumed onto subunit surfaces, gradually encasing and freezing previously acquired components. The model predicts that appropriate rRNA fragments have inherited local autonomy of folding and local autonomy of assembly with ribosomal proteins (rProteins), and that the rProtein and rRNA are co-chaperones. To test these predictions, we investigate the rRNA interactions of rProtein uL23 and its tail, uL23, which is a β-hairpin that penetrates deep into the core of the large ribosomal subunit. In the assembled ribosome, uL23 associates with Domain III of the rRNA and a subdomain called "DIII". Here using band shift assays, fluorescence Job plots, and yeast three-hybrid assays, we investigate the interactions of rProtein uL23 and its tail with Domain III and with DIII rRNA. We observe rRNA-uL23 complexes in the absence of Mg ions and rRNA-uL23 (n > 1) complexes in the presence of Mg ions. By contrast, the intact uL23 rProtein binds in slightly anticooperative complexes of various stoichiometries. The globular and tail regions of rProtein uL23 are distinctive in their folding behaviors and the ion dependences of their association with rRNA. For the globular region of the rProtein, folding is independent of rRNA, and rRNA association is predominantly by nonelectrostatic mechanisms. For the tail region of the protein, folding requires rRNA, and association is predominantly by electrostatic mechanisms. We believe these protein capabilities could have roots in ancient evolution and could be mechanistically important in co-chaperoning the assembly of the ribosome.

Lipid vesicles chaperone an encapsulated RNA aptamer

“…To the extent that fitness depends on proper folding, encapsulation would also ‘flatten’ the fitness landscape, permitting greater sequence diversity. The importance of chaperone-like activity has been emphasized in the early co-evolution of ribosomal RNA and protein 73 . Our results suggest that encapsulation could act as a primitive chaperone for RNA, favoring folded structures inside a protocell.…”

Multidomain ribosomal protein trees and the planctobacterial origin of neomura (eukaryotes, archaebacteria)

“…Such a piecemeal neomuran RP changeover is mechanistically much more plausible than assuming that LUCA had only the 34 universal RPs and eubacteria evolved 23 and neomura 33 unique RPs simultaneously as each diverged from an imaginary ancestor positioned on the neomuran stem as Klein et al (2004) and Forterre (2015) speculated. More likely, the first ribosomes had much smaller rRNAs with stabilising cations but no RPs, the large subunit being a small self-folding peptidyl transferase core and as soon as translation and the genetic code evolved crudely, extra RNA helices and associated RPs were added simultaneously to produce the complete cenancestral eubacterial ribosome (Lanier et al 2017;Petrov et al 2015). That accretionary expansion to a full eubacterial ribosome with 57 RPs involved coevolution of rRNA helices and RPs and must have been complete before LUCA.…”

Deducing putative ancestral forms of GNRA/receptor interactions from the ribosome

“…We hypothesized that ancestral forms of the ribosome likely relied on more stable RNA/RNA interactions for folding and assembling into their native structures. Indeed, the L39/H89 interaction might have evolved through time to become dependent on additional factors like proteins and/or post-transcriptional modifications within the context of the ribosome (8,13,26). Therefore, an outstanding question is whether stable and more ancestral versions of this universally conserved ribosomal interaction can be recovered by taking advantage of the present structural knowledge of RNA, and more specifically, GNRA/receptor interaction.…”