Abstract
A vestige of an RNA apparatus with presumed ribozyme capabilities was detected within the core of contemporary ribosome, the contemporary catalytic center. This embedded architectural element is a dimer of RNA chains with a pocket-like structure, which functions in peptide bond formation. We suggest that it represents an ancient apparatus for performing chemical reactions required in the RNA world era, with peptide bond formation capabilities, called here the proto-ribosome. It is conceivable that proto-ribosome pocket was produced by a prebiotic process that originated from a pool of oligonucleotides and proceeds via a self-folded unit into a self-assembled dimer resembling the contemporary ribosomal catalytic center, which is built of two symmetrically related halves. This proto-ribosome could have evolved into more specialized apparatus once its products, namely short, uncoded “primitive” polypeptides, could play some role either in chemical reactions or in its stabilization and consequently led to the development of a simple code for their replication. These advances could have led to simultaneous developments in the nature of the apparatus, by the addition of new RNA features or by the interactions of the proto-ribosome with other RNA chains, and could have also contributed to the stability of the evolving more sophisticated machinery. This suggested pathway may shed light on the emergence of the contemporary genetic translation apparatus from the original rather short RNA oligomers. The tendency to dimerize of the sequences designed to mimic the proto-ribosome was found to vary significantly between the similar constructs. This suggested natural selection in the prebiotic era and advocated for a homodimer as the initial proto-ribosome, which could have been created by gene duplication. Thus, we have developed structural tools for investigating possible pathways in the evolution from the prebiotic era into modern life. These tools, together with biochemical investigations, are also useful for approaching key questions in prebiotic evolution. Among those are: Did the ancient translation apparatus survive selection pressure? Does its relic reside within the modern ribosome? What was the evolution conduit leading to its successive optimization?
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Acknowledgments
We thank Ilana Agmon and all members and guests of the ribosome group at the Weizmann Institute for continuous interest, fruitful discussions, experimental design, and excellent technical assistance. Support was provided by the US National Institute of Health (GM34360) and the Kimmelman Center for Macromolecular Assemblies. AY holds the Martin and Helen Kimmel Professorial Chair.
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Yonath, A. (2013). A Vestige of an RNA Apparatus With Ribozyme Capabilities Embedded and Functions Within the Modern Ribosome. In: Trueba, G., Montúfar, C. (eds) Evolution from the Galapagos. Social and Ecological Interactions in the Galapagos Islands, vol 2. Springer, New York, NY. https://doi.org/10.1007/978-1-4614-6732-8_4
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