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Luo X, Reiter MA, d'Espaux L, Wong J, Denby CM, Lechner A, Zhang Y, Grzybowski AT, Harth S, Lin W, Lee H, Yu C, Shin J, Deng K, Benites VT, Wang G, Baidoo EEK, Chen Y, Dev I, Petzold CJ, Keasling JD. Author Correction: Complete biosynthesis of cannabinoids and their unnatural analogues in yeast. Nature 2020; 580:E2. [PMID: 32269333 DOI: 10.1038/s41586-020-2109-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
An amendment to this paper has been published and can be accessed via a link at the top of the paper.
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Affiliation(s)
- Xiaozhou Luo
- California Institute of Quantitative Biosciences (QB3), University of California, Berkeley, CA, USA
| | - Michael A Reiter
- California Institute of Quantitative Biosciences (QB3), University of California, Berkeley, CA, USA.,Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Leo d'Espaux
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,Demetrix, Inc., Emeryville, CA, USA
| | - Jeff Wong
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,Demetrix, Inc., Emeryville, CA, USA
| | - Charles M Denby
- California Institute of Quantitative Biosciences (QB3), University of California, Berkeley, CA, USA.,Berkeley Brewing Science, Inc., Berkeley, CA, USA
| | - Anna Lechner
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA, USA.,Department of Bioengineering, University of California, Berkeley, CA, USA.,Genomatica, Inc., San Diego, CA, USA
| | - Yunfeng Zhang
- California Institute of Quantitative Biosciences (QB3), University of California, Berkeley, CA, USA.,Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China
| | - Adrian T Grzybowski
- California Institute of Quantitative Biosciences (QB3), University of California, Berkeley, CA, USA
| | - Simon Harth
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Weiyin Lin
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Hyunsu Lee
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,Department of Chemistry, University of California, Berkeley, CA, USA
| | - Changhua Yu
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,Department of Bioengineering, University of California, Berkeley, CA, USA
| | - John Shin
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA, USA
| | - Kai Deng
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA.,Biotechnology and Bioengineering Department, Sandia National Laboratories, Livermore, CA, USA
| | - Veronica T Benites
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - George Wang
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Edward E K Baidoo
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Yan Chen
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Ishaan Dev
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA, USA
| | - Christopher J Petzold
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Jay D Keasling
- California Institute of Quantitative Biosciences (QB3), University of California, Berkeley, CA, USA. .,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA. .,Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA, USA. .,Department of Bioengineering, University of California, Berkeley, CA, USA. .,Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark. .,Center for Synthetic Biochemistry, Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technologies, Shenzhen, China.
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Wong J, d'Espaux L, Dev I, van der Horst C, Keasling J. De novo synthesis of the sedative valerenic acid in Saccharomyces cerevisiae. Metab Eng 2018; 47:94-101. [PMID: 29545148 DOI: 10.1016/j.ymben.2018.03.005] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Revised: 03/03/2018] [Accepted: 03/05/2018] [Indexed: 12/20/2022]
Abstract
Valeriana officinalis (Valerian) root extracts have been used by European and Asian cultures for millennia for their anxiolytic and sedative properties. However, the efficacy of these extracts suffers from variable yields and composition, making these extracts a prime candidate for microbial production. Recently, valerenic acid, a C15 sesquiterpenoid, was identified as the active compound that modulates the GABAA channel. Although the first committed step, valerena-4,7(11)-diene synthase, has been identified and described, the complete valerenic acid biosynthetic pathway remains to be elucidated. Sequence homology and tissue-specific expression profiles of V. officinalis putative P450s led to the discovery of a V. officinalis valerena-4,7(11)-diene oxidase, VoCYP71DJ1, which required coexpression with a V. officinalis alcohol dehydrogenase and aldehyde dehydrogenase to complete valerenic acid biosynthesis in yeast. Further, we demonstrated the stable integration of all pathway enzymes in yeast, resulting in the production of 140 mg/L of valerena-4,7(11)-diene and 4 mg/L of valerenic acid in milliliter plates. These findings showcase Saccharomyces cerevisiae's potential as an expression platform for facilitating multiply-oxidized medicinal terpenoid pathway discovery, possibly paving the way for scale up and FDA approval of valerenic acid and other active compounds from plant-derived herbal medicines.
