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History of the Ribosome and the Origin of Translation

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History of the Ribosome and the Origin of Translation History of the ribosome and the origin of translation Anton S. Petrova,1, Burak Gulena, Ashlyn M. Norrisa, Nicholas A. Kovacsa, Chad R. Berniera, Kathryn A. Laniera, George E. Foxb, Stephen C. Harveyc, Roger M. Wartellc, Nicholas V. Huda, and Loren Dean Williamsa,1 aSchool of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332; bDepartment of Biology and Biochemistry, University of Houston, Houston, TX, 77204; and cSchool of Biology, Georgia Institute of Technology, Atlanta, GA 30332 Edited by David M. Hillis, The University of Texas at Austin, Austin, TX, and approved November 6, 2015 (received for review May 18, 2015) We present a molecular-level model for the origin and evolution of building up of the functional centers, proceeds to the establishment the translation system, using a 3D comparative method. In this model, of the common core, and continues to the development of large the ribosome evolved by accretion, recursively adding expansion metazoan rRNAs. segments, iteratively growing, subsuming, and freezing the rRNA. Incremental evolution of function is mapped out by stepwise Functions of expansion segments in the ancestral ribosome are accretion of rRNA. In the extant ribosome, specific segments of assigned by correspondence with their functions in the extant rRNA perform specific functions including peptidyl transfer, ribosome. The model explains the evolution of the large ribosomal subunit association, decoding, and energy-driven translocation subunit, the small ribosomal subunit, tRNA, and mRNA. Prokaryotic (11). The model assumes that the correlations of rRNA segments ribosomes evolved in six phases, sequentially acquiring capabilities with their functions have been reasonably maintained over the for RNA folding, catalysis, subunit association, correlated evolution, broad course of ribosomal evolution. Therefore the model maps decoding, energy-driven translocation, and surface proteinization. out the time course of acquisition of function. Breadth of function Two additional phases exclusive to eukaryotes led to tentacle-like increased as the ribosome grew in size. rRNA expansions. In this model, ribosomal proteinization was a driving force for the broad adoption of proteins in other biological rRNA Variation processes. The exit tunnel was clearly a central theme of all phases of Expansion segments (“ES” indicates LSU expansion segments, ribosomal evolution and was continuously extended and rigidified. In “ ” the primitive noncoding ribosome, proto-mRNA and the small and es indicates SSU expansion segments) (7, 8, 12, 13) are ribosomal subunit acted as cofactors, positioning the activated ends small, folding-competent RNA fragments that are inserted into of tRNAs within the peptidyl transferase center. This association common core rRNA over evolution, increasing rRNA length linked the evolution of the large and small ribosomal subunits, proto- without substantially perturbing the structure of the common mRNA, and tRNA. core. Recursive insertion of expansion segments leads to varia- tion in the length of rRNAs. In extant species, rRNA lengths RNA evolution | translation | origin of life | A-minor interactions vary according to well-defined rules. (i) rRNA length tends to increase from bacteria/archaea, which approximate the common he ribosome retains interpretable molecular records of a world of core, to protists, to metazoa (9, 10). (ii) Size variation is signif- Tprimordial molecules (1) from around 4 billion years ago (2–9). icantly greater in eukaryotes than in prokaryotes and in LSU The records are maintained in rRNA secondary and 3D structures, rRNAs than in SSU rRNAs (8). (iii) Variation is focused at a few which are fully conserved throughout the tree of life, and in rRNA specific sites of the common core (7–10, 14, 15). (iv) Variation is sequences, which are more variable (SI Appendix,Fig.S1). Here we excluded from the interior and from functional regions of the use information within ribosomes from each major branch of the tree rRNA such as the PTC, the decoding center, the core of the of life to reconstruct much of the emergence of the universal subunit interface, and tRNA-binding sites (16). (v) rRNA size translational machinery. generally increases with organismal complexity (10). Here, we consider ancestral expansion segments, which are found within Large Ribosomal Subunit Evolution Previously, we reported a 3D comparative method that revealed a Significance molecular level chronology of the evolution of the large ribosomal subunit (LSU) rRNA (10). Insertion fingerprints are evident when The ribosome, in analogy with a tree, contains a record of comparing3DstructuresofLSUrRNAsofvarioussizesfrom its history, spanning 4 billion years of life on earth. The in- various species. These insertion fingerprints mark sites where formation contained within ribosomes connects us to the rRNA expands, recording growth steps on a