1
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Bradley SA, Hansson FG, Lehka BJ, Rago D, Pinho P, Peng H, Adhikari KB, Haidar AK, Hansen LG, Volkova D, Holtz M, Muyo Abad S, Ma X, Koudounas K, Besseau S, Gautron N, Mélin C, Marc J, Birer Williams C, Courdavault V, Jensen ED, Keasling JD, Zhang J, Jensen MK. Yeast Platforms for Production and Screening of Bioactive Derivatives of Rauwolscine. ACS Synth Biol 2024; 13:1498-1512. [PMID: 38635307 DOI: 10.1021/acssynbio.4c00039] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/19/2024]
Abstract
Monoterpene indole alkaloids (MIAs) make up a highly bioactive class of metabolites produced by a range of tropical and subtropical plants. The corynanthe-type MIAs are a stereochemically complex subclass with therapeutic potential against a large number of indications including cancer, psychotic disorders, and erectile dysfunction. Here, we report yeast-based cell factories capable of de novo production of corynanthe-type MIAs rauwolscine, yohimbine, tetrahydroalstonine, and corynanthine. From this, we demonstrate regioselective biosynthesis of 4 fluorinated derivatives of these compounds and de novo biosynthesis of 7-chlororauwolscine by coexpression of a halogenase with the biosynthetic pathway. Finally, we capitalize on the ability of these cell factories to produce derivatives of these bioactive scaffolds to establish a proof-of-principle drug discovery pipeline in which the corynanthe-type MIAs are screened for bioactivity on human drug targets, expressed in yeast. In doing so, we identify antagonistic and agonistic behavior against the human adrenergic G protein-coupled receptors ADRA2A and ADRA2B, and the serotonergic receptor 5HT4b, respectively. This study thus demonstrates a proto-drug discovery pipeline for bioactive plant-inspired small molecules based on one-pot biocatalysis of natural and new-to-nature corynanthe-type MIAs in yeast.
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Affiliation(s)
- Samuel A Bradley
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Lyngby, Denmark
| | - Frederik G Hansson
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Lyngby, Denmark
| | - Beata J Lehka
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Lyngby, Denmark
| | - Daniela Rago
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Lyngby, Denmark
| | - Pedro Pinho
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Lyngby, Denmark
| | - Huadong Peng
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Lyngby, Denmark
| | - Khem B Adhikari
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Lyngby, Denmark
| | - Ahmad K Haidar
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Lyngby, Denmark
| | - Lea G Hansen
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Lyngby, Denmark
- Biomia ApS, DK-2100 Copenhagen, Denmark
| | - Daria Volkova
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Lyngby, Denmark
| | - Maxence Holtz
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Lyngby, Denmark
| | - Sergi Muyo Abad
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Lyngby, Denmark
| | - Xin Ma
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Lyngby, Denmark
| | - Konstantinos Koudounas
- EA2106 Biomolécules et Biotechnologies Végétales, Université de Tours, F-37200 Tours, France
| | - Sébastien Besseau
- EA2106 Biomolécules et Biotechnologies Végétales, Université de Tours, F-37200 Tours, France
| | - Nicolas Gautron
- EA2106 Biomolécules et Biotechnologies Végétales, Université de Tours, F-37200 Tours, France
| | - Céline Mélin
- EA2106 Biomolécules et Biotechnologies Végétales, Université de Tours, F-37200 Tours, France
| | - Jillian Marc
- EA2106 Biomolécules et Biotechnologies Végétales, Université de Tours, F-37200 Tours, France
| | - Caroline Birer Williams
- EA2106 Biomolécules et Biotechnologies Végétales, Université de Tours, F-37200 Tours, France
| | - Vincent Courdavault
- EA2106 Biomolécules et Biotechnologies Végétales, Université de Tours, F-37200 Tours, France
| | - Emil D Jensen
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Lyngby, Denmark
| | - Jay D Keasling
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Lyngby, Denmark
- Joint BioEnergy Institute, Emeryville, California 94608,United States
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720,United States
- Department of Chemical and Biomolecular Engineering, Department of Bioengineering, University of California, Berkeley, California 94720, United States
- Center for Synthetic Biochemistry, Institute for Synthetic Biology, Shenzhen Institutes of Advanced Technologies, Shenzhen 518055, China
| | - Jie Zhang
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Lyngby, Denmark
- Biomia ApS, DK-2100 Copenhagen, Denmark
| | - Michael K Jensen
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Lyngby, Denmark
- Biomia ApS, DK-2100 Copenhagen, Denmark
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Cano-Prieto C, Undabarrena A, de Carvalho AC, Keasling JD, Cruz-Morales P. Triumphs and Challenges of Natural Product Discovery in the Postgenomic Era. Annu Rev Biochem 2024. [PMID: 38639989 DOI: 10.1146/annurev-biochem-032620-104731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/20/2024]
Abstract
Natural products have played significant roles as medicine and food throughout human history. Here, we first provide a brief historical overview of natural products, their classification, biosynthetic origins, and the microbiological and genetic methods used for their discovery. We also describe and discuss the technologies that revolutionized the field, which transitioned from classic genetics to genome-centric discovery approximately two decades ago. We then highlight the most recent advancements and approaches in the current postgenomic era, in which genome mining is a standard operation and high-throughput analytical methods allow parallel discovery of genes and molecules at an unprecedented pace. Finally, we discuss the new challenges faced by the field of natural products and the future of systematic heterologous expression and strain-independent discovery, which promises to deliver more molecules in vials than ever before.
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Affiliation(s)
- Carolina Cano-Prieto
- 1Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark;
| | - Agustina Undabarrena
- 1Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark;
| | - Ana Calheiros de Carvalho
- 1Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark;
| | - Jay D Keasling
- 1Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark;
- 2Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
- 3Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, California, USA
- 4Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California, USA
- 5Department of Bioengineering, University of California, Berkeley, California, USA
- 6Center for Synthetic Biochemistry, Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Shenzhen, China
| | - Pablo Cruz-Morales
- 1Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark;
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3
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Crowe SA, Zhao X, Gan F, Chen X, Hudson GA, Astolfi MCT, Scheller HV, Liu Y, Keasling JD. Engineered Saccharomyces cerevisiae as a Biosynthetic Platform of Nucleotide Sugars. ACS Synth Biol 2024; 13:1215-1224. [PMID: 38467016 DOI: 10.1021/acssynbio.3c00666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/13/2024]
Abstract
Glycosylation of biomolecules can greatly alter their physicochemical properties, cellular recognition, subcellular localization, and immunogenicity. Glycosylation reactions rely on the stepwise addition of sugars using nucleotide diphosphate (NDP)-sugars. Making these substrates readily available will greatly accelerate the characterization of new glycosylation reactions, elucidation of their underlying regulation mechanisms, and production of glycosylated molecules. In this work, we engineered Saccharomyces cerevisiae to heterologously express nucleotide sugar synthases to access a wide variety of uridine diphosphate (UDP)-sugars from simple starting materials (i.e., glucose and galactose). Specifically, activated glucose, uridine diphosphate d-glucose (UDP-d-Glc), can be converted to UDP-d-glucuronic acid (UDP-d-GlcA), UDP-d-xylose (UDP-d-Xyl), UDP-d-apiose (UDP-d-Api), UDP-d-fucose (UDP-d-Fuc), UDP-l-rhamnose (UDP-l-Rha), UDP-l-arabinopyranose (UDP-l-Arap), and UDP-l-arabinofuranose (UDP-l-Araf) using the corresponding nucleotide sugar synthases of plant and microbial origins. We also expressed genes encoding the salvage pathway to directly activate free sugars to achieve the biosynthesis of UDP-l-Arap and UDP-l-Araf. We observed strong inhibition of UDP-d-Glc 6-dehydrogenase (UGD) by the downstream product UDP-d-Xyl, which we circumvented using an induction system (Tet-On) to delay the production of UDP-d-Xyl to maintain the upstream UDP-sugar pool. Finally, we performed a time-course study using strains containing the biosynthetic pathways to produce five non-native UDP-sugars to elucidate their time-dependent interconversion and the role of UDP-d-Xyl in regulating UDP-sugar metabolism. These engineered yeast strains are a robust platform to (i) functionally characterize sugar synthases in vivo, (ii) biosynthesize a diverse selection of UDP-sugars, (iii) examine the regulation of intracellular UDP-sugar interconversions, and (iv) produce glycosylated secondary metabolites and proteins.
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Affiliation(s)
- Samantha A Crowe
- Department of Chemical & Biomolecular Engineering, University of California, Berkeley, California 94720, United States
- California Institute of Quantitative Biosciences (QB3), University of California, Berkeley, California 94720, United States
- Joint BioEnergy Institute, Emeryville, California 94608, United States
| | - Xixi Zhao
- California Institute of Quantitative Biosciences (QB3), University of California, Berkeley, California 94720, United States
- Joint BioEnergy Institute, Emeryville, California 94608, United States
| | - Fei Gan
- California Institute of Quantitative Biosciences (QB3), University of California, Berkeley, California 94720, United States
- Joint BioEnergy Institute, Emeryville, California 94608, United States
| | - Xiaoyue Chen
- Joint BioEnergy Institute, Emeryville, California 94608, United States
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, United States
| | - Graham A Hudson
- California Institute of Quantitative Biosciences (QB3), University of California, Berkeley, California 94720, United States
- Joint BioEnergy Institute, Emeryville, California 94608, United States
| | - Maria C T Astolfi
- Joint BioEnergy Institute, Emeryville, California 94608, United States
- Department of Bioengineering, University of California, Berkeley, California 94720, United States
| | - Henrik V Scheller
- Joint BioEnergy Institute, Emeryville, California 94608, United States
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, United States
| | - Yuzhong Liu
- California Institute of Quantitative Biosciences (QB3), University of California, Berkeley, California 94720, United States
- Joint BioEnergy Institute, Emeryville, California 94608, United States
| | - Jay D Keasling
- Department of Chemical & Biomolecular Engineering, University of California, Berkeley, California 94720, United States
- California Institute of Quantitative Biosciences (QB3), University of California, Berkeley, California 94720, United States
- Joint BioEnergy Institute, Emeryville, California 94608, United States
- Department of Bioengineering, University of California, Berkeley, California 94720, United States
- Division of Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
- Center for Synthetic Biochemistry, Shenzhen Institutes for Advanced Technologies, Shenzhen 518071, China
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4
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Wang X, Chen N, Cruz-Morales P, Zhong B, Zhang Y, Wang J, Xiao Y, Fu X, Lin Y, Acharya S, Li Z, Deng H, Sun Y, Bai L, Tang X, Keasling JD, Luo X. Elucidation of genes enhancing natural product biosynthesis through co-evolution analysis. Nat Metab 2024:10.1038/s42255-024-01024-9. [PMID: 38609677 DOI: 10.1038/s42255-024-01024-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 03/06/2024] [Indexed: 04/14/2024]
Abstract
Streptomyces has the largest repertoire of natural product biosynthetic gene clusters (BGCs), yet developing a universal engineering strategy for each Streptomyces species is challenging. Given that some Streptomyces species have larger BGC repertoires than others, we proposed that a set of genes co-evolved with BGCs to support biosynthetic proficiency must exist in those strains, and that their identification may provide universal strategies to improve the productivity of other strains. We show here that genes co-evolved with natural product BGCs in Streptomyces can be identified by phylogenomics analysis. Among the 597 genes that co-evolved with polyketide BGCs, 11 genes in the 'coenzyme' category have been examined, including a gene cluster encoding for the cofactor pyrroloquinoline quinone. When the pqq gene cluster was engineered into 11 Streptomyces strains, it enhanced production of 16,385 metabolites, including 36 known natural products with up to 40-fold improvement and several activated silent gene clusters. This study provides an innovative engineering strategy for improving polyketide production and finding previously unidentified BGCs.