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Affiliation(s)
- Jeff Wong
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, United States; DOE Joint BioEnergy Institute, Emeryville, CA 94608, United States; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Leo d'Espaux
- DOE Joint BioEnergy Institute, Emeryville, CA 94608, United States; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Ishaan Dev
- DOE Joint BioEnergy Institute, Emeryville, CA 94608, United States; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States; Department of Chemical Engineering and Bioengineering, University of California at Berkeley, Berkeley, CA, USA Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA Joint BioEnergy Institute, Emeryville, CA, United States
| | - Cas van der Horst
- DOE Joint BioEnergy Institute, Emeryville, CA 94608, United States; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Jay Keasling
- DOE Joint BioEnergy Institute, Emeryville, CA 94608, United States; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States; Department of Chemical Engineering and Bioengineering, University of California at Berkeley, Berkeley, CA, USA Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA Joint BioEnergy Institute, Emeryville, CA, United States.
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Wong J, de Rond T, d’Espaux L, van der Horst C, Dev I, Rios-Solis L, Kirby J, Scheller H, Keasling J. High-titer production of lathyrane diterpenoids from sugar by engineered Saccharomyces cerevisiae. Metab Eng 2018; 45:142-148. [DOI: 10.1016/j.ymben.2017.12.007] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Revised: 10/24/2017] [Accepted: 12/10/2017] [Indexed: 10/18/2022]
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d'Espaux L, Ghosh A, Runguphan W, Wehrs M, Xu F, Konzock O, Dev I, Nhan M, Gin J, Reider Apel A, Petzold CJ, Singh S, Simmons BA, Mukhopadhyay A, García Martín H, Keasling JD. Engineering high-level production of fatty alcohols by Saccharomyces cerevisiae from lignocellulosic feedstocks. Metab Eng 2017; 42:115-125. [PMID: 28606738 DOI: 10.1016/j.ymben.2017.06.004] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Revised: 05/26/2017] [Accepted: 06/05/2017] [Indexed: 11/17/2022]
Abstract
Fatty alcohols in the C12-C18 range are used in personal care products, lubricants, and potentially biofuels. These compounds can be produced from the fatty acid pathway by a fatty acid reductase (FAR), yet yields from the preferred industrial host Saccharomyces cerevisiae remain under 2% of the theoretical maximum from glucose. Here we improved titer and yield of fatty alcohols using an approach involving quantitative analysis of protein levels and metabolic flux, engineering enzyme level and localization, pull-push-block engineering of carbon flux, and cofactor balancing. We compared four heterologous FARs, finding highest activity and endoplasmic reticulum localization from a Mus musculus FAR. After screening an additional twenty-one single-gene edits, we identified increasing FAR expression; deleting competing reactions encoded by DGA1, HFD1, and ADH6; overexpressing a mutant acetyl-CoA carboxylase; limiting NADPH and carbon usage by the glutamate dehydrogenase encoded by GDH1; and overexpressing the Δ9-desaturase encoded by OLE1 as successful strategies to improve titer. Our final strain produced 1.2g/L fatty alcohols in shake flasks, and 6.0g/L in fed-batch fermentation, corresponding to ~ 20% of the maximum theoretical yield from glucose, the highest titers and yields reported to date in S. cerevisiae. We further demonstrate high-level production from lignocellulosic feedstocks derived from ionic-liquid treated switchgrass and sorghum, reaching 0.7g/L in shake flasks. Altogether, our work represents progress towards efficient and renewable microbial production of fatty acid-derived products.
