Journal Article

Community science designed ribosomes with beneficial phenotypes

Anderson-Lee, Jeff, Townley, Jill, Krüger, Antje, d’Aquino, Anne E., Kim, Yejun, Das, Rhiju, DeFoe, Alysse, Romano, Jonathan, Wellington-Oguri, Roger, Jewett, Michael C., Fisker, Eli, Kofman, Camila, Watkins, Andrew M.

2023

Overview

Functional design of ribosomes with mutant ribosomal RNA (rRNA) can expand opportunities for understanding molecular translation, building cells from the bottom-up, and engineering ribosomes with altered capabilities. However, such efforts are hampered by cell viability constraints, an enormous combinatorial sequence space, and limitations on large-scale, 3D design of RNA structures and functions. To address these challenges, we develop an integrated community science and experimental screening approach for rational design of ribosomes. This approach couples Eterna, an online video game that crowdsources RNA sequence design to community scientists in the form of puzzles, with in vitro ribosome synthesis, assembly, and translation in multiple design-build-test-learn cycles. We apply our framework to discover mutant rRNA sequences that improve protein synthesis in vitro and cell growth in vivo, relative to wild type ribosomes, under diverse environmental conditions. This work provides insights into rRNA sequence-function relationships and has implications for synthetic biology. While the ribosome has been harnessed for synthetic biology, designing ribosomes has remained challenging. Here, the authors demonstrate a community science approach for rational design of ribosomes with beneficial properties.

• Publisher: Nature Publishing Group UK,Nature Publishing Group,Nature Portfolio
• Subject: 49 / 49/40 / 631/337 / 631/61/338/552 / 82/80 / Biology / Cell viability / Combinatorial analysis / Computer & video games / Design / Environmental conditions / Humanities and Social Sciences / In vivo methods and tests / multidisciplinary / Mutants / Nucleotide sequence / Phenotype / Phenotypes / Protein biosynthesis / Protein synthesis / Ribosomal Proteins - metabolism / Ribosomes / Ribosomes - metabolism / RNA, Ribosomal - metabolism / rRNA / Science / Science (multidisciplinary) / Synthetic Biology / Translation