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University of Illinois – Urbana-Champaign

1. Chen, Ke. Evolution and assembly of the ribosome.

Degree: PhD, 0319, 2014, University of Illinois – Urbana-Champaign

The ribosome is a large macromolecular assembly responsible for protein synthesis in all living cells. A typical bacterial ribosome consists of three ribosomal RNA (rRNA) molecules and approximately fifty ribosomal proteins (r-proteins), which are arranged into two subunits of unequal size and distinct function. The large subunit promotes formation of the peptide bond, and the small subunit enforces the recognition between the mRNA codons and the tRNA anticodons. With the availability of the ribosome crystal structure, it becomes clear that the two major functions, peptide bond formation and decoding, are performed within an entire RNA environment devoid of proteins. Combining with the fact that the majority of the ribosomal components are conserved across all three domains of life, it is believed that the ribosome has its origin deep in the RNA world before the last universal common ancestor (LUCA). Further evolutionary studies lead to the hypothesis that the evolution of the ribosome begins with a prototype ribozyme that catalyzes peptidyl-transferase reaction. Structural and sequence analysis suggests that the small ribozyme capable of catalyzing formation of short peptides may still exist in the core of the modern ribosome. Accordingly, a proto-ribosome model is constructed computationally using RNA fragments near the peptidyl-transferase center (PTC), and is proven to be stable throughout the micro-second molecular dynamics (MD) simulations. The model is capable of incorporating freely diffusing substrates spontaneously into its binding site, and holds them in both pockets long enough to reach a transition intermediate favorable for peptide bond formation. This in silico designed proto-ribosome is then subjected to experimental investigations to test its ability to assemble and bind potential substrates in solution. The successful design of the proto-ribosome presents a possible scenario for the initial development of the early translation apparatus. The proto-ribosome coupled with the probable parallel evolution of ancient tRNAs might have driven the emergence of the oldest coded protein shortly afterwards. The universally conserved r-protein S4 is likely an ancient protein due to its role in the initiation of the 30S assembly, control of the translational accuracy, and regulation of the conserved operon. However, the N-terminal domain of S4 is identified as a “molecular signature” that distinguishes between Bacteria and Archaea, and hence might be a newer addition to the protein. The presence of both an old and a new component in the same protein makes it an extremely interesting case to study for the ribosomal evolution. Therefore, we perform phylogenetic analysis of S4 in relation to a broad sharing of zinc/non-zinc binding sequence in the N-terminal domain of the protein, and study the scope of horizontal gene transfer (HGT) of S4 during bacterial evolution. The complex history presented for “core” protein S4 suggests the existence of a gene pool before the emergence of bacterial lineages and reflects… Advisors/Committee Members: Luthey-Schulten, Zaida A. (advisor), Martin Gruebele (Committee Chair), Luthey-Schulten, Zaida A. (committee member), Ha, Taekjip (committee member), Schulten, Klaus J. (committee member).

Subjects/Keywords: the RNA world; last universal common ancestor (LUCA); ribosomal evolution; ribosomal signature; ribosomal assembly; ribosomal RNA (rRNA); r-proteins; r-protein S4; RNA folding; protein binding; ligand binding; fly-casting mechanism; single-molecule Förster resonance energy transfer (smFRET); selective 20-hydroxyl acylation analyzed by primer extension (SHAPE); footprinting; molecular dynamics simulation; structure-based Go potential; micro-second simulation

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APA (6th Edition):

Chen, K. (2014). Evolution and assembly of the ribosome. (Doctoral Dissertation). University of Illinois – Urbana-Champaign. Retrieved from

Chicago Manual of Style (16th Edition):

Chen, Ke. “Evolution and assembly of the ribosome.” 2014. Doctoral Dissertation, University of Illinois – Urbana-Champaign. Accessed March 01, 2021.

MLA Handbook (7th Edition):

Chen, Ke. “Evolution and assembly of the ribosome.” 2014. Web. 01 Mar 2021.


Chen K. Evolution and assembly of the ribosome. [Internet] [Doctoral dissertation]. University of Illinois – Urbana-Champaign; 2014. [cited 2021 Mar 01]. Available from:

Council of Science Editors:

Chen K. Evolution and assembly of the ribosome. [Doctoral Dissertation]. University of Illinois – Urbana-Champaign; 2014. Available from: