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A roadmap to establish a comprehensive platform for sustainable manufacturing of natural products in yeast

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  • Gita Naseri

    (Max Planck Unit for the Science of Pathogens
    Humboldt-Universität zu Berlin)

Abstract

Secondary natural products (NPs) are a rich source for drug discovery. However, the low abundance of NPs makes their extraction from nature inefficient, while chemical synthesis is challenging and unsustainable. Saccharomyces cerevisiae and Pichia pastoris are excellent manufacturing systems for the production of NPs. This Perspective discusses a comprehensive platform for sustainable production of NPs in the two yeasts through system-associated optimization at four levels: genetics, temporal controllers, productivity screening, and scalability. Additionally, it is pointed out critical metabolic building blocks in NP bioengineering can be identified through connecting multilevel data of the optimized system using deep learning.

Suggested Citation

  • Gita Naseri, 2023. "A roadmap to establish a comprehensive platform for sustainable manufacturing of natural products in yeast," Nature Communications, Nature, vol. 14(1), pages 1-13, December.
    • Handle: RePEc:nat:natcom:v:14:y:2023:i:1:d:10.1038_s41467-023-37627-1
    DOI: 10.1038/s41467-023-37627-1
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    References listed on IDEAS

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    1. Prashanth Srinivasan & Christina D. Smolke, 2020. "Biosynthesis of medicinal tropane alkaloids in yeast," Nature, Nature, vol. 585(7826), pages 614-619, September.
    2. Gita Naseri & Mattheos A. G. Koffas, 2020. "Application of combinatorial optimization strategies in synthetic biology," Nature Communications, Nature, vol. 11(1), pages 1-14, December.
    3. François Bertaux & Sebastián Sosa-Carrillo & Viktoriia Gross & Achille Fraisse & Chetan Aditya & Mariela Furstenheim & Gregory Batt, 2022. "Enhancing bioreactor arrays for automated measurements and reactive control with ReacSight," Nature Communications, Nature, vol. 13(1), pages 1-12, December.
    4. Adam L. Meadows & Kristy M. Hawkins & Yoseph Tsegaye & Eugene Antipov & Youngnyun Kim & Lauren Raetz & Robert H. Dahl & Anna Tai & Tina Mahatdejkul-Meadows & Lan Xu & Lishan Zhao & Madhukar S. Dasika , 2016. "Rewriting yeast central carbon metabolism for industrial isoprenoid production," Nature, Nature, vol. 537(7622), pages 694-697, September.
    5. Gita Naseri & Jessica Behrend & Lisa Rieper & Bernd Mueller-Roeber, 2019. "COMPASS for rapid combinatorial optimization of biochemical pathways based on artificial transcription factors," Nature Communications, Nature, vol. 10(1), pages 1-18, December.
    6. Chae Won Kang & Hyun Gyu Lim & Jaehyuk Won & Sanghak Cha & Giyoung Shin & Jae-Seong Yang & Jaeyoung Sung & Gyoo Yeol Jung, 2022. "Circuit-guided population acclimation of a synthetic microbial consortium for improved biochemical production," Nature Communications, Nature, vol. 13(1), pages 1-9, December.
    7. Michael A. Skinnider & Chad W. Johnston & Mathusan Gunabalasingam & Nishanth J. Merwin & Agata M. Kieliszek & Robyn J. MacLellan & Haoxin Li & Michael R. M. Ranieri & Andrew L. H. Webster & My P. T. C, 2020. "Comprehensive prediction of secondary metabolite structure and biological activity from microbial genome sequences," Nature Communications, Nature, vol. 11(1), pages 1-9, December.
    8. Jie Zhang & Lea G. Hansen & Olga Gudich & Konrad Viehrig & Lærke M. M. Lassen & Lars Schrübbers & Khem B. Adhikari & Paulina Rubaszka & Elena Carrasquer-Alvarez & Ling Chen & Vasil D’Ambrosio & Beata , 2022. "A microbial supply chain for production of the anti-cancer drug vinblastine," Nature, Nature, vol. 609(7926), pages 341-347, September.
    9. Dirk Benzinger & Mustafa Khammash, 2018. "Pulsatile inputs achieve tunable attenuation of gene expression variability and graded multi-gene regulation," Nature Communications, Nature, vol. 9(1), pages 1-10, December.
    10. Mingtao Huang & Jichen Bao & Björn M. Hallström & Dina Petranovic & Jens Nielsen, 2017. "Efficient protein production by yeast requires global tuning of metabolism," Nature Communications, Nature, vol. 8(1), pages 1-12, December.
    11. Lin Wang & Xi Zhang & Chenwang Tang & Pengcheng Li & Runtao Zhu & Jing Sun & Yunfeng Zhang & Hua Cui & Jiajia Ma & Xinyu Song & Weiwen Zhang & Xiang Gao & Xiaozhou Luo & Lingchong You & Ye Chen & Zhuo, 2022. "Engineering consortia by polymeric microbial swarmbots," Nature Communications, Nature, vol. 13(1), pages 1-13, December.
    12. Thomas A. Dixon & Paul S. Freemont & Richard A. Johnson & Isak S. Pretorius, 2022. "A global forum on synthetic biology: the need for international engagement," Nature Communications, Nature, vol. 13(1), pages 1-5, December.
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