Directed evolution of rRNA improves translation kinetics and recombinant protein yield
Journal article, 2021

In bacteria, ribosome kinetics are considered rate-limiting for protein synthesis and cell growth. Enhanced ribosome kinetics may augment bacterial growth and biomanufacturing through improvements to overall protein yield, but whether this can be achieved by ribosome-specific modifications remains unknown. Here, we evolve 16S ribosomal RNAs (rRNAs) from Escherichia coli, Pseudomonas aeruginosa, and Vibrio cholerae towards enhanced protein synthesis rates. We find that rRNA sequence origin significantly impacted evolutionary trajectory and generated rRNA mutants with augmented protein synthesis rates in both natural and engineered contexts, including the incorporation of noncanonical amino acids. Moreover, discovered consensus mutations can be ported onto phylogenetically divergent rRNAs, imparting improved translational activities. Finally, we show that increased translation rates in vivo coincide with only moderately reduced translational fidelity, but do not enhance bacterial population growth. Together, these findings provide a versatile platform for development of unnatural ribosomal functions in vivo.

Author

Fan Liu

Broad Institute

Sinisa Bratulic

Chalmers, Biology and Biological Engineering, Systems and Synthetic Biology

Broad Institute

Alan Costello

Broad Institute

Scripps Research Institute

Teemu P. Miettinen

Massachusetts Institute of Technology (MIT)

Ahmed H. Badran

Scripps Research Institute

Broad Institute

Nature Communications

2041-1723 (ISSN) 20411723 (eISSN)

Vol. 12 1 5638

Subject Categories

Biochemistry and Molecular Biology

Microbiology

Medical Biotechnology (with a focus on Cell Biology (including Stem Cell Biology), Molecular Biology, Microbiology, Biochemistry or Biopharmacy)

DOI

10.1038/s41467-021-25852-5

PubMed

34561441

More information

Latest update

10/5/2021