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Affiliation(s)
- Xinran Wang
- Shenzhen Key Laboratory for the Intelligent Microbial Manufacturing of Medicines, Key Laboratory of Quantitative Synthetic Biology, Center for Synthetic Biochemistry, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Ningxin Chen
- Shenzhen Key Laboratory for the Intelligent Microbial Manufacturing of Medicines, Key Laboratory of Quantitative Synthetic Biology, Center for Synthetic Biochemistry, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Pablo Cruz-Morales
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Biming Zhong
- Shenzhen Key Laboratory for the Intelligent Microbial Manufacturing of Medicines, Key Laboratory of Quantitative Synthetic Biology, Center for Synthetic Biochemistry, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Yangming Zhang
- Shenzhen Key Laboratory for the Intelligent Microbial Manufacturing of Medicines, Key Laboratory of Quantitative Synthetic Biology, Center for Synthetic Biochemistry, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Jian Wang
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Ministry of Education), Wuhan University, Wuhan, China
| | - Yifan Xiao
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Xinnan Fu
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Yang Lin
- Institute of Chemical Biology, Shenzhen Bay Laboratory, Shenzhen, China
| | - Suneil Acharya
- Department of Chemical and Biomolecular Engineering and Department of Bioengineering, University of California, Berkeley, CA, USA
| | - Zhibo Li
- Shenzhen Key Laboratory for the Intelligent Microbial Manufacturing of Medicines, Key Laboratory of Quantitative Synthetic Biology, Center for Synthetic Biochemistry, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Huaxiang Deng
- Shenzhen Key Laboratory for the Intelligent Microbial Manufacturing of Medicines, Key Laboratory of Quantitative Synthetic Biology, Center for Synthetic Biochemistry, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Yuhui Sun
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Ministry of Education), Wuhan University, Wuhan, China
- School of Pharmacy, Huazhong University of Science and Technology, Wuhan, China
| | - Linquan Bai
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Xiaoyu Tang
- Institute of Chemical Biology, Shenzhen Bay Laboratory, Shenzhen, China.
| | - Jay D Keasling
- Shenzhen Key Laboratory for the Intelligent Microbial Manufacturing of Medicines, Key Laboratory of Quantitative Synthetic Biology, Center for Synthetic Biochemistry, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China.
- Department of Chemical and Biomolecular Engineering and Department of Bioengineering, University of California, Berkeley, CA, USA.
- Joint BioEnergy Institute, Emeryville, CA, USA.
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
| | - Xiaozhou Luo
- Shenzhen Key Laboratory for the Intelligent Microbial Manufacturing of Medicines, Key Laboratory of Quantitative Synthetic Biology, Center for Synthetic Biochemistry, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China.
- Shenzhen Infrastructure for Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China.
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5
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Martin LBB, Kikuchi S, Rejzek M, Owen C, Reed J, Orme A, Misra RC, El-Demerdash A, Hill L, Hodgson H, Liu Y, Keasling JD, Field RA, Truman AW, Osbourn A. Complete biosynthesis of the potent vaccine adjuvant QS-21. Nat Chem Biol 2024; 20:493-502. [PMID: 38278997 PMCID: PMC10972754 DOI: 10.1038/s41589-023-01538-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2023] [Accepted: 12/20/2023] [Indexed: 01/28/2024]
Abstract
QS-21 is a potent vaccine adjuvant currently sourced by extraction from the Chilean soapbark tree. It is a key component of human vaccines for shingles, malaria, coronavirus disease 2019 and others under development. The structure of QS-21 consists of a glycosylated triterpene scaffold coupled to a complex glycosylated 18-carbon acyl chain that is critical for immunostimulant activity. We previously identified the early pathway steps needed to make the triterpene glycoside scaffold; however, the biosynthetic route to the acyl chain, which is needed for stimulation of T cell proliferation, was unknown. Here, we report the biogenic origin of the acyl chain, characterize the series of enzymes required for its synthesis and addition and reconstitute the entire 20-step pathway in tobacco, thereby demonstrating the production of QS-21 in a heterologous expression system. This advance opens up unprecedented opportunities for bioengineering of vaccine adjuvants, investigating structure-activity relationships and understanding the mechanisms by which these compounds promote the human immune response.
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Affiliation(s)
| | | | - Martin Rejzek
- John Innes Centre, Norwich Research Park, Norwich, UK
| | | | - James Reed
- John Innes Centre, Norwich Research Park, Norwich, UK
| | | | | | - Amr El-Demerdash
- John Innes Centre, Norwich Research Park, Norwich, UK
- Department of Chemistry, Faculty of Sciences, Mansoura University, Mansoura, Egypt
| | - Lionel Hill
- John Innes Centre, Norwich Research Park, Norwich, UK
| | | | - Yuzhong Liu
- California Institute of Quantitative Biosciences (QB3), University of California, Berkeley, Berkeley, CA, USA
- Joint BioEnergy Institute, Emeryville, CA, USA
| | - Jay D Keasling
- California Institute of Quantitative Biosciences (QB3), University of California, Berkeley, Berkeley, CA, USA
- Joint BioEnergy Institute, Emeryville, CA, USA
- Department of Chemical & Biomolecular Engineering, University of California, Berkeley, Berkeley, CA, USA
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA
- Center for Biosustainability, Danish Technical University, Lyngby, Denmark
- Center for Synthetic Biochemistry, Shenzhen Institutes for Advanced Technologies, Shenzhen, China
| | - Robert A Field
- Department of Chemistry and Manchester Institute of Biotechnology, University of Manchester, Manchester, UK
| | | | - Anne Osbourn
- John Innes Centre, Norwich Research Park, Norwich, UK.
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6
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Deng H, Yu H, Deng Y, Qiu Y, Li F, Wang X, He J, Liang W, Lan Y, Qiao L, Zhang Z, Zhang Y, Keasling JD, Luo X. Pathway Evolution Through a Bottlenecking-Debottlenecking Strategy and Machine Learning-Aided Flux Balancing. Adv Sci (Weinh) 2024; 11:e2306935. [PMID: 38321783 PMCID: PMC11005738 DOI: 10.1002/advs.202306935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 12/24/2023] [Indexed: 02/08/2024]
Abstract
The evolution of pathway enzymes enhances the biosynthesis of high-value chemicals, crucial for pharmaceutical, and agrochemical applications. However, unpredictable evolutionary landscapes of pathway genes often hinder successful evolution. Here, the presence of complex epistasis is identifued within the representative naringenin biosynthetic pathway enzymes, hampering straightforward directed evolution. Subsequently, a biofoundry-assisted strategy is developed for pathway bottlenecking and debottlenecking, enabling the parallel evolution of all pathway enzymes along a predictable evolutionary trajectory in six weeks. This study then utilizes a machine learning model, ProEnsemble, to further balance the pathway by optimizing the transcription of individual genes. The broad applicability of this strategy is demonstrated by constructing an Escherichia coli chassis with evolved and balanced pathway genes, resulting in 3.65 g L-1 naringenin. The optimized naringenin chassis also demonstrates enhanced production of other flavonoids. This approach can be readily adapted for any given number of enzymes in the specific metabolic pathway, paving the way for automated chassis construction in contemporary biofoundries.
