DOE OSTI · 3382431
Probing the limits of genetic recoding using multi-omics-guided evolution
Abstract
Engineering the genetic code—by reassigning multiple of the 64 natural codons—enables making organisms resistant to all viruses, preventing genetic information exchange, and allowing the biosynthesis of genetically encoded unnatural polymers. However, synonymous codon replacement—recoding—is frequently lethal, and how recoding impacts fitness remains poorly explored. Here, we explore these effects using genome synthesis, directed evolution, and genome-transcriptome-translatome-proteome co-profiling on multiple synthetic Escherichia coli genomes. We construct six partially recoded E. coli strains bearing up to 45.8% of a synthetic genome with a deleterious 57-codon genetic code. As our analyses revealed widespread defects—including unassigned codons in Syn61 and Syn57—we apply multi-omics to revise our genome design and mitigate defects. Using multi-omics, we show that recoding induces transcriptional and translational changes leading to fitness defects under hundreds of conditions. Finally, we develop a multi-omics-guided evolution strategy that rapidly restores fitness, enabling genome synthesis with radical changes.
Keep this discovery
Explore connections, maps & timelines
Nyerges, Akos [Harvard Medical School, Boston, MA (United States)] (ORCID:000000021581490X), Chiappino-Pepe, Anush [Harvard Medical School, Boston, MA (United States)] (ORCID:000000023993907X), Budnik, Bogdan [Harvard Univ., Boston, MA (United States)] (ORCID:0000000336222003), Baas-Thomas, Maximilien [Harvard Medical School, Boston, MA (United States)] (ORCID:0000000198219585), Rhuby, Elissa [Harvard Medical School, Boston, MA (United States)], Flynn, Regan [Harvard Medical School, Boston, MA (United States)], Yan, Shirui [Harvard Medical School, Boston, MA (United States); BGI Research, Shenzhen (China)], Ostrov, Nili [Harvard Medical School, Boston, MA (United States)], Liu, Min [GenScript USA Inc., Piscataway, NJ (United States)], Wang, Meizhou [GenScript USA Inc., Piscataway, NJ (United States)], Zheng, Qingmei [GenScript USA Inc., Piscataway, NJ (United States)], Hu, Fangxiang [GenScript USA Inc., Piscataway, NJ (United States)], Chen, Kangming [GenScript USA Inc., Piscataway, NJ (United States)], Rudolph, Alexandra [Harvard Medical School, Boston, MA (United States)], Chen, Dawn [Harvard Medical School, Boston, MA (United States)] (ORCID:0000000181276014), Ahn, Jenny [Harvard Medical School, Boston, MA (United States)] (ORCID:0009000039127162), Spencer, Owen [Harvard Medical School, Boston, MA (United States)], Ayalavarapu, Venkat [Harvard Medical School, Boston, MA (United States)], Tarver, Angela [USDOE Joint Genome Institute (JGI), Berkeley, CA (United States); Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)], Harmon-Smith, Miranda [USDOE Joint Genome Institute (JGI), Berkeley, CA (United States); Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)] (ORCID:0000000239801820), Hamilton, Matthew [USDOE Joint Genome Institute (JGI), Berkeley, CA (United States); Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)], Blaby, Ian [USDOE Joint Genome Institute (JGI), Berkeley, CA (United States); Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)] (ORCID:0000000216313154), Yoshikuni, Yasuo [USDOE Joint Genome Institute (JGI), Berkeley, CA (United States); Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)] (ORCID:000000028372640X), Hajian, Behnoush [Broad Institute of MIT and Harvard, Cambridge, MA (United States)], Jin, Adeline [GenScript USA Inc., Piscataway, NJ (United States)], Kintses, Balint [HUN-REN Biological Research Centre (HUN-REN BRC), Szeged (Hungary)] (ORCID:0000000308440310), Szamel, Monika [HUN-REN Biological Research Centre (HUN-REN BRC), Szeged (Hungary)], Seregi, Viktoria [HUN-REN Biological Research Centre (HUN-REN BRC), Szeged (Hungary)], Shen, Yue [BGI Research, Shenzhen (China); BGI Research, Changzhou (China)] (ORCID:0000000232767295), Li, Zilong [GenScript USA Inc., Piscataway, NJ (United States)], Church, George M. [Harvard Medical School, Boston, MA (United States); Harvard Univ., Boston, MA (United States)] (ORCID:0000000162329969). 2026-06-22. Probing the limits of genetic recoding using multi-omics-guided evolution. https://doi.org/10.1038/s41467-026-74300-9
Cite the original work for its findings. Save a collection to share your selection of sources.