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Advancing the scale of synthetic biology via cross-species transfer of cellular functions enabled by iModulon engraftment

Author

Listed:
  • Donghui Choe

    (University of California San Diego)

  • Connor A. Olson

    (University of California San Diego)

  • Richard Szubin

    (University of California San Diego)

  • Hannah Yang

    (University of California San Diego)

  • Jaemin Sung

    (University of California San Diego)

  • Adam M. Feist

    (University of California San Diego
    Technical University of Denmark)

  • Bernhard O. Palsson

    (University of California San Diego
    Technical University of Denmark)

Abstract

Machine learning applied to large compendia of transcriptomic data has enabled the decomposition of bacterial transcriptomes to identify independently modulated sets of genes, such iModulons represent specific cellular functions. The identification of iModulons enables accurate identification of genes necessary and sufficient for cross-species transfer of cellular functions. We demonstrate cross-species transfer of: 1) the biotransformation of vanillate to protocatechuate, 2) a malonate catabolic pathway, 3) a catabolic pathway for 2,3-butanediol, and 4) an antimicrobial resistance to ampicillin found in multiple Pseudomonas species to Escherichia coli. iModulon-based engineering is a transformative strategy as it includes all genes comprising the transferred cellular function, including genes without functional annotation. Adaptive laboratory evolution was deployed to optimize the cellular function transferred, revealing mutations in the host. Combining big data analytics and laboratory evolution thus enhances the level of understanding of systems biology, and synthetic biology for strain design and development.

Suggested Citation

  • Donghui Choe & Connor A. Olson & Richard Szubin & Hannah Yang & Jaemin Sung & Adam M. Feist & Bernhard O. Palsson, 2024. "Advancing the scale of synthetic biology via cross-species transfer of cellular functions enabled by iModulon engraftment," Nature Communications, Nature, vol. 15(1), pages 1-10, December.
    • Handle: RePEc:nat:natcom:v:15:y:2024:i:1:d:10.1038_s41467-024-46486-3
    DOI: 10.1038/s41467-024-46486-3
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    References listed on IDEAS

    as
    1. Riyaz Maderbocus & Blanche L. Fields & Keith Hamilton & Shukun Luo & Timothy H. Tran & Lars E. P. Dietrich & Liang Tong, 2017. "Crystal structure of a Pseudomonas malonate decarboxylase holoenzyme hetero-tetramer," Nature Communications, Nature, vol. 8(1), pages 1-12, December.
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    3. Kaihang Wang & Julius Fredens & Simon F. Brunner & Samuel H. Kim & Tiongsun Chia & Jason W. Chin, 2016. "Defining synonymous codon compression schemes by genome recoding," Nature, Nature, vol. 539(7627), pages 59-64, November.
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    5. Anand V. Sastry & Ye Gao & Richard Szubin & Ying Hefner & Sibei Xu & Donghyuk Kim & Kumari Sonal Choudhary & Laurence Yang & Zachary A. King & Bernhard O. Palsson, 2019. "The Escherichia coli transcriptome mostly consists of independently regulated modules," Nature Communications, Nature, vol. 10(1), pages 1-14, December.
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