Measuring the tolerance of the genetic code to altered codon size
- Massachusetts Institue of Technology, United States
- Yale University, United States
- Massachusetts Institute of Technology, United States
Abstract
Translation using four-base codons occurs in both natural and synthetic systems. What constraints contributed to the universal adoption of a triplet-codon, rather than quadruplet-codon, genetic code? Here, we investigate the tolerance of the Escherichia coli genetic code to tRNA mutations that increase codon size. We found that tRNAs from all twenty canonical isoacceptor classes can be converted to functional quadruplet tRNAs (qtRNAs). Many of these selectively incorporate a single amino acid in response to a specified four-base codon, as confirmed with mass spectrometry. However, efficient quadruplet codon translation often requires multiple tRNA mutations. Moreover, while tRNAs were largely amenable to quadruplet conversion, only nine of the twenty aminoacyl tRNA synthetases tolerate quadruplet anticodons. These may constitute a functional and mutually orthogonal set, but one that sharply limits the chemical alphabet available to a nascent all-quadruplet code. Our results suggest that the triplet codon code was selected because it is simpler and sufficient, not because a quadruplet codon code is unachievable. These data provide a blueprint for synthetic biologists to deliberately engineer an all-quadruplet expanded genetic code.
Data availability
All luminescence raw data are compiled in Figure 5A and provided as Source Data 1. Raw spectra have been deposited in the PRIDE database, dataset identifier PXD031925 and 10.6019/PXD031925.
Article and author information
Author details
Erika Alden DeBenedictis
Funding
National Institute of General Medical Sciences (R35GM122560)
- Dieter Söll
National Institute of General Medical Sciences (3R35GM122560-05W1)
- Dieter Söll
National Institute of Allergy and Infectious Diseases (F31 AI145181-01)
- Erika Alden DeBenedictis
National Institute of Diabetes and Digestive and Kidney Diseases (R00 DK102669-01)
- Kevin M Esvelt
The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
Copyright
© 2022, DeBenedictis et al.
This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.
Metrics
-
- 3,837
- views
-
- 636
- downloads
-
- 23
- citations
Views, downloads and citations are aggregated across all versions of this paper published by eLife.
Citations by DOI
-
- 23
- citations for umbrella DOI https://doi.org/10.7554/eLife.76941
Download links
A two-part list of links to download the article, or parts of the article, in various formats.
Downloads (link to download the article as PDF)
Open citations (links to open the citations from this article in various online reference manager services)
Cite this article (links to download the citations from this article in formats compatible with various reference manager tools)
Measuring the tolerance of the genetic code to altered codon size
eLife 11:e76941.
https://doi.org/10.7554/eLife.76941
