We present a molecular-level model for the origin and evolution of the translation system, using a 3D comparative method. In this model, the ribosome evolved by accretion, recursively adding expansion segments, iteratively growing, subsuming, and freezing the rRNA. Functions of expansion segments in the ancestral ribosome are assigned by correspondence with their functions in the extant ribosome. The model explains the evolution of the large ribosomal subunit, the small ribosomal subunit, tRNA, and mRNA. Prokaryotic ribosomes evolved in six phases, sequentially acquiring capabilities for RNA folding, catalysis, subunit association, correlated evolution, decoding, energy-driven translocation, and surface proteinization. Two additional phases exclusive to eukaryotes led to tentacle-like rRNA expansions. In this model, ribosomal proteinization was a driving force for the broad adoption of proteins in other biological processes. The exit tunnel was clearly a central theme of all phases of ribosomal evolution and was continuously extended and rigidified. In the primitive noncoding ribosome, proto-mRNA and the small ribosomal subunit acted as cofactors, positioning the activated ends of tRNAs within the peptidyl transferase center. This association linked the evolution of the large and small ribosomal subunits, protomRNA, and tRNA.RNA evolution | translation | origin of life | A-minor interactions T he ribosome retains interpretable molecular records of a world of primordial molecules (1) from around 4 billion years ago (2-9). The records are maintained in rRNA secondary and 3D structures, which are fully conserved throughout the tree of life, and in rRNA sequences, which are more variable (SI Appendix, Fig. S1). Here we use information within ribosomes from each major branch of the tree of life to reconstruct much of the emergence of the universal translational machinery. Large Ribosomal Subunit EvolutionPreviously, we reported a 3D comparative method that revealed a molecular level chronology of the evolution of the large ribosomal subunit (LSU) rRNA (10). Insertion fingerprints are evident when comparing 3D structures of LSU rRNAs of various sizes from various species. These insertion fingerprints mark sites where rRNA expands, recording growth steps on a molecular level.Within the common core of the LSU rRNA, insertion fingerprints were used to identify ancient growth sites. We showed that insertion fingerprints provide a roadmap from the first steps in the formation of the peptidyl transferase center (PTC) (10) located in the ancient heart of the LSU (2-6), culminating in the common core.Small Ribosomal Subunit, LSU, tRNA, and mRNA Evolution Here, using the 3D comparative method, we establish a comprehensive and coherent model for the evolution of the entire ribosome. This model covers the LSU rRNA, small ribosomal subunit (SSU) rRNA, tRNA, and mRNA. The evolution of each of these components is reconciled at the molecular level to a common chronology. This evolutionary model, which we call the "accretion model," ...

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.RNA evolution | C value | origin of life | translation | phylogeny T he translation system, one of life's universal processes, synthesizes all coded protein in living systems. Our understanding of translation has advanced over the last decade and a half with the explosion in sequencing data and by the determination of 3D structures (1-4). X-ray crystallography and cryoelectron microscopy (cryo-EM) have provided atomic resolution structures of ribosomes from all three domains of life. Eukaryotic ribosomal structures are now available from protists (5), fungi (6), plants (7), insects, and humans (8). Here we describe an atomic level model of the evolution of ribosomal RNA (rRNA) from the large ribosomal subunit (LSU). Our evolutionary model is grounded in patterns of rRNA growth in relatively recent ribosomal expansions, for which there is an extensive, atomicresolution record.The common core LSU rRNA (9, 10), which is approximated here by the rRNA of Escherichia coli, is conserved over the entire phylogenetic tree, in sequence, and especially in secondary structure (11) and 3D structure (12). By contrast, the surface regions and the sizes of ribosomes are variable (13,14). Most of the size variability is found in eukaryotic LSUs (Fig. 1). The integrated rRNA size in the LSU follows the trend Bacteria ≤ Archaea < Eukarya. The added rRNA in eukaryotes interacts with eukaryotic-specific proteins (5, 8, 9) (SI Appendix, Fig. S1 and Dataset S1).Bacterial and archaeal LSU rRNAs are composed entirely of the common core, with only subtle deviations from it. By contrast, eukaryotic LSU rRNAs are expanded beyond the common core. Sacccharomyce...

Mitochondrial ribosomes (mitoribosomes) are essential components of all mitochondria that synthesize proteins encoded by the mitochondrial genome. Unlike other ribosomes, mitoribosomes are highly variable across species. The basis for this diversity is not known. Here, we examine the composition and evolutionary history of mitoribosomes across the phylogenetic tree by combining three-dimensional structural information with a comparative analysis of the secondary structures of mitochondrial rRNAs (mt-rRNAs) and available proteomic data. We generate a map of the acquisition of structural variation and reconstruct the fundamental stages that shaped the evolution of the mitoribosomal large subunit and led to this diversity. Our analysis suggests a critical role for ablation and expansion of rapidly evolving mt-rRNA. These changes cause structural instabilities that are “patched” by the acquisition of pre-existing compensatory elements, thus providing opportunities for rapid evolution. This mechanism underlies the incorporation of mt-tRNA into the central protuberance of the mammalian mitoribosome, and the altered path of the polypeptide exit tunnel of the yeast mitoribosome. We propose that since the toolkits of elements utilized for structural patching differ between mitochondria of different species, it fosters the growing divergence of mitoribosomes.

We describe a case of relapsing babesiosis in an immunocompromised patient. A point mutation in the Babesia microti 23S rRNA gene predicted resistance to azithromycin and clindamycin whereas an amino acid change in the parasite cytochrome b predicted resistance to atovaquone. Following initiation of tafenoquine, symptoms and parasitemia resolved.

The assembled bacterial ribosome contains around 50 proteins and many counterions. Here, focusing on rRNA from the large ribosomal subunit, we demonstrate that Mg 2+ causes structural collapse in the absence of ribosomal proteins. The collapsed rRNA forms many native-like RNA-RNA interactions, similar to those observed in the assembled ribosome. We assayed rRNA structure by chemical footprinting in the presence and absence of Mg 2+. Our results indicate that Mg 2+ -dependent conformational change is focused in nonhelical regions, consistent with tertiary interactions. In the presence of Mg 2+ , the large subunit rRNA adopts a state that includes the core inter-domain architecture of the assembled ribosome. We infer that the rRNA-Mg 2+ state represents the core architecture of the LSU which, while not catalytically active, positions the residues of the LSU rRNA in such a way as to promote native interactions with rProteins to ultimately form a functional LSU.