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Metabolic repair through emergence of new pathways in Escherichia coli

Nature Chemical Biology volume 14, pages 1005–1009 (2018)Cite this article

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Abstract

Escherichia coli can derive all essential metabolites and cofactors through a highly evolved metabolic system. Damage of pathways may affect cell growth and physiology, but the strategies by which damaged metabolic pathways can be circumvented remain intriguing. Here, we use a ΔpanD (encoding for aspartate 1-decarboxylase) strain of E. coli that is unable to produce the β-alanine required for CoA biosynthesis to demonstrate that metabolic systems can overcome pathway damage by extensively rerouting metabolic pathways and modifying existing enzymes for unnatural functions. Using directed cell evolution, rewiring and repurposing of uracil metabolism allowed formation of an alternative β-alanine biosynthetic pathway. After this pathway was deleted, a second was evolved that used a gain-of-function mutation on ornithine decarboxylase (SpeC) to alter reaction and substrate specificity toward an oxidative decarboxylation–deamination reaction. After deletion of both pathways, yet another independent pathway emerged using polyamine biosynthesis, demonstrating the vast capacity of metabolic repair.

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Fig. 1: β-alanine biosynthesis through uracil degradation.
Fig. 2: Characterization of mutations that contribute to the degradation of uracil into β-alanine.
Fig. 3: Emergence of β-alanine synthesis pathway using evolved ornithine decarboxylase.
Fig. 4: β-alanine pathway using SpeC and pathway reconstruction.

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Data availability

The data that support the findings of this study are available from the corresponding author upon reasonable request. All genomic sequences are available at NCBI under BioProject ID PRJNA485586.

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Acknowledgements

This research was supported in part by a grant from National Science Foundation (MCB-1139318) for JP-US “Metabolomics for Low Carbon Society” (received by J.C.L.), and Japan Science and Technology’s Strategic International Collaborative Research Program (received by E.F). S.F.-G. acknowledges support from a QCB Collaboratory Postdoctoral Fellowship, and the QCB Collaboratory community directed by M. Pellegrini.

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Authors and Affiliations

  1. Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, Los Angeles, CA, USA

    Sammy Pontrelli, Riley C. B. Fricke & Matthew Chung

  2. Department of Biotechnology, Graduate School of Engineering, Osaka University, Suita, Osaka, Japan

    Shao Thing Teoh, Walter A. Laviña, Sastia Prama Putri & Eiichiro Fukusaki

  3. Microbiology Division, Institute of Biological Sciences, College of Arts and Sciences, University of the Philippines Los Baños, Los Baños, Laguna, Philippines

    Walter A. Laviña

  4. Institute of Genomics and Proteomics, University of California, Los Angeles, Los Angeles, CA, USA

    Sorel Fitz-Gibbon & Matteo Pellegrini

  5. Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, Los Angeles, CA, USA

    Matteo Pellegrini

  6. Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan

    James C. Liao

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Contributions

J.C.L. and S.P. conceived the idea of this project and wrote the manuscript. S.P. designed all experiments and performed evolution, RT-qPCR, enzyme assays, gene deletions, genome sequencing library generation, mass spec verification and measured growth phenotypes. R.C.B.F. performed evolution, enzyme assays, point mutation reversions, and growth curve analysis. S.T.T., W.A.L., S.P.P. and E.F. performed metabolomic analysis and data analysis. M.C. performed evolution. S.F.-G. and M.P. performed genomic sequencing and analysis.

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Correspondence to James C. Liao.

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Supplementary Figures 1–9, Supplementary Tables 1–10

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Pontrelli, S., Fricke, R.C.B., Teoh, S.T. et al. Metabolic repair through emergence of new pathways in Escherichia coli. Nat Chem Biol 14, 1005–1009 (2018). https://doi.org/10.1038/s41589-018-0149-6

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