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Affiliation(s)
- Huaxiang Deng
- Shenzhen Key Laboratory for the Intelligent Microbial Manufacturing of Medicines, Shenzhen Institute of Advanced TechnologyChinese Academy of SciencesShenzhen518055P. R. China
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced TechnologyChinese Academy of SciencesShenzhen518055P. R. China
- Center for Synthetic Biochemistry, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced TechnologyChinese Academy of SciencesShenzhen518055P. R. China
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of BiotechnologyJiangnan UniversityWuxi214122P. R. China
| | - Han Yu
- Shenzhen Key Laboratory for the Intelligent Microbial Manufacturing of Medicines, Shenzhen Institute of Advanced TechnologyChinese Academy of SciencesShenzhen518055P. R. China
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced TechnologyChinese Academy of SciencesShenzhen518055P. R. China
- Center for Synthetic Biochemistry, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced TechnologyChinese Academy of SciencesShenzhen518055P. R. China
- University of Chinese Academy of SciencesBeijing100049P. R. China
| | - Yanwu Deng
- Shenzhen Key Laboratory for the Intelligent Microbial Manufacturing of Medicines, Shenzhen Institute of Advanced TechnologyChinese Academy of SciencesShenzhen518055P. R. China
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced TechnologyChinese Academy of SciencesShenzhen518055P. R. China
- Center for Synthetic Biochemistry, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced TechnologyChinese Academy of SciencesShenzhen518055P. R. China
| | - Yulan Qiu
- Shenzhen Key Laboratory for the Intelligent Microbial Manufacturing of Medicines, Shenzhen Institute of Advanced TechnologyChinese Academy of SciencesShenzhen518055P. R. China
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced TechnologyChinese Academy of SciencesShenzhen518055P. R. China
- Center for Synthetic Biochemistry, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced TechnologyChinese Academy of SciencesShenzhen518055P. R. China
| | - Feifei Li
- Shenzhen Key Laboratory for the Intelligent Microbial Manufacturing of Medicines, Shenzhen Institute of Advanced TechnologyChinese Academy of SciencesShenzhen518055P. R. China
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced TechnologyChinese Academy of SciencesShenzhen518055P. R. China
- Center for Synthetic Biochemistry, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced TechnologyChinese Academy of SciencesShenzhen518055P. R. China
| | - Xinran Wang
- Shenzhen Key Laboratory for the Intelligent Microbial Manufacturing of Medicines, Shenzhen Institute of Advanced TechnologyChinese Academy of SciencesShenzhen518055P. R. China
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced TechnologyChinese Academy of SciencesShenzhen518055P. R. China
- Center for Synthetic Biochemistry, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced TechnologyChinese Academy of SciencesShenzhen518055P. R. China
| | - Jiahui He
- Shenzhen Key Laboratory for the Intelligent Microbial Manufacturing of Medicines, Shenzhen Institute of Advanced TechnologyChinese Academy of SciencesShenzhen518055P. R. China
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced TechnologyChinese Academy of SciencesShenzhen518055P. R. China
- Center for Synthetic Biochemistry, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced TechnologyChinese Academy of SciencesShenzhen518055P. R. China
| | - Weiyue Liang
- Shenzhen Key Laboratory for the Intelligent Microbial Manufacturing of Medicines, Shenzhen Institute of Advanced TechnologyChinese Academy of SciencesShenzhen518055P. R. China
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced TechnologyChinese Academy of SciencesShenzhen518055P. R. China
- Center for Synthetic Biochemistry, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced TechnologyChinese Academy of SciencesShenzhen518055P. R. China
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of BiotechnologyJiangnan UniversityWuxi214122P. R. China
| | - Yunquan Lan
- Shenzhen Infrastructure for Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced TechnologyChinese Academy of SciencesShenzhen518055P. R. China
| | - Longjiang Qiao
- Shenzhen Infrastructure for Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced TechnologyChinese Academy of SciencesShenzhen518055P. R. China
| | - Zhiyu Zhang
- Shenzhen Infrastructure for Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced TechnologyChinese Academy of SciencesShenzhen518055P. R. China
| | - Yunfeng Zhang
- Shenzhen Key Laboratory for the Intelligent Microbial Manufacturing of Medicines, Shenzhen Institute of Advanced TechnologyChinese Academy of SciencesShenzhen518055P. R. China
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced TechnologyChinese Academy of SciencesShenzhen518055P. R. China
- Center for Synthetic Biochemistry, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced TechnologyChinese Academy of SciencesShenzhen518055P. R. China
| | - Jay D. Keasling
- Center for Synthetic Biochemistry, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced TechnologyChinese Academy of SciencesShenzhen518055P. R. China
- Joint BioEnergy InstituteEmeryvilleCA94608USA
- Biological Systems and Engineering DivisionLawrence Berkeley National LaboratoryBerkeleyCA94720USA
- Department of Chemical and Biomolecular Engineering & Department of BioengineeringUniversity of CaliforniaBerkeleyCA94720USA
- Novo Nordisk Foundation Center for BiosustainabilityTechnical University of DenmarkKgs. Lyngby2800Denmark
| | - Xiaozhou Luo
- Shenzhen Key Laboratory for the Intelligent Microbial Manufacturing of Medicines, Shenzhen Institute of Advanced TechnologyChinese Academy of SciencesShenzhen518055P. R. China
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced TechnologyChinese Academy of SciencesShenzhen518055P. R. China
- Center for Synthetic Biochemistry, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced TechnologyChinese Academy of SciencesShenzhen518055P. R. China
- University of Chinese Academy of SciencesBeijing100049P. R. China
- Shenzhen Infrastructure for Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced TechnologyChinese Academy of SciencesShenzhen518055P. R. China
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7
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Maini Rekdal V, van der Luijt CRB, Chen Y, Kakumanu R, Baidoo EEK, Petzold CJ, Cruz-Morales P, Keasling JD. Edible mycelium bioengineered for enhanced nutritional value and sensory appeal using a modular synthetic biology toolkit. Nat Commun 2024; 15:2099. [PMID: 38485948 PMCID: PMC10940619 DOI: 10.1038/s41467-024-46314-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 02/21/2024] [Indexed: 03/18/2024] Open
Abstract
Filamentous fungi are critical in the transition to a more sustainable food system. While genetic modification of these organisms has promise for enhancing the nutritional value, sensory appeal, and scalability of fungal foods, genetic tools and demonstrated use cases for bioengineered food production by edible strains are lacking. Here, we develop a modular synthetic biology toolkit for Aspergillus oryzae, an edible fungus used in fermented foods, protein production, and meat alternatives. Our toolkit includes a CRISPR-Cas9 method for gene integration, neutral loci, and tunable promoters. We use these tools to elevate intracellular levels of the nutraceutical ergothioneine and the flavor-and color molecule heme in the edible biomass. The strain overproducing heme is red in color and is readily formulated into imitation meat patties with minimal processing. These findings highlight the promise of synthetic biology to enhance fungal foods and provide useful genetic tools for applications in food production and beyond.
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Affiliation(s)
- Vayu Maini Rekdal
- Department of Bioengineering, University of California, Berkeley, CA, 94720, USA
- Miller Institute for Basic Research in Science, University of California, Berkeley, CA, 94720, USA
- Joint BioEnergy Institute, Emeryville, CA, 94608, USA
| | - Casper R B van der Luijt
- Joint BioEnergy Institute, Emeryville, CA, 94608, USA
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kgs. Lyngby, Denmark
- Department of Food Science, University of Copenhagen, 1958, Frederiksberg, Denmark
- Lawrence Berkeley National Laboratory, Biological Systems and Engineering Division, Berkeley, CA, 94720, USA
| | - Yan Chen
- Joint BioEnergy Institute, Emeryville, CA, 94608, USA
- Lawrence Berkeley National Laboratory, Biological Systems and Engineering Division, Berkeley, CA, 94720, USA
| | - Ramu Kakumanu
- Joint BioEnergy Institute, Emeryville, CA, 94608, USA
- Lawrence Berkeley National Laboratory, Biological Systems and Engineering Division, Berkeley, CA, 94720, USA
| | - Edward E K Baidoo
- Joint BioEnergy Institute, Emeryville, CA, 94608, USA
- Lawrence Berkeley National Laboratory, Biological Systems and Engineering Division, Berkeley, CA, 94720, USA
| | - Christopher J Petzold
- Joint BioEnergy Institute, Emeryville, CA, 94608, USA
- Lawrence Berkeley National Laboratory, Biological Systems and Engineering Division, Berkeley, CA, 94720, USA
| | - Pablo Cruz-Morales
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kgs. Lyngby, Denmark
| | - Jay D Keasling
- Department of Bioengineering, University of California, Berkeley, CA, 94720, USA.
- Joint BioEnergy Institute, Emeryville, CA, 94608, USA.
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kgs. Lyngby, Denmark.
- Lawrence Berkeley National Laboratory, Biological Systems and Engineering Division, Berkeley, CA, 94720, USA.
- California Institute of Quantitative Biosciences (QB3), University of California, Berkeley, CA, 94720, USA.
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA, 94720, USA.
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8
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Petersen SD, Levassor L, Pedersen CM, Madsen J, Hansen LG, Zhang J, Haidar AK, Frandsen RJN, Keasling JD, Weber T, Sonnenschein N, K. Jensen M. teemi: An open-source literate programming approach for iterative design-build-test-learn cycles in bioengineering. PLoS Comput Biol 2024; 20:e1011929. [PMID: 38457467 PMCID: PMC10954146 DOI: 10.1371/journal.pcbi.1011929] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 03/20/2024] [Accepted: 02/17/2024] [Indexed: 03/10/2024] Open
Abstract
Synthetic biology dictates the data-driven engineering of biocatalysis, cellular functions, and organism behavior. Integral to synthetic biology is the aspiration to efficiently find, access, interoperate, and reuse high-quality data on genotype-phenotype relationships of native and engineered biosystems under FAIR principles, and from this facilitate forward-engineering strategies. However, biology is complex at the regulatory level, and noisy at the operational level, thus necessitating systematic and diligent data handling at all levels of the design, build, and test phases in order to maximize learning in the iterative design-build-test-learn engineering cycle. To enable user-friendly simulation, organization, and guidance for the engineering of biosystems, we have developed an open-source python-based computer-aided design and analysis platform operating under a literate programming user-interface hosted on Github. The platform is called teemi and is fully compliant with FAIR principles. In this study we apply teemi for i) designing and simulating bioengineering, ii) integrating and analyzing multivariate datasets, and iii) machine-learning for predictive engineering of metabolic pathway designs for production of a key precursor to medicinal alkaloids in yeast. The teemi platform is publicly available at PyPi and GitHub.
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Affiliation(s)
- Søren D. Petersen
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Lucas Levassor
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Christine M. Pedersen
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Jan Madsen
- Department of Applied Mathematics and Computer Science, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Lea G. Hansen
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Jie Zhang
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Ahmad K. Haidar
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Rasmus J. N. Frandsen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Jay D. Keasling
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark
- Joint BioEnergy Institute, Emeryville, California, United States of America
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
- Department of Chemical and Biomolecular Engineering, Department of Bioengineering, University of California, Berkeley, California, United States of America
- Center for Synthetic Biochemistry, Institute for Synthetic Biology, Shenzhen Institutes of Advanced Technologies, Shenzhen, China
| | - Tilmann Weber
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Nikolaus Sonnenschein
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Michael K. Jensen
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark
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9
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Roberts JB, Nava AA, Pearson AN, Incha MR, Valencia LE, Ma M, Rao A, Keasling JD. Foldy: An open-source web application for interactive protein structure analysis. PLoS Comput Biol 2024; 20:e1011171. [PMID: 38306398 PMCID: PMC10866462 DOI: 10.1371/journal.pcbi.1011171] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 02/14/2024] [Accepted: 01/05/2024] [Indexed: 02/04/2024] Open
Abstract
Foldy is a cloud-based application that allows non-computational biologists to easily utilize advanced AI-based structural biology tools, including AlphaFold and DiffDock. With many deployment options, it can be employed by individuals, labs, universities, and companies in the cloud without requiring hardware resources, but it can also be configured to utilize locally available computers. Foldy enables scientists to predict the structure of proteins and complexes up to 6000 amino acids with AlphaFold, visualize Pfam annotations, and dock ligands with AutoDock Vina and DiffDock. In our manuscript, we detail Foldy's interface design, deployment strategies, and optimization for various user scenarios. We demonstrate its application through case studies including rational enzyme design and analyzing proteins with domains of unknown function. Furthermore, we compare Foldy's interface and management capabilities with other open and closed source tools in the field, illustrating its practicality in managing complex data and computation tasks. Our manuscript underlines the benefits of Foldy as a day-to-day tool for life science researchers, and shows how Foldy can make modern tools more accessible and efficient.
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Affiliation(s)
- Jacob B. Roberts
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, California, United States of America
- Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
- Department of Bioengineering, University of California, Berkeley, Berkeley, California, United States of America
| | - Alberto A. Nava
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, California, United States of America
- Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, California, United States of America
| | - Allison N. Pearson
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, California, United States of America
- Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, California, United States of America
| | - Matthew R. Incha
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, California, United States of America
- Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, California, United States of America
| | - Luis E. Valencia
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, California, United States of America
- Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, California, United States of America
| | - Melody Ma
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California, United States of America
| | - Abhay Rao
- Department of Bioengineering, University of California, Berkeley, Berkeley, California, United States of America
| | - Jay D. Keasling
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, California, United States of America
- Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
- Department of Bioengineering, University of California, Berkeley, Berkeley, California, United States of America
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, California, United States of America
- Center for Synthetic Biochemistry, Shenzhen Institutes for Advanced Technologies, Shenzhen, People’s Republic of China
- The Novo Nordisk Foundation Center for Biosustainability, Technical University Denmark, Kemitorvet, Denmark
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10
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Pearson AN, Incha MR, Ho CN, Schmidt M, Roberts JB, Nava AA, Keasling JD. Characterization and Diversification of AraC/XylS Family Regulators Guided by Transposon Sequencing. ACS Synth Biol 2024; 13:206-219. [PMID: 38113125 DOI: 10.1021/acssynbio.3c00441] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2023]
Abstract
In this study, we explored the development of engineered inducible systems. Publicly available data from previous transposon sequencing assays were used to identify regulators of metabolism in Pseudomonas putida KT2440. For AraC family regulators (AFRs) represented in these data, we posited AFR/promoter/inducer groupings. Twelve promoters were characterized for a response to their proposed inducers in P. putida, and the resultant data were used to create and test nine two-plasmid sensor systems in Escherichia coli. Several of these were further developed into a palette of single-plasmid inducible systems. From these experiments, we observed an unreported inducer response from a previously characterized AFR, demonstrated that the addition of a P. putida transporter improved the sensor dynamics of an AFR in E. coli, and identified an uncharacterized AFR with a novel potential inducer specificity. Finally, targeted mutations in an AFR, informed by structural predictions, enabled the further diversification of these inducible plasmids.