molecular level. prehistory of biology. Details of ribosomal RNA variation, Within the common core of the LSU rRNA, insertion fingerprints observed by comparing three-dimensional structures of ribo- were used to identify ancient growth sites. We showed that insertion somes across the tree of life, form the basis of our molecular- fingerprints provide a roadmap from the first steps in the formation level model of the origins and evolution of the translational of the peptidyl transferase center (PTC) (10) located in the ancient system. We infer many steps in the evolution of translation, heartoftheLSU(2–6), culminating in the common core. mapping out acquisition of structure and function, revealing much about how modern biology originated from ancestral Small Ribosomal Subunit, LSU, tRNA, and mRNA Evolution chemical systems. Here, using the 3D comparative method, we establish a compre- hensive and coherent model for the evolution of the entire ribosome. Author contributions: A.S.P., C.R.B., G.E.F., S.C.H., R.M.W., N.V.H., and L.D.W. designed research; This model covers the LSU rRNA, small ribosomal subunit (SSU) A.S.P., B.G., A.M.N., N.A.K., and K.A.L. performed research; C.R.B. contributed new reagents/ analytic tools; A.S.P., B.G., A.M.N., N.A.K., C.R.B., and K.A.L. analyzed data; A.S.P. and B.G. rRNA, tRNA, and mRNA. The evolution of each of these compo- prepared the figures; and A.S.P., G.E.F., S.C.H., R.M.W., N.V.H., and L.D.W. wrote the paper. nents is reconciled at the molecular level to a common chronology. The authors declare no conflict of interest. “ ” This evolutionary model, which we call the accretion model, is fully This article is a PNAS Direct Submission. grounded in structural data in the form of insertion fingerprints and 1To whom correspondence may be addressed. Email: [email protected] molecular interactions. The model describes iterative accretion of or [email protected]. rRNA fragments in the form of expansion segments. The timeline of This article contains supporting information online at www.pnas.org/lookup/suppl/doi:10. the accretion model initiates in ancient proto-biology in the initial 1073/pnas.1509761112/-/DCSupplemental. 15396–15401 | PNAS | December 15, 2015 | vol. 112 | no. 50 www.pnas.org/cgi/doi/10.1073/pnas.1509761112 Downloaded by guest on October 1, 2021 the common core (10) and are denoted as “AES” (LSU) and have used a comparison of S. cerevisiae and E. coli SSU rRNAs to “aes” (SSU). detect insertion fingerprints of eukaryotic expansions on the surface of the common core as shown in SI Appendix,TableS1. Thus, Results eukaryotic expansions and their insertion fingerprints observed Using a 3D comparative method, we establish the order of acqui- within the SSU rRNA follow patterns previously established within sition of AES and aes. This chronology assimilates serial AES/aes the LSU (10). accretion at the sites of expansion marked by insertion fingerprints. The model assumes that the rRNA of an ancestor can be Function is acquired commensurate with structural growth. approximated by rRNA components common to its progeny and typically is most similar to the smaller rRNA among progeny (10, 21). The SSU from the Common Core to Extant Biology. To illustrate SSU Although the growth of rRNA by accretion is a general phenomenon, expansions that took place after formation of the common core, we the progression of increasing size does not hold universally. In rare use the region of helices 7–10 (Fig. 1 A and B). In the bacterium cases, homologous expansions occur in parallel, leading to small Escherichia coli, helices 7–10 are 92 nt in length (17). This region of uncertainties in the model. In some instances rRNA does not follow the E. coli SSU is a reasonable approximation of the corresponding localized monotonic growth in size over evolution. For example, es6 region of the common core except for an eight-nucleotide addition of Drosophila melanogaster (20) contains a helix (21es6b1 as defined to helix 10. In the archaean Pyrococcus furiosus, helix 9 is expanded in refs. 22 and 23) which is extended further in Trypanosoma brucei by 11 nt (18) relative to E. coli (Dataset S1). This rRNA is ex- (15)butisabsentinthemammalianSSU. panded further in eukaryotes by the addition of three helices constituting expansion segment es3. Helices 7–10 and es3 have a The SSU from Its Origins to the Common Core. Insertion fingerprints combined length of 174 nt in Saccharomyces cerevisiae (19). This are found throughout the ancient SSU common core and are segment of the rRNA is maintained at nearly that size in protists, indistinguishable in form from those at sites of recent eukaryotic plants, and invertebrate animals. Helices 7–10 and es3 are expanded expansions. Using these insertion fingerprints, we decompose further in mammals, reaching a length of 223 nt in Homo sapiens SSU rRNA into ancestral expansion segments (Fig. 2A and SI (20). Comparison of rRNAs in three dimensions indicates that from Appendix, Fig. S2 and Table S2). In the common core we observe the common core (approximated by E.
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