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Engineering yeast metabolism for the discovery and production of polyamines and polyamine analogues

Abstract

Structurally complex and diverse polyamines and polyamine analogues are potential therapeutics and agrochemicals that can address grand societal challenges, for example, healthy ageing and sustainable food production. However, their structural complexity and low abundance in nature hampers either bulk chemical synthesis or extraction from natural resources. Here we reprogrammed the metabolism of baker’s yeast Saccharomyces cerevisiae and recruited nature’s diverse reservoir of biochemical tools to enable a complete biosynthesis of multiple polyamines and polyamine analogues. Specifically, we adopted a systematic engineering strategy to enable gram-per-litre-scale titres of spermidine, a central metabolite in polyamine metabolism. To demonstrate the potential of our polyamine platform, various polyamine synthases and ATP-dependent amide-bond-forming systems were introduced for the biosynthesis of natural and unnatural polyamine analogues. The yeast platform serves as a resource to accelerate the discovery and production of polyamines and polyamine analogues, and thereby unlocks this chemical space for further pharmacological and insecticidal studies.

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Fig. 1: Illustration of the modularized platform for the discovery and production of polyamines and polyamine analogues.
Fig. 2: Systematic engineering of yeast metabolism for the high-level production of spermidine.
Fig. 3: Biosynthesis of complex polyamines by elongating the spermidine carbon skeleton.
Fig. 4: Biocatalysis platform for amide-bond-containing natural polyamine analogues.

Data availability

Raw sequencing data is available on ArrayExpress with accession number E-MTAB- 9898. Data supporting the findings of this study are available within the article and its Supplementary Information files: the accession numbers and nucleotide sequences (codon optimized or original) of the enzymes referenced in this study are provided in this paper; source data are provided with this paper as Source Data files. All other data that support the findings of this study are available from the corresponding author upon reasonable request. All plasmids and strains used in this study are available from the corresponding author under a material transfer agreement. Source data are provided with this paper.

Code availability

All code used in the model simulations is available in GitHub (https://github.com/foodgeoff2010/Polyamine_platform).

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Acknowledgements

This work was funded by the Novo Nordisk Foundation (NNF10CC1016517), the Swedish Foundation for Strategic Research and the Knut and Alice Wallenberg Foundation. We thank J. Zhang, I. Borodina and Q-L. Liu for helpful discussions, J. Zhang for kindly providing plasmids from the CRISPR/Cas9 genome editing system, Q-L. Liu and Y. Chen for kindly providing aromatic chemical overproducing strains, A. Hoffmeyer for genome sequencing, M. Gossing, D. Romero-Suarez, the Chalmers Mass Spectrometry Infrastructure and the Analytical Core Facility of the Novo Nordisk Foundation Center for Biosustainability at Technical University of Denmark for assistance with metabolite analysis.

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Authors

Contributions

J.Q. and J.N. conceived the study with input from A.K. (spermidine section). J.Q. designed and performed the experiments, analysed the data and drafted the manuscript. M.K. assisted with the MS-based metabolite analysis. B.J., Y.C. and E.Ö. assisted with the computational and bioinformatic analysis. M.K.J., J.D.K., A.K. and B.J. assisted with the data analysis and interpretation. J.N., M.K.J. and J.D.K. supervised the study. All the authors revised and approved the manuscript.

Corresponding author

Correspondence to Jens Nielsen.

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Competing interests

J.Q., J.N. and A.K. are listed as inventors on patent applications related to microbial production of polyamines and/or polyamine analogues. J.Q. and J.N. are scientific co-founders of Chrysea Ltd. A.K. and J.N. are shareholders in Biopetrolia AB. J.D.K. has interests in Amyris, Lygos, Demetrix, Napigen, Maple Bio, Apertor Labs, Ansa Biosiences and Berkeley Brewing Sciences. All the other authors declare no competing interests.

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Peer review information Nature Catalysis thanks Rajib Saha and the other, anonymous, reviewer(s) for their contribution to the peer review of this work.

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Supplementary Information

Supplementary methods, references and Figs. 1–.45.

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Supplementary Tables 1–15.

Supplementary Data

Source Data for Supplementary Figs. 2–8.

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Statistical Source Data for Fig. 2.

Source Data Fig. 3

Statistical Source Data for Fig. 3.

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Qin, J., Krivoruchko, A., Ji, B. et al. Engineering yeast metabolism for the discovery and production of polyamines and polyamine analogues. Nat Catal 4, 498–509 (2021). https://doi.org/10.1038/s41929-021-00631-z

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