Probing the limits of genetic recoding using multi-omics-guided evolution
12 affiliations
- 1Department of Genetics, Harvard Medical School, Boston, MA, USA. [email protected]
- 2Department of Genetics, Harvard Medical School, Boston, MA, USA
- 3Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
- 4BGI Research, Shenzhen, China
- 5GenScript USA Inc., Piscataway, NJ, USA
- 6DOE Joint Genome Institute (JGI), Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- 7Center for the Development of Therapeutics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- 8Institute of Biochemistry, HUN-REN Biological Research Centre, Szeged, Hungary
- 9BGI Research, Changzhou, China
- 10Guangdong Provincial Key Laboratory of Genome Read and Write, BGI Research, Shenzhen, China
- 11Department of Genetics, Harvard Medical School, Boston, MA, USA. [email protected]
- 12Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA. [email protected]
Abstract
Engineering the genetic code of an organism provides the basis for (i) making any organism safely resistant to natural viruses and (ii) preventing genetic information flow into and out of genetically modified organisms while (iii) allowing the biosynthesis of genetically encoded unnatural polymers 1–4 . Achieving these three goals requires the reassignment of multiple of the 64 codons nature uses to encode proteins. However, synonymous codon replacement—recoding—is frequently lethal, and how recoding impacts fitness remains poorly explored. Here, we explore these effects using whole-genome synthesis, multiplexed directed evolution, and genome-transcriptome-translatome-proteome co-profiling on multiple recoded genomes. Using this information, we assemble a synthetic Escherichia coli genome in seven sections using only 57 codons to encode proteins. By discovering the rules responsible for the lethality of synonymous recoding and developing a data-driven multi-omics-based genome construction workflow that troubleshoots synthetic genomes, we overcome the lethal effects of 62,007 synonymous codon swaps and 11,108 additional genomic edits. We show that synonymous recoding induces transcriptional noise including new antisense RNAs, leading to drastic transcriptome and proteome perturbation. As the elimination of select codons from an organism’s genetic code results in the widespread appearance of cryptic promoters, we show that synonymous codon choice may naturally evolve to minimize transcriptional noise. Our work provides the first genome-scale description of how synonymous codon changes influence organismal fitness and paves the way for the construction of functional genomes that provide genetic firewalls from natural ecosystems and safely produce biopolymers, drugs, and enzymes with an expanded chemistry.
Related
- Probe Before You Edit: Probing-Guided Molecular Optimization for LLM Agents in Structure-Based Drug Design
- Kinetics and Evolution-guided Design of High Fidelity CRISPR-Cas Endonucleases
- bL9 prevents recoding in collided ribosomes
- Structure and evolution-guided design of minimal RNA-guided nucleases
- CEM 2.0: Co-evolution-guided mining of superior extremophilic proteins via a curated proteome database and protein language model.
BibTeX
@article{nyerges2026probing,
title = {{Probing the limits of genetic recoding using multi-omics-guided evolution}},
author = {Ákos Nyerges and Anush Chiappino-Pepe and Bogdan Budnik and Maximilien S. Baas-Thomas and Elissa Rhuby and Regan Flynn and Shirui Yan and Nili Ostrov and Min Liu and Meizhou Wang and Qingmei Zheng and Fangxiang Hu and Kangming Chen and Alexandra Rudolph and Xi Dawn Chen and Jenny J. Ahn and Owen Spencer and Venkat Ayalavarapu and Angela Tarver and Miranda Harmon‐Smith and Matthew Hamilton and Ian K. Blaby and Yasuo Yoshikuni and Behnoush Hajian and Adeline Jin and Bálint Kintses and Mónika Számel and Viktória Seregi and Yue Shen and Zilong Li and George McDonald Church},
journal = {Nature Communications},
year = {2026},
month = jun,
doi = {10.1038/s41467-026-74300-9},
url = {https://doi.org/10.1038/s41467-026-74300-9},
note = {CC BY-NC-ND},
}
RIS
TY - JOUR
TI - Probing the limits of genetic recoding using multi-omics-guided evolution
AU - Ákos Nyerges
AU - Anush Chiappino-Pepe
AU - Bogdan Budnik
AU - Maximilien S. Baas-Thomas
AU - Elissa Rhuby
AU - Regan Flynn
AU - Shirui Yan
AU - Nili Ostrov
AU - Min Liu
AU - Meizhou Wang
AU - Qingmei Zheng
AU - Fangxiang Hu
AU - Kangming Chen
AU - Alexandra Rudolph
AU - Xi Dawn Chen
AU - Jenny J. Ahn
AU - Owen Spencer
AU - Venkat Ayalavarapu
AU - Angela Tarver
AU - Miranda Harmon‐Smith
AU - Matthew Hamilton
AU - Ian K. Blaby
AU - Yasuo Yoshikuni
AU - Behnoush Hajian
AU - Adeline Jin
AU - Bálint Kintses
AU - Mónika Számel
AU - Viktória Seregi
AU - Yue Shen
AU - Zilong Li
AU - George McDonald Church
PY - 2026
DA - 2026/06/22
JO - Nature Communications
DO - 10.1038/s41467-026-74300-9
UR - https://doi.org/10.1038/s41467-026-74300-9
AB - Engineering the genetic code of an organism provides the basis for (i) making any organism safely resistant to natural viruses and (ii) preventing genetic information flow into and out of genetically modified organisms while (iii) allowing the biosynthesis of genetically encoded unnatural polymers 1–4 . Achieving these three goals requires the reassignment of multiple of the 64 codons nature uses to encode proteins. However, synonymous codon replacement—recoding—is frequently lethal, and how recoding impacts fitness remains poorly explored. Here, we explore these effects using whole-genome synthesis, multiplexed directed evolution, and genome-transcriptome-translatome-proteome co-profiling on multiple recoded genomes. Using this information, we assemble a synthetic Escherichia coli genome in seven sections using only 57 codons to encode proteins. By discovering the rules responsible for the lethality of synonymous recoding and developing a data-driven multi-omics-based genome construction workflow that troubleshoots synthetic genomes, we overcome the lethal effects of 62,007 synonymous codon swaps and 11,108 additional genomic edits. We show that synonymous recoding induces transcriptional noise including new antisense RNAs, leading to drastic transcriptome and proteome perturbation. As the elimination of select codons from an organism’s genetic code results in the widespread appearance of cryptic promoters, we show that synonymous codon choice may naturally evolve to minimize transcriptional noise. Our work provides the first genome-scale description of how synonymous codon changes influence organismal fitness and paves the way for the construction of functional genomes that provide genetic firewalls from natural ecosystems and safely produce biopolymers, drugs, and enzymes with an expanded chemistry.
SN - 2041-1723
ER -