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bioRxiv · 10.1101/2023.11.09.566451

Minimization of the E. coli ribosome, aided and optimized by community science

Tangpradabkul, T.·Palo, M. Z.·Townley, J.·Hsu, K. B.·Eterna Participants,·Smaga, S.·Das, R.·Schepartz, A.
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Abstract

The ribosome is a ribonucleoprotein complex found in all domains of life. Its role is to catalyze protein synthesis, the messenger RNA (mRNA)-templated formation of amide bonds between -amino acid monomers. Amide bond formation occurs within a highly conserved region of the large ribosomal subunit known as the peptidyl transferase center (PTC). Here we describe the stepwise design and characterization of mini-PTC 1.1, a 284-nucleotide RNA that recapitulates many essential features of the Escherichia coli PTC. Mini-PTC 1.1 folds into a PTC-like structure under physiological conditions, even in the absence of r-proteins, and engages small molecule analogs of A- and P-site tRNAs. The sequence of mini-PTC 1.1 differs from the wild type E. coli ribosome at 12 nucleotides that were installed by a cohort of citizen scientists using the on-line video game Eterna. These base changes improve both the secondary structure and tertiary folding of mini-PTC 1.1 as well as its ability to bind small molecule substrate analogs. Here, the combined input from Eterna citizen-scientists and RNA structural analysis provides a robust workflow for the design of a minimal PTC that recapitulates many features of an intact ribosome.

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Tangpradabkul, T., Palo, M. Z., Townley, J., Hsu, K. B., Eterna Participants,, Smaga, S., Das, R., Schepartz, A.. 2023-11-10. Minimization of the E. coli ribosome, aided and optimized by community science. https://doi.org/10.1101/2023.11.09.566451

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