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Affiliation(s)
- Allison N Pearson
- Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, California 94608, United States
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, United States
| | - Matthew R Incha
- Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, California 94608, United States
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, United States
| | - Cindy N Ho
- Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, California 94608, United States
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Matthias Schmidt
- Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, California 94608, United States
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- Institute of Applied Microbiology-iAMB, Aachen Biology and Biotechnology-ABBt, RWTH Aachen University, Aachen 52062, Germany
| | - Jacob B Roberts
- Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, California 94608, United States
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- Joint Program in Bioengineering, University of California, Berkeley/San Francisco, California 94720, United States
| | - Alberto A Nava
- Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, California 94608, United States
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720, United States
| | - Jay D Keasling
- Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, California 94608, United States
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- Joint Program in Bioengineering, University of California, Berkeley/San Francisco, California 94720, United States
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720, United States
- Institute for Quantitative Biosciences, University of California, Berkeley, California 94720, United States
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby 2800, Denmark
- Center for Synthetic Biochemistry, Institute for Synthetic Biology, Shenzhen Institutes for Advanced Technologies, Shenzhen 518055, China
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11
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Chen R, Wang M, Keasling JD, Hu T, Yin X. Expanding the structural diversity of terpenes by synthetic biology approaches. Trends Biotechnol 2024:S0167-7799(23)00345-1. [PMID: 38233232 DOI: 10.1016/j.tibtech.2023.12.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 12/08/2023] [Accepted: 12/11/2023] [Indexed: 01/19/2024]
Abstract
Terpenoids display chemical and structural diversities as well as important biological activities. Despite their extreme variability, the range of these structures is limited by the scope of natural products that canonically derive from interconvertible five-carbon (C5) isoprene units. New approaches have recently been developed to expand their structural diversity. This review systematically explores the combinatorial biosynthesis of noncanonical building blocks via the coexpression of the canonical mevalonate (MVA) pathway and C-methyltransferases (C-MTs), or by using the lepidopteran mevalonate (LMVA) pathway. Unnatural terpenoids can be created from farnesyl diphosphate (FPP) analogs by chemobiological synthesis and terpene cyclopropanation by artificial metalloenzymes (ArMs). Advanced technologies to accelerate terpene biosynthesis are discussed. This review provides a valuable reference for increasing the diversity of valuable terpenoids and their derivatives, as well as for expanding their potential applications.
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Affiliation(s)
- Rong Chen
- Key Laboratory of Elemene Class Anti-Cancer Chinese Medicine of Zhejiang Province, School of Pharmacy, School of Public Health, Hangzhou Normal University, Hangzhou 310000, China; Joint BioEnergy Institute, Emeryville, CA 94608, USA.
| | - Ming Wang
- Key Laboratory of Elemene Class Anti-Cancer Chinese Medicine of Zhejiang Province, School of Pharmacy, School of Public Health, Hangzhou Normal University, Hangzhou 310000, China
| | - Jay D Keasling
- Joint BioEnergy Institute, Emeryville, CA 94608, USA; California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA 94720, USA; Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA 94720, USA; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Department of Bioengineering, University of California, Berkeley, CA 94720, USA; Center for Synthetic Biochemistry, Institute for Synthetic Biology, Shenzhen Institutes of Advanced Technologies, Shenzhen 518055, China; Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Tianyuan Hu
- Key Laboratory of Elemene Class Anti-Cancer Chinese Medicine of Zhejiang Province, School of Pharmacy, School of Public Health, Hangzhou Normal University, Hangzhou 310000, China
| | - Xiaopu Yin
- Key Laboratory of Elemene Class Anti-Cancer Chinese Medicine of Zhejiang Province, School of Pharmacy, School of Public Health, Hangzhou Normal University, Hangzhou 310000, China.
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12
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Luckie BA, Kashyap M, Pearson AN, Chen Y, Liu Y, Valencia LE, Carrillo Romero A, Hudson GA, Tao XB, Wu B, Petzold CJ, Keasling JD. Development of Corynebacterium glutamicum as a monoterpene production platform. Metab Eng 2024; 81:110-122. [PMID: 38056688 DOI: 10.1016/j.ymben.2023.11.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2023] [Revised: 11/29/2023] [Accepted: 11/30/2023] [Indexed: 12/08/2023]
Abstract
Monoterpenes are commonly known for their role in the flavors and fragrances industry and are also gaining attention for other uses like insect repellant and as potential renewable fuels for aviation. Corynebacterium glutamicum, a Generally Recognized as Safe microbe, has been a choice organism in industry for the annual million ton-scale bioproduction of amino acids for more than 50 years; however, efforts to produce monoterpenes in C. glutamicum have remained relatively limited. In this study, we report a further expansion of the C. glutamicum biosynthetic repertoire through the development and optimization of a mevalonate-based monoterpene platform. In the course of our plasmid design iterations, we increased flux through the mevalonate-based bypass pathway, measuring isoprenol production as a proxy for monoterpene precursor abundance and demonstrating the highest reported titers in C. glutamicum to date at 1504.6 mg/L. Our designs also evaluated the effects of backbone, promoter, and GPP synthase homolog origin on monoterpene product titers. Monoterpene production was further improved by disrupting competing pathways for isoprenoid precursor supply and by implementing a biphasic production system to prevent volatilization. With this platform, we achieved 321.1 mg/L of geranoids, 723.6 mg/L of 1,8-cineole, and 227.8 mg/L of linalool. Furthermore, we determined that C. glutamicum first oxidizes geraniol through an aldehyde intermediate before it is asymmetrically reduced to citronellol. Additionally, we demonstrate that the aldehyde reductase, AdhC, possesses additional substrate promiscuity for acyclic monoterpene aldehydes.
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Affiliation(s)
- Bridget A Luckie
- Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, CA, 94608, USA; Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA; Department of Molecular and Cell Biology, University of California, Berkeley, CA, 94720, USA
| | - Meera Kashyap
- Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, CA, 94608, USA; Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Allison N Pearson
- Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, CA, 94608, USA; Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA; Department of Plant and Microbial Biology, University of California, Berkeley, CA, 94720, USA
| | - Yan Chen
- Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, CA, 94608, USA; Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Yuzhong Liu
- Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, CA, 94608, USA; Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA; Institute for Quantitative Biosciences, University of California, Berkeley, CA, 94720, USA
| | - Luis E Valencia
- Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, CA, 94608, USA; Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA; Joint Program in Bioengineering, University of California, Berkeley, San Francisco, CA, 94720, USA
| | - Alexander Carrillo Romero
- Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, CA, 94608, USA; Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Graham A Hudson
- Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, CA, 94608, USA; Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA; Institute for Quantitative Biosciences, University of California, Berkeley, CA, 94720, USA
| | - Xavier B Tao
- Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, CA, 94608, USA; Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Bryan Wu
- Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, CA, 94608, USA; Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Christopher J Petzold
- Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, CA, 94608, USA; Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Jay D Keasling
- Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, CA, 94608, USA; Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA; Institute for Quantitative Biosciences, University of California, Berkeley, CA, 94720, USA; Joint Program in Bioengineering, University of California, Berkeley, San Francisco, CA, 94720, USA; Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA, 94720, USA; The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Denmark; Center for Synthetic Biochemistry, Institute for Synthetic Biology, Shenzhen Institutes for Advanced Technologies, Shenzhen, China.
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13
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Huang J, Keasling JD. Carbene chemistry for unnatural biosynthesis. Sci China Life Sci 2024; 67:204-207. [PMID: 37955778 DOI: 10.1007/s11427-023-2470-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Accepted: 10/16/2023] [Indexed: 11/14/2023]
Affiliation(s)
- Jing Huang
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, 94720, USA
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, 94608, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, 94720, USA
| | - Jay D Keasling
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, 94720, USA.
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, 94608, USA.
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, 94720, USA.
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, 2800, Denmark.
- Department of Bioengineering, University of California, Berkeley, 94720, USA.
- Synthetic Biochemistry Center, Institute for Synthetic Biology, Shenzhen Institutes for Advanced Technologies, Shenzhen, 518055, China.
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14
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Wu J, Zhou L, Peng H, Wang Z, Wang Z, Keasling JD, Liu S, Zhou G, Ding S, Wang Q, Wang X, Chen X, Lang Y, Xia M, Guan X, Dong M, Zhou J, Chen J. A General and Convenient Peptide Self-Assembling Mechanism for Developing Supramolecular Versatile Nanomaterials Based on The Biosynthetic Hybrid Amyloid-Resilin Protein. Adv Mater 2024; 36:e2304364. [PMID: 37885340 DOI: 10.1002/adma.202304364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 10/17/2023] [Indexed: 10/28/2023]
Abstract
Self-assembling peptides are valuable building blocks to fabricate supramolecular biomaterials, which have broad applications from biomedicine to biotechnology. However, limited choices to induce different globular proteins into hydrogels hinder these designs. Here, an easy-to-implement and tunable self-assembling strategy, which employs Ure2 amyloidogenic peptide, are described to induce any target proteins to assemble into supramolecular hydrogels alone or in combination with notable compositional control. Furthermore, the collective effect of nanoscale interactions among amyloid nanofibrils and partially disordered elastomeric polypeptides are investigated. This led to many useful macroscopic material properties simultaneously emerging from one pure protein material, i.e. strong adhesion to any substrates under wet conditions, rapidly self--assembling into robust and porous hydrogels, adaptation to remodeling processes, strongly promoting cell adhesion, proliferation and differentiation. Moreover, he demonstrated this supramolecular material's robust performance in vitro and vivo for tissue engineering, cosmetic and hemostasis applications and exhibited superior performance compared to corresponding commercial counterparts. To the best of his knowledge, few pure protein-based materials could meet such seemingly mutually exclusive properties simultaneously. Such versatility renders this novel supramolecular nanomaterial as next-generation functional protein-based materials, and he demonstrated the sequence level modulation of structural order and disorder as an untapped principle to design new proteins.