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Affiliation(s)
- Leo d'Espaux
- DOE Joint BioEnergy Institute, Emeryville, CA 94608, United States; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Amit Ghosh
- DOE Joint BioEnergy Institute, Emeryville, CA 94608, United States; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Weerawat Runguphan
- DOE Joint BioEnergy Institute, Emeryville, CA 94608, United States; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Maren Wehrs
- DOE Joint BioEnergy Institute, Emeryville, CA 94608, United States; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Feng Xu
- DOE Joint BioEnergy Institute, Emeryville, CA 94608, United States; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States; Biomass Science and Conversion Technology Department, Sandia National Laboratories, Livermore, CA 94551, United States; Biological and Materials Science Center, Sandia National Laboratories, Livermore, CA 94551, United States
| | - Oliver Konzock
- DOE Joint BioEnergy Institute, Emeryville, CA 94608, United States; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Ishaan Dev
- DOE Joint BioEnergy Institute, Emeryville, CA 94608, United States; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States; Department of Chemical & Biomolecular Engineering, University of California, Berkeley, CA 94720, United States
| | - Melissa Nhan
- DOE Joint BioEnergy Institute, Emeryville, CA 94608, United States; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Jennifer Gin
- DOE Joint BioEnergy Institute, Emeryville, CA 94608, United States; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Amanda Reider Apel
- DOE Joint BioEnergy Institute, Emeryville, CA 94608, United States; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Christopher J Petzold
- DOE Joint BioEnergy Institute, Emeryville, CA 94608, United States; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Seema Singh
- DOE Joint BioEnergy Institute, Emeryville, CA 94608, United States; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States; Biomass Science and Conversion Technology Department, Sandia National Laboratories, Livermore, CA 94551, United States; Biological and Materials Science Center, Sandia National Laboratories, Livermore, CA 94551, United States
| | - Blake A Simmons
- DOE Joint BioEnergy Institute, Emeryville, CA 94608, United States; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States; Biomass Science and Conversion Technology Department, Sandia National Laboratories, Livermore, CA 94551, United States; Biological and Materials Science Center, Sandia National Laboratories, Livermore, CA 94551, United States
| | - Aindrila Mukhopadhyay
- DOE Joint BioEnergy Institute, Emeryville, CA 94608, United States; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Héctor García Martín
- DOE Joint BioEnergy Institute, Emeryville, CA 94608, United States; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Jay D Keasling
- DOE Joint BioEnergy Institute, Emeryville, CA 94608, United States; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States; Department of Chemical & Biomolecular Engineering, University of California, Berkeley, CA 94720, United States; Department of Bioengineering, University of California, Berkeley, CA 94720, United States; The Novo Nordisk Foundation Center for Sustainability, Technical University of Denmark, Denmark.
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Kievit E, Bershad E, Ng E, Sethna P, Dev I, Lawrence TS, Rehemtulla A. Superiority of yeast over bacterial cytosine deaminase for enzyme/prodrug gene therapy in colon cancer xenografts. Cancer Res 1999; 59:1417-21. [PMID: 10197605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Abstract
The enzyme/prodrug strategy using bacterial cytosine deaminase (bCD) and 5-fluorocytosine (5-FC) is currently under investigation for cancer gene therapy. A major limitation for the use of bCD is that it is inefficient in the conversion of 5-FC into 5-fluorouracil. In the present study, we show that the K(m) of yeast cytosine deaminase (yCD) for 5-FC was 22-fold lower when compared with that of bCD. HT29 human colon cancer cells transduced with yCD (HT29/yCD) were significantly more sensitive to 5-FC in vitro than HT29 cells transduced with bCD (HT29/bCD). In tumor-bearing nude mice, complete tumor regression was observed in 6 of 13 HT29/yCD tumors in response to 5-FC treatment (500 mg/kg i.p. daily, 5 days a week for 2 weeks), whereas 0 of 10 HT29/bCD tumors were cured. Our study demonstrates an improved efficacy of the CD/5-FC treatment strategy when yCD was used. This enzyme has, therefore, a high potential to increase the therapeutic outcome of the enzyme/prodrug strategy in cancer patients.
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Affiliation(s)
- E Kievit
- Department of Radiation Oncology, University of Michigan Medical Center, Ann Arbor 48109-0582, USA
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