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Affiliation(s)
- Junjun Wu
- School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, China
| | - Lin Zhou
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
| | - Hu Peng
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
| | - Zhaojun Wang
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
| | - Zhaoshi Wang
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
| | - Jay D Keasling
- Departments of Chemical & Biomolecular Engineering and of Bioengineering, University of California Berkeley, Berkeley, CA, 94720, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Center for Biosustainability, Technical University of Denmark, Lyngby, 2800, Denmark
| | - Shike Liu
- Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China
| | - Guanghong Zhou
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
| | - Shijie Ding
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
| | - Qiong Wang
- School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, China
| | - Xuejian Wang
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
| | - Xinxiu Chen
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
| | - Yifei Lang
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
| | - Mo Xia
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
| | - Xin Guan
- Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China
| | - Mingsheng Dong
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
| | - Jingwen Zhou
- Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China
| | - Jian Chen
- Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China
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15
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Li F, Chen Q, Deng H, Ye S, Chen R, Keasling JD, Luo X. One-pot selective biosynthesis of Tyrian purple in Escherichia coli. Metab Eng 2024; 81:100-109. [PMID: 38000548 DOI: 10.1016/j.ymben.2023.11.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 11/17/2023] [Accepted: 11/19/2023] [Indexed: 11/26/2023]
Abstract
Tyrian purple (6,6'-Dibromoindigo) is an ancient precious dye, which possesses remarkable properties as a biocompatible semiconductor material. Recently, biosynthesis has emerged as an alternative for the sustainable production of Tyrian purple from a natural substrate. However, the selectivity issue in enzymatic tryptophan (Trp) and bromotryptophan (6-Br-Trp) degradation was an obstacle for obtaining high-purity Tyrian purple in a single cell biosynthesis. In this study, we present a simplified one-pot process for the production of Tyrian purple from Trp in Escherichia coli (E. coli) using Trp 6-halogenase from Streptomyces toxytricini (SttH), tryptophanase from E. coli (TnaA) and a two-component indole oxygenase from Providencia Rettgeri GS-2 (GS-C and GS-D). To enhance the in vivo solubility and activity of SttH and flavin reductase (Fre) fusion enzyme (Fre-L3-SttH), a chaperone system of GroEL/GroES (pGro7) was introduced in addition to the implementation of a set of optimization strategies, including fine-tuning the expression vector, medium, concentration of bromide salt and inducer. To overcome the selectivity issue and achieve a higher conversion yield of Tyrian purple with minimal indigo formation, we applied the λpL/pR-cI857 thermoinducible system to temporally control the bifunctional fusion enzyme of TnaA and monooxygenase GS-C (TnaA-L3-GS-C). Through optimization of the fermentation process, we were able to achieve a Tyrian purple titer of 44.5 mg L-1 with minimal indigo byproduct from 500 μM Trp. To the best of our knowledge, this is the first report of the selective production of Tyrian purple in E. colivia a one-pot process.
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Affiliation(s)
- Feifei Li
- Shenzhen Key Laboratory for the Intelligent Microbial Manufacturing of Medicines, CAS Key Laboratory of Quantitative Engineering Biology, Center for Synthetic Biochemistry, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China; School of Life Sciences, Inner Mongolia University, Hohhot, 150100, China
| | - Que Chen
- Shenzhen Key Laboratory for the Intelligent Microbial Manufacturing of Medicines, CAS Key Laboratory of Quantitative Engineering Biology, Center for Synthetic Biochemistry, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Huaxiang Deng
- Shenzhen Key Laboratory for the Intelligent Microbial Manufacturing of Medicines, CAS Key Laboratory of Quantitative Engineering Biology, Center for Synthetic Biochemistry, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Shumei Ye
- Shenzhen Key Laboratory for the Intelligent Microbial Manufacturing of Medicines, CAS Key Laboratory of Quantitative Engineering Biology, Center for Synthetic Biochemistry, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China; School of Life Sciences, Inner Mongolia University, Hohhot, 150100, China; Basic Medical College, Inner Mongolia Medical University, Hohhot, 150100, China
| | - Ruidong Chen
- Shenzhen Key Laboratory for the Intelligent Microbial Manufacturing of Medicines, CAS Key Laboratory of Quantitative Engineering Biology, Center for Synthetic Biochemistry, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Jay D Keasling
- Shenzhen Key Laboratory for the Intelligent Microbial Manufacturing of Medicines, CAS Key Laboratory of Quantitative Engineering Biology, Center for Synthetic Biochemistry, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China; Center for Synthetic Biochemistry, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA; QB3 Institute, University of California, Berkeley, CA, 94720, USA; Department of Chemical and Biomolecular Engineering and Department of Bioengineering, University of California, Berkeley, CA, 94720, USA; The Novo Nordisk Foundation Center for Biosustainability, Technical University Denmark, Kemitorvet, Building 220, Kongens Lyngby, 2800, Denmark
| | - Xiaozhou Luo
- Shenzhen Key Laboratory for the Intelligent Microbial Manufacturing of Medicines, CAS Key Laboratory of Quantitative Engineering Biology, Center for Synthetic Biochemistry, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China; School of Life Sciences, Inner Mongolia University, Hohhot, 150100, China.
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16
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Nava A, Fear AL, Lee N, Mellinger P, Lan G, McCauley J, Tan S, Kaplan N, Goyal G, Coates RC, Roberts J, Johnson Z, Hu R, Wu B, Ahn J, Kim WE, Wan Y, Yin K, Hillson N, Haushalter RW, Keasling JD. Automated Platform for the Plasmid Construction Process. ACS Synth Biol 2023; 12:3506-3513. [PMID: 37948662 PMCID: PMC10729297 DOI: 10.1021/acssynbio.3c00292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2023] [Indexed: 11/12/2023]
Abstract
There is a growing need for applications capable of handling large synthesis biology experiments. At the core of synthetic biology is the process of cloning and manipulating DNA as plasmids. Here, we report the development of an application named DNAda capable of writing automation instructions for any given DNA construct design generated by the J5 DNA assembly program. We also describe the automation pipeline and several useful features. The pipeline is particularly useful for the construction of combinatorial DNA assemblies. Furthermore, we demonstrate the platform by constructing a library of polyketide synthase parts, which includes 120 plasmids ranging in size from 7 to 14 kb from 4 to 7 DNA fragments.
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Affiliation(s)
- Alberto
A. Nava
- Joint
BioEnergy Institute, Lawrence Berkeley National
Laboratory, Emeryville, California 94608, United States
- Biological
Systems and Engineering Division, Lawrence
Berkeley National Laboratory, Berkeley, California 94720, United States
- Department
of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, California 94720, United States
| | - Anna Lisa Fear
- Joint
BioEnergy Institute, Lawrence Berkeley National
Laboratory, Emeryville, California 94608, United States
- Biological
Systems and Engineering Division, Lawrence
Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Namil Lee
- Joint
BioEnergy Institute, Lawrence Berkeley National
Laboratory, Emeryville, California 94608, United States
- Biological
Systems and Engineering Division, Lawrence
Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Peter Mellinger
- Joint
BioEnergy Institute, Lawrence Berkeley National
Laboratory, Emeryville, California 94608, United States
- Biological
Systems and Engineering Division, Lawrence
Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Guangxu Lan
- Joint
BioEnergy Institute, Lawrence Berkeley National
Laboratory, Emeryville, California 94608, United States
- Biological
Systems and Engineering Division, Lawrence
Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Joshua McCauley
- Joint
BioEnergy Institute, Lawrence Berkeley National
Laboratory, Emeryville, California 94608, United States
- Biological
Systems and Engineering Division, Lawrence
Berkeley National Laboratory, Berkeley, California 94720, United States
- DOE
Agile BioFoundry, Emeryville, California 94608, United States
| | - Stephen Tan
- Joint
BioEnergy Institute, Lawrence Berkeley National
Laboratory, Emeryville, California 94608, United States
- Biological
Systems and Engineering Division, Lawrence
Berkeley National Laboratory, Berkeley, California 94720, United States
- DOE
Agile BioFoundry, Emeryville, California 94608, United States
| | - Nurgul Kaplan
- Joint
BioEnergy Institute, Lawrence Berkeley National
Laboratory, Emeryville, California 94608, United States
- Biological
Systems and Engineering Division, Lawrence
Berkeley National Laboratory, Berkeley, California 94720, United States
- DOE
Agile BioFoundry, Emeryville, California 94608, United States
| | - Garima Goyal
- Joint
BioEnergy Institute, Lawrence Berkeley National
Laboratory, Emeryville, California 94608, United States
- Biological
Systems and Engineering Division, Lawrence
Berkeley National Laboratory, Berkeley, California 94720, United States
- DOE
Agile BioFoundry, Emeryville, California 94608, United States
| | - R. Cameron Coates
- Joint
BioEnergy Institute, Lawrence Berkeley National
Laboratory, Emeryville, California 94608, United States
- Biological
Systems and Engineering Division, Lawrence
Berkeley National Laboratory, Berkeley, California 94720, United States
- DOE
Agile BioFoundry, Emeryville, California 94608, United States
| | - Jacob Roberts
- Joint
BioEnergy Institute, Lawrence Berkeley National
Laboratory, Emeryville, California 94608, United States
- Biological
Systems and Engineering Division, Lawrence
Berkeley National Laboratory, Berkeley, California 94720, United States
- Department
of Bioengineering, University of California,
Berkeley, Berkeley, California 94720, United States
| | - Zahmiria Johnson
- Department
of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, California 94720, United States
| | - Romina Hu
- Department
of Bioengineering, University of California,
Berkeley, Berkeley, California 94720, United States
| | - Bryan Wu
- Department
of Bioengineering, University of California,
Berkeley, Berkeley, California 94720, United States
| | - Jared Ahn
- Department
of Bioengineering, University of California,
Berkeley, Berkeley, California 94720, United States
| | - Woojoo E. Kim
- Joint
BioEnergy Institute, Lawrence Berkeley National
Laboratory, Emeryville, California 94608, United States
- Biological
Systems and Engineering Division, Lawrence
Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Yao Wan
- Joint
BioEnergy Institute, Lawrence Berkeley National
Laboratory, Emeryville, California 94608, United States
- Biological
Systems and Engineering Division, Lawrence
Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Kevin Yin
- Joint
BioEnergy Institute, Lawrence Berkeley National
Laboratory, Emeryville, California 94608, United States
- Biological
Systems and Engineering Division, Lawrence
Berkeley National Laboratory, Berkeley, California 94720, United States
- Department
of Plant and Microbial Biology, University
of California, Berkeley, Berkeley, California 94720, United States
| | - Nathan Hillson
- Joint
BioEnergy Institute, Lawrence Berkeley National
Laboratory, Emeryville, California 94608, United States
- Biological
Systems and Engineering Division, Lawrence
Berkeley National Laboratory, Berkeley, California 94720, United States
- DOE
Agile BioFoundry, Emeryville, California 94608, United States
| | - Robert W. Haushalter
- Joint
BioEnergy Institute, Lawrence Berkeley National
Laboratory, Emeryville, California 94608, United States
- Biological
Systems and Engineering Division, Lawrence
Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Jay D. Keasling
- Joint
BioEnergy Institute, Lawrence Berkeley National
Laboratory, Emeryville, California 94608, United States
- Biological
Systems and Engineering Division, Lawrence
Berkeley National Laboratory, Berkeley, California 94720, United States
- Department
of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, California 94720, United States
- Department
of Bioengineering, University of California,
Berkeley, Berkeley, California 94720, United States
- Center
for Synthetic Biochemistry, Shenzhen Institutes
for Advanced Technologies, Shenzhen 518055, P.R. China
- The
Novo Nordisk Foundation Center for Biosustainability, Technical University Denmark, Kemitorvet, Building 220, Kongens Lyngby 2800, Denmark
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17
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Abstract
Prediction of enzyme kinetic parameters is essential for designing and optimizing enzymes for various biotechnological and industrial applications, but the limited performance of current prediction tools on diverse tasks hinders their practical applications. Here, we introduce UniKP, a unified framework based on pretrained language models for the prediction of enzyme kinetic parameters, including enzyme turnover number (kcat), Michaelis constant (Km), and catalytic efficiency (kcat / Km), from protein sequences and substrate structures. A two-layer framework derived from UniKP (EF-UniKP) has also been proposed to allow robust kcat prediction in considering environmental factors, including pH and temperature. In addition, four representative re-weighting methods are systematically explored to successfully reduce the prediction error in high-value prediction tasks. We have demonstrated the application of UniKP and EF-UniKP in several enzyme discovery and directed evolution tasks, leading to the identification of new enzymes and enzyme mutants with higher activity. UniKP is a valuable tool for deciphering the mechanisms of enzyme kinetics and enables novel insights into enzyme engineering and their industrial applications.
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Affiliation(s)
- Han Yu
- Shenzhen Key Laboratory for the Intelligent Microbial Manufacturing of Medicines, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
- Center for Synthetic Biochemistry, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Huaxiang Deng
- Shenzhen Key Laboratory for the Intelligent Microbial Manufacturing of Medicines, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
- Center for Synthetic Biochemistry, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Jiahui He
- Shenzhen Key Laboratory for the Intelligent Microbial Manufacturing of Medicines, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
- Center for Synthetic Biochemistry, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Jay D Keasling
- Center for Synthetic Biochemistry, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
- Joint BioEnergy Institute, Emeryville, CA, 94608, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Department of Chemical and Biomolecular Engineering & Department of Bioengineering, University of California, Berkeley, CA, 94720, USA
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kgs, Lyngby, Denmark
| | - Xiaozhou Luo
- Shenzhen Key Laboratory for the Intelligent Microbial Manufacturing of Medicines, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China.
- Center for Synthetic Biochemistry, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China.
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18
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Li X, Gadar-Lopez AE, Chen L, Jayachandran S, Cruz-Morales P, Keasling JD. Mining natural products for advanced biofuels and sustainable bioproducts. Curr Opin Biotechnol 2023; 84:103003. [PMID: 37769513 DOI: 10.1016/j.copbio.2023.103003] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 09/03/2023] [Accepted: 09/03/2023] [Indexed: 10/03/2023]
Abstract
Recently, there has been growing interest in the sustainable production of biofuels and bioproducts derived from renewable sources. Natural products, the largest and more structurally diverse group of metabolites, hold significant promise as sources for such bio-based products. However, there are two primary challenges in harnessing natural products' potential: precise mining of biosynthetic gene clusters (BGCs) that can be used as scaffolds or bioparts and their functional expression for biofuel and bioproduct manufacture. In this review, we explore recent advances in the development of bioinformatic tools for BGC mining and the manipulation of various hosts for natural product-based biofuels and bioproducts manufacture. Moreover, we discuss potential strategies for expanding the chemical diversity of biofuels and bioproducts and enhancing their overall yield.
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Affiliation(s)
- Xiaowei Li
- Novo Nordisk Foundation Center for Biosustainability, Danmarks Tekniske Universitet, Kongens Lyngby, Denmark
| | - Adrian E Gadar-Lopez
- Novo Nordisk Foundation Center for Biosustainability, Danmarks Tekniske Universitet, Kongens Lyngby, Denmark
| | - Ling Chen
- Novo Nordisk Foundation Center for Biosustainability, Danmarks Tekniske Universitet, Kongens Lyngby, Denmark
| | - Sidharth Jayachandran
- Novo Nordisk Foundation Center for Biosustainability, Danmarks Tekniske Universitet, Kongens Lyngby, Denmark
| | - Pablo Cruz-Morales
- Novo Nordisk Foundation Center for Biosustainability, Danmarks Tekniske Universitet, Kongens Lyngby, Denmark.
| | - Jay D Keasling
- Novo Nordisk Foundation Center for Biosustainability, Danmarks Tekniske Universitet, Kongens Lyngby, Denmark; Lawrence Berkeley National Laboratory, Biological Systems and Engineering Division, Berkeley, CA, USA; Joint BioEnergy Institute, Emeryville, CA, USA; Departments of Chemical & Biomolecular Engineering and of Bioengineering, University of California, Berkeley, CA 94720, USA; Center for Synthetic Biochemistry, Shenzhen Institutes for Advanced Technologies, Shenzhen, China.
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19
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Bradley SA, Lehka BJ, Hansson FG, Adhikari KB, Rago D, Rubaszka P, Haidar AK, Chen L, Hansen LG, Gudich O, Giannakou K, Lengger B, Gill RT, Nakamura Y, de Bernonville TD, Koudounas K, Romero-Suarez D, Ding L, Qiao Y, Frimurer TM, Petersen AA, Besseau S, Kumar S, Gautron N, Melin C, Marc J, Jeanneau R, O'Connor SE, Courdavault V, Keasling JD, Zhang J, Jensen MK. Biosynthesis of natural and halogenated plant monoterpene indole alkaloids in yeast. Nat Chem Biol 2023; 19:1551-1560. [PMID: 37932529 PMCID: PMC10667104 DOI: 10.1038/s41589-023-01430-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 08/25/2023] [Indexed: 11/08/2023]
Abstract
Monoterpenoid indole alkaloids (MIAs) represent a large class of plant natural products with marketed pharmaceutical activities against a wide range of indications, including cancer, malaria and hypertension. Halogenated MIAs have shown improved pharmaceutical properties; however, synthesis of new-to-nature halogenated MIAs remains a challenge. Here we demonstrate a platform for de novo biosynthesis of two MIAs, serpentine and alstonine, in baker's yeast Saccharomyces cerevisiae and deploy it to systematically explore the biocatalytic potential of refactored MIA pathways for the production of halogenated MIAs. From this, we demonstrate conversion of individual haloindole derivatives to a total of 19 different new-to-nature haloserpentine and haloalstonine analogs. Furthermore, by process optimization and heterologous expression of a modified halogenase in the microbial MIA platform, we document de novo halogenation and biosynthesis of chloroalstonine. Together, this study highlights a microbial platform for enzymatic exploration and production of complex natural and new-to-nature MIAs with therapeutic potential.
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Affiliation(s)
- Samuel A Bradley
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Beata J Lehka
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Frederik G Hansson
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Khem B Adhikari
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Daniela Rago
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Paulina Rubaszka
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Ahmad K Haidar
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Ling Chen
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Lea G Hansen
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Olga Gudich
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Konstantina Giannakou
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Bettina Lengger
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Ryan T Gill
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Yoko Nakamura
- Department of Natural Product Biosynthesis, Max Planck Institute for Chemical Ecology, Jena, Germany
| | | | | | - David Romero-Suarez
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Ling Ding
- Department of Bioengineering, Technical University of Denmark, Lyngby, Denmark
| | - Yijun Qiao
- Department of Bioengineering, Technical University of Denmark, Lyngby, Denmark
| | - Thomas M Frimurer
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
| | - Anja A Petersen
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
| | - Sébastien Besseau
- EA2106 Biomolécules et Biotechnologies Végétales, Université de Tours, Tours, France
| | - Sandeep Kumar
- EA2106 Biomolécules et Biotechnologies Végétales, Université de Tours, Tours, France
| | - Nicolas Gautron
- EA2106 Biomolécules et Biotechnologies Végétales, Université de Tours, Tours, France
| | - Celine Melin
- EA2106 Biomolécules et Biotechnologies Végétales, Université de Tours, Tours, France
| | - Jillian Marc
- EA2106 Biomolécules et Biotechnologies Végétales, Université de Tours, Tours, France
| | | | - Sarah E O'Connor
- Department of Natural Product Biosynthesis, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Vincent Courdavault
- EA2106 Biomolécules et Biotechnologies Végétales, Université de Tours, Tours, France
| | - Jay D Keasling
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
- Joint BioEnergy Institute, Emeryville, CA, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, CA, USA
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA
- Center for Synthetic Biochemistry, Institute for Synthetic Biology, Shenzhen Institutes of Advanced Technologies, Shenzhen, China
| | - Jie Zhang
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark.
| | - Michael K Jensen
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark.
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20
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Garber ME, Frank V, Kazakov AE, Incha MR, Nava AA, Zhang H, Valencia LE, Keasling JD, Rajeev L, Mukhopadhyay A. REC protein family expansion by the emergence of a new signaling pathway. mBio 2023; 14:e0262223. [PMID: 37991384 PMCID: PMC10746176 DOI: 10.1128/mbio.02622-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 10/20/2023] [Indexed: 11/23/2023] Open
Abstract
IMPORTANCE We explore when and why large classes of proteins expand into new sequence space. We used an unsupervised machine learning approach to observe the sequence landscape of REC domains of bacterial response regulator proteins. We find that within-gene recombination can switch effector domains and, consequently, change the regulatory context of the duplicated protein.
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Affiliation(s)
- Megan E. Garber
- Department of Comparative Biochemistry, University of California, Berkeley, California, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Vered Frank
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Alexey E. Kazakov
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Matthew R. Incha
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
- Department of Plant and Microbial Biology, University of California, Berkeley, California, USA
| | - Alberto A. Nava
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California, USA
| | - Hanqiao Zhang
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
- Department of Bioengineering, University of California, Berkeley, California, USA
| | - Luis E. Valencia
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
- Department of Bioengineering, University of California, Berkeley, California, USA
| | - Jay D. Keasling
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
- Department of Plant and Microbial Biology, University of California, Berkeley, California, USA
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California, USA
- Department of Bioengineering, University of California, Berkeley, California, USA
- Center for Biosustainability, Danish Technical University, Lyngby, Denmark
- Center for Synthetic Biochemistry, Shenzhen Institutes for Advanced Technologies, Shenzhen, China
| | - Lara Rajeev
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Aindrila Mukhopadhyay
- Department of Comparative Biochemistry, University of California, Berkeley, California, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
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21
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Nava A, Roberts J, Haushalter RW, Wang Z, Keasling JD. Module-Based Polyketide Synthase Engineering for de Novo Polyketide Biosynthesis. ACS Synth Biol 2023; 12:3148-3155. [PMID: 37871264 PMCID: PMC10661043 DOI: 10.1021/acssynbio.3c00282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Indexed: 10/25/2023]
Abstract
Polyketide retrobiosynthesis, where the biosynthetic pathway of a given polyketide can be reversibly engineered due to the colinearity of the polyketide synthase (PKS) structure and function, has the potential to produce millions of organic molecules. Mixing and matching modules from natural PKSs is one of the routes to produce many of these molecules. Evolutionary analysis of PKSs suggests that traditionally used module boundaries may not lead to the most productive hybrid PKSs and that new boundaries around and within the ketosynthase domain may be more active when constructing hybrid PKSs. As this is still a nascent area of research, the generality of these design principles based on existing engineering efforts remains inconclusive. Recent advances in structural modeling and synthetic biology present an opportunity to accelerate PKS engineering by re-evaluating insights gained from previous engineering efforts with cutting edge tools.
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Affiliation(s)
- Alberto
A. Nava
- Joint
BioEnergy Institute, Lawrence Berkeley National
Laboratory, Emeryville, California 94608, United States
- Biological
Systems and Engineering Division, Lawrence
Berkeley National Laboratory, Berkeley, California 94720, United States
- Department
of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, California 94720, United States
| | - Jacob Roberts
- Joint
BioEnergy Institute, Lawrence Berkeley National
Laboratory, Emeryville, California 94608, United States
- Biological
Systems and Engineering Division, Lawrence
Berkeley National Laboratory, Berkeley, California 94720, United States
- Department
of Bioengineering, University of California,
Berkeley, Berkeley, California 94720, United States
| | - Robert W. Haushalter
- Joint
BioEnergy Institute, Lawrence Berkeley National
Laboratory, Emeryville, California 94608, United States
- Biological
Systems and Engineering Division, Lawrence
Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Zilong Wang
- Joint
BioEnergy Institute, Lawrence Berkeley National
Laboratory, Emeryville, California 94608, United States
- Biological
Systems and Engineering Division, Lawrence
Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Jay D. Keasling
- Joint
BioEnergy Institute, Lawrence Berkeley National
Laboratory, Emeryville, California 94608, United States
- Biological
Systems and Engineering Division, Lawrence
Berkeley National Laboratory, Berkeley, California 94720, United States
- Department
of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, California 94720, United States
- Department
of Bioengineering, University of California,
Berkeley, Berkeley, California 94720, United States
- Center
for Synthetic Biochemistry, Shenzhen Institutes
for Advanced Technologies, Shenzhen 518055, P.R. China
- The
Novo
Nordisk Foundation Center for Biosustainability, Technical University Denmark, Kemitorvet, Building 220, Kongens Lyngby 2800, Denmark
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22
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Schmidt M, Lee N, Zhan C, Roberts JB, Nava AA, Keiser LS, Vilchez AA, Chen Y, Petzold CJ, Haushalter RW, Blank LM, Keasling JD. Maximizing Heterologous Expression of Engineered Type I Polyketide Synthases: Investigating Codon Optimization Strategies. ACS Synth Biol 2023; 12:3366-3380. [PMID: 37851920 PMCID: PMC10661030 DOI: 10.1021/acssynbio.3c00367] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Indexed: 10/20/2023]
Abstract
Type I polyketide synthases (T1PKSs) hold enormous potential as a rational production platform for the biosynthesis of specialty chemicals. However, despite great progress in this field, the heterologous expression of PKSs remains a major challenge. One of the first measures to improve heterologous gene expression can be codon optimization. Although controversial, choosing the wrong codon optimization strategy can have detrimental effects on the protein and product levels. In this study, we analyzed 11 different codon variants of an engineered T1PKS and investigated in a systematic approach their influence on heterologous expression in Corynebacterium glutamicum, Escherichia coli, and Pseudomonas putida. Our best performing codon variants exhibited a minimum 50-fold increase in PKS protein levels, which also enabled the production of an unnatural polyketide in each of these hosts. Furthermore, we developed a free online tool (https://basebuddy.lbl.gov) that offers transparent and highly customizable codon optimization with up-to-date codon usage tables. In this work, we not only highlight the significance of codon optimization but also establish the groundwork for the high-throughput assembly and characterization of PKS pathways in alternative hosts.
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Affiliation(s)
- Matthias Schmidt
- Joint
BioEnergy Institute, 5885 Hollis Street, Emeryville, California 94608, United States
- Biological
Systems & Engineering Division, Lawrence
Berkeley National Laboratory, Berkeley, California 94720, United States
- Institute
of Applied Microbiology (iAMB), Aachen Biology and Biotechnology (ABBt), RWTH Aachen University, 52062 Aachen, Germany
- California
Institute for Quantitative Biosciences (QB3), University of California, Berkeley, California 94720, United States
| | - Namil Lee
- Joint
BioEnergy Institute, 5885 Hollis Street, Emeryville, California 94608, United States
- Biological
Systems & Engineering Division, Lawrence
Berkeley National Laboratory, Berkeley, California 94720, United States
- California
Institute for Quantitative Biosciences (QB3), University of California, Berkeley, California 94720, United States
| | - Chunjun Zhan
- Joint
BioEnergy Institute, 5885 Hollis Street, Emeryville, California 94608, United States
- Biological
Systems & Engineering Division, Lawrence
Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Jacob B. Roberts
- Joint
BioEnergy Institute, 5885 Hollis Street, Emeryville, California 94608, United States
- Biological
Systems & Engineering Division, Lawrence
Berkeley National Laboratory, Berkeley, California 94720, United States
- Joint
Program in Bioengineering, University of
California, Berkeley, California 94720, United States
| | - Alberto A. Nava
- Joint
BioEnergy Institute, 5885 Hollis Street, Emeryville, California 94608, United States
- Biological
Systems & Engineering Division, Lawrence
Berkeley National Laboratory, Berkeley, California 94720, United States
- Department
of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720, United States
| | - Leah S. Keiser
- Joint
BioEnergy Institute, 5885 Hollis Street, Emeryville, California 94608, United States
- Biological
Systems & Engineering Division, Lawrence
Berkeley National Laboratory, Berkeley, California 94720, United States
- Department
of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720, United States
| | - Aaron A. Vilchez
- Joint
BioEnergy Institute, 5885 Hollis Street, Emeryville, California 94608, United States
- Biological
Systems & Engineering Division, Lawrence
Berkeley National Laboratory, Berkeley, California 94720, United States
- Department
of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720, United States
| | - Yan Chen
- Joint
BioEnergy Institute, 5885 Hollis Street, Emeryville, California 94608, United States
- Biological
Systems & Engineering Division, Lawrence
Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Christopher J. Petzold
- Joint
BioEnergy Institute, 5885 Hollis Street, Emeryville, California 94608, United States
- Biological
Systems & Engineering Division, Lawrence
Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Robert W. Haushalter
- Joint
BioEnergy Institute, 5885 Hollis Street, Emeryville, California 94608, United States
- Biological
Systems & Engineering Division, Lawrence
Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Lars M. Blank
- Institute
of Applied Microbiology (iAMB), Aachen Biology and Biotechnology (ABBt), RWTH Aachen University, 52062 Aachen, Germany
| | - Jay D. Keasling
- Joint
BioEnergy Institute, 5885 Hollis Street, Emeryville, California 94608, United States
- Biological
Systems & Engineering Division, Lawrence
Berkeley National Laboratory, Berkeley, California 94720, United States
- Joint
Program in Bioengineering, University of
California, Berkeley, California 94720, United States
- Department
of Chemistry, University of California, Berkeley, California 94720, United States
- Environmental
Genomics and Systems Biology Division, Lawrence
Berkeley National Laboratory, Berkeley, California 94720, United States
- Department
of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720, United States
- The
Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
- Center
for Synthetic Biochemistry, Institute for
Synthetic Biology, Shenzhen Institutes for Advanced Technologies, Shenzhen 518071, China
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23
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Chen X, Hudson GA, Mineo C, Amer B, Baidoo EEK, Crowe SA, Liu Y, Keasling JD, Scheller HV. Deciphering triterpenoid saponin biosynthesis by leveraging transcriptome response to methyl jasmonate elicitation in Saponaria vaccaria. Nat Commun 2023; 14:7101. [PMID: 37925486 PMCID: PMC10625584 DOI: 10.1038/s41467-023-42877-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 10/24/2023] [Indexed: 11/06/2023] Open
Abstract
Methyl jasmonate (MeJA) is a known elicitor of plant specialized metabolism, including triterpenoid saponins. Saponaria vaccaria is an annual herb used in traditional Chinese medicine, containing large quantities of oleanane-type triterpenoid saponins with anticancer properties and structural similarities to the vaccine adjuvant QS-21. Leveraging the MeJA-elicited saponin biosynthesis, we identify multiple enzymes catalyzing the oxidation and glycosylation of triterpenoids in S. vaccaria. This exploration is aided by Pacbio full-length transcriptome sequencing and gene expression analysis. A cellulose synthase-like enzyme can not only glucuronidate triterpenoid aglycones but also alter the product profile of a cytochrome P450 monooxygenase via preference for the aldehyde intermediate. Furthermore, the discovery of a UDP-glucose 4,6-dehydratase and a UDP-4-keto-6-deoxy-glucose reductase reveals the biosynthetic pathway for the rare nucleotide sugar UDP-D-fucose, a likely sugar donor for fucosylation of plant natural products. Our work enables the production and optimization of high-value saponins in microorganisms and plants through synthetic biology approaches.
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Affiliation(s)
- Xiaoyue Chen
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, 94720, USA
- Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, CA, 94608, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Graham A Hudson
- Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, CA, 94608, USA
- California Institute of Quantitative Biosciences (QB3), University of California, Berkeley, CA, 94720, USA
| | - Charlotte Mineo
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, 94720, USA
- Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, CA, 94608, USA
| | - Bashar Amer
- Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, CA, 94608, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Edward E K Baidoo
- Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, CA, 94608, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Samantha A Crowe
- Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, CA, 94608, USA
- California Institute of Quantitative Biosciences (QB3), University of California, Berkeley, CA, 94720, USA
- Department of Chemical & Biomolecular Engineering, University of California, Berkeley, CA, 94720, USA
| | - Yuzhong Liu
- Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, CA, 94608, USA
- California Institute of Quantitative Biosciences (QB3), University of California, Berkeley, CA, 94720, USA
| | - Jay D Keasling
- Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, CA, 94608, USA
- California Institute of Quantitative Biosciences (QB3), University of California, Berkeley, CA, 94720, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
- Department of Chemical & Biomolecular Engineering, University of California, Berkeley, CA, 94720, USA
- Department of Bioengineering, University of California, Berkeley, CA, 94720, USA
- Technical University of Denmark, DK-2800, Kongens Lyngby, Denmark
- Center for Synthetic Biochemistry, Shenzhen Institutes for Advanced Technologies, Shenzhen, China
| | - Henrik V Scheller
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, 94720, USA.
- Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, CA, 94608, USA.
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA.
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24
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Yang J, Liu Y, Zhong D, Xu L, Gao H, Keasling JD, Luo X, Chou HH. Combinatorial optimization and spatial remodeling of CYPs to control product profile. Metab Eng 2023; 80:119-129. [PMID: 37703999 DOI: 10.1016/j.ymben.2023.09.004] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 09/07/2023] [Accepted: 09/08/2023] [Indexed: 09/15/2023]
Abstract
Activating inert substrates is a challenge in nature and synthetic chemistry, but essential for creating functionally active molecules. In this work, we used a combinatorial optimization approach to assemble cytochrome P450 monooxygenases (CYPs) and reductases (CPRs) to achieve a target product profile. By creating 110 CYP-CPR pairs and iteratively screening different pairing libraries, we demonstrated a framework for establishing a CYP network that catalyzes six oxidation reactions at three different positions of a chemical scaffold. Target product titer was improved by remodeling endoplasmic reticulum (ER) size and spatially controlling the CYPs' configuration on the ER. Out of 47 potential products that could be synthesized, 86% of the products synthesized by the optimized network was our target compound quillaic acid (QA), the aglycone backbone of many pharmaceutically important saponins, and fermentation achieved QA titer 2.23 g/L.
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Affiliation(s)
- Jiazeng Yang
- Shenzhen Key Laboratory for the Intelligent Microbial Manufacturing of Medicines, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China; CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China; Center for Synthetic Biochemistry, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, 518055, China
| | - Yuguang Liu
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China; Center for Synthetic Biochemistry, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, 518055, China
| | - Dacai Zhong
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China; Center for Synthetic Biochemistry, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, 518055, China
| | - Linlin Xu
- Center for Synthetic Biochemistry, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, 518055, China
| | - Haixin Gao
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China; Center for Synthetic Biochemistry, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, 518055, China
| | - Jay D Keasling
- Center for Synthetic Biochemistry, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, 518055, China; Joint BioEnergy Institute, Emeryville, CA, 94608, USA; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA; Department of Chemical and Biomolecular Engineering & Department of Bioengineering, University of California, Berkeley, CA, 94720, USA; Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kgs. Lyngby, Denmark
| | - Xiaozhou Luo
- Shenzhen Key Laboratory for the Intelligent Microbial Manufacturing of Medicines, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China; CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China; Center for Synthetic Biochemistry, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, 518055, China
| | - Howard H Chou
- Shenzhen Key Laboratory for the Intelligent Microbial Manufacturing of Medicines, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China; CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China; Center for Synthetic Biochemistry, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, 518055, China.
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25
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Backman TWH, Schenk C, Radivojevic T, Ando D, Singh J, Czajka JJ, Costello Z, Keasling JD, Tang Y, Akhmatskaya E, Garcia Martin H. BayFlux: A Bayesian method to quantify metabolic Fluxes and their uncertainty at the genome scale. PLoS Comput Biol 2023; 19:e1011111. [PMID: 37948450 PMCID: PMC10664898 DOI: 10.1371/journal.pcbi.1011111] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 11/22/2023] [Accepted: 09/27/2023] [Indexed: 11/12/2023] Open
Abstract
Metabolic fluxes, the number of metabolites traversing each biochemical reaction in a cell per unit time, are crucial for assessing and understanding cell function. 13C Metabolic Flux Analysis (13C MFA) is considered to be the gold standard for measuring metabolic fluxes. 13C MFA typically works by leveraging extracellular exchange fluxes as well as data from 13C labeling experiments to calculate the flux profile which best fit the data for a small, central carbon, metabolic model. However, the nonlinear nature of the 13C MFA fitting procedure means that several flux profiles fit the experimental data within the experimental error, and traditional optimization methods offer only a partial or skewed picture, especially in "non-gaussian" situations where multiple very distinct flux regions fit the data equally well. Here, we present a method for flux space sampling through Bayesian inference (BayFlux), that identifies the full distribution of fluxes compatible with experimental data for a comprehensive genome-scale model. This Bayesian approach allows us to accurately quantify uncertainty in calculated fluxes. We also find that, surprisingly, the genome-scale model of metabolism produces narrower flux distributions (reduced uncertainty) than the small core metabolic models traditionally used in 13C MFA. The different results for some reactions when using genome-scale models vs core metabolic models advise caution in assuming strong inferences from 13C MFA since the results may depend significantly on the completeness of the model used. Based on BayFlux, we developed and evaluated novel methods (P-13C MOMA and P-13C ROOM) to predict the biological results of a gene knockout, that improve on the traditional MOMA and ROOM methods by quantifying prediction uncertainty.
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Affiliation(s)
- Tyler W. H. Backman
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
- Biofuels and Bioproducts Division, Joint BioEnergy Institute, Emeryville, California, United States of America
| | - Christina Schenk
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
- BCAM, Basque Center for Applied Mathematics, Bilbao, Spain
- DOE Agile BioFoundry, Emeryville, California, United States of America
| | - Tijana Radivojevic
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
- Biofuels and Bioproducts Division, Joint BioEnergy Institute, Emeryville, California, United States of America
- DOE Agile BioFoundry, Emeryville, California, United States of America
| | - David Ando
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
- Biofuels and Bioproducts Division, Joint BioEnergy Institute, Emeryville, California, United States of America
| | - Jahnavi Singh
- Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, California, United States of America
| | - Jeffrey J. Czajka
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri, United States of America
| | - Zak Costello
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
- Biofuels and Bioproducts Division, Joint BioEnergy Institute, Emeryville, California, United States of America
- DOE Agile BioFoundry, Emeryville, California, United States of America
| | - Jay D. Keasling
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
- Biofuels and Bioproducts Division, Joint BioEnergy Institute, Emeryville, California, United States of America
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California, United States of America
- Department of Bioengineering, University of California, Berkeley, California, United States of America
- QB3 Institute, University of California, Berkeley, California, United States of America
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Copenhagen, Denmark
- Center for Synthetic Biochemistry, Institute for Synthetic Biology, Shenzhen Institutes for Advanced Technologies, Shenzhen, China
| | - Yinjie Tang
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri, United States of America
| | - Elena Akhmatskaya
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
- BCAM, Basque Center for Applied Mathematics, Bilbao, Spain
- IKERBASQUE, Basque Foundation for Science, Bilbao, Spain
| | - Hector Garcia Martin
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
- Biofuels and Bioproducts Division, Joint BioEnergy Institute, Emeryville, California, United States of America
- BCAM, Basque Center for Applied Mathematics, Bilbao, Spain
- DOE Agile BioFoundry, Emeryville, California, United States of America
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26
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Zhang Y, Guo J, Gao P, Yan W, Shen J, Luo X, Keasling JD. Development of an efficient yeast platform for cannabigerolic acid biosynthesis. Metab Eng 2023; 80:232-240. [PMID: 37890610 DOI: 10.1016/j.ymben.2023.10.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 10/16/2023] [Accepted: 10/18/2023] [Indexed: 10/29/2023]
Abstract
Cannabinoids are important therapeutical molecules for human ailments, cancer treatment, and SARS-CoV-2. The central cannabinoid, cannabigerolic acid (CBGA), is generated from geranyl pyrophosphate and olivetolic acid by Cannabis sativa prenyltransferase (CsPT4). Despite efforts to engineer microorganisms such as Saccharomyces cerevisiae (S. cerevisiae) for CBGA production, their titers remain suboptimal because of the low conversion of hexanoate into olivetolic acid and the limited activity and stability of the CsPT4. To address the low hexanoate conversion, we eliminated hexanoate consumption by the beta-oxidation pathway and reduced its incorporation into fatty acids. To address CsPT4 limitations, we expanded the endoplasmic reticulum and fused an auxiliary protein to CsPT4. Consequently, the engineered S. cerevisiae chassis showed a marked improvement of 78.64-fold in CBGA production, reaching a titer of 510.32 ± 10.70 mg l-1 from glucose and hexanoate.
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Affiliation(s)
- Yunfeng Zhang
- Shenzhen Key Laboratory for the Intelligent Microbial Manufacturing of Medicines, CAS Key Laboratory of Quantitative Engineering Biology, Center for Synthetic Biochemistry, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Jiulong Guo
- Synceres Biosciences (Shenzhen) CO., LTD, China
| | - PeiZhen Gao
- Synceres Biosciences (Shenzhen) CO., LTD, China
| | - Wei Yan
- Synceres Biosciences (Shenzhen) CO., LTD, China
| | - Junfeng Shen
- Shenzhen Key Laboratory for the Intelligent Microbial Manufacturing of Medicines, CAS Key Laboratory of Quantitative Engineering Biology, Center for Synthetic Biochemistry, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Xiaozhou Luo
- Shenzhen Key Laboratory for the Intelligent Microbial Manufacturing of Medicines, CAS Key Laboratory of Quantitative Engineering Biology, Center for Synthetic Biochemistry, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China.
| | - Jay D Keasling
- Center for Synthetic Biochemistry, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China; Joint BioEnergy Institute, Emeryville, CA, 94608, USA; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA; Department of Chemical and Biomolecular Engineering & Department of Bioengineering, University of California, Berkeley, CA, 94720, USA; Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kgs. Lyngby, Denmark.
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27
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Eng T, Banerjee D, Menasalvas J, Chen Y, Gin J, Choudhary H, Baidoo E, Chen JH, Ekman A, Kakumanu R, Diercks YL, Codik A, Larabell C, Gladden J, Simmons BA, Keasling JD, Petzold CJ, Mukhopadhyay A. Maximizing microbial bioproduction from sustainable carbon sources using iterative systems engineering. Cell Rep 2023; 42:113087. [PMID: 37665664 DOI: 10.1016/j.celrep.2023.113087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 07/10/2023] [Accepted: 08/18/2023] [Indexed: 09/06/2023] Open
Abstract
Maximizing the production of heterologous biomolecules is a complex problem that can be addressed with a systems-level understanding of cellular metabolism and regulation. Specifically, growth-coupling approaches can increase product titers and yields and also enhance production rates. However, implementing these methods for non-canonical carbon streams is challenging due to gaps in metabolic models. Over four design-build-test-learn cycles, we rewire Pseudomonas putida KT2440 for growth-coupled production of indigoidine from para-coumarate. We explore 4,114 potential growth-coupling solutions and refine one design through laboratory evolution and ensemble data-driven methods. The final growth-coupled strain produces 7.3 g/L indigoidine at 77% maximum theoretical yield in para-coumarate minimal medium. The iterative use of growth-coupling designs and functional genomics with experimental validation was highly effective and agnostic to specific hosts, carbon streams, and final products and thus generalizable across many systems.
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Affiliation(s)
- Thomas Eng
- The Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA 94608, USA; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Deepanwita Banerjee
- The Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA 94608, USA; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Javier Menasalvas
- The Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA 94608, USA; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Yan Chen
- The Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA 94608, USA; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Jennifer Gin
- The Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA 94608, USA; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Hemant Choudhary
- The Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA 94608, USA; Biomanufacturing and Biomaterials Department, Sandia National Laboratories, Livermore, CA, USA
| | - Edward Baidoo
- The Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA 94608, USA; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Jian Hua Chen
- Department of Anatomy, University of California, San Francisco, San Francisco, CA, USA; National Center for X-ray Tomography, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Axel Ekman
- Department of Anatomy, University of California, San Francisco, San Francisco, CA, USA; National Center for X-ray Tomography, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Ramu Kakumanu
- The Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA 94608, USA; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Yuzhong Liu Diercks
- The Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA 94608, USA; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Alex Codik
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Carolyn Larabell
- Department of Anatomy, University of California, San Francisco, San Francisco, CA, USA; National Center for X-ray Tomography, Lawrence Berkeley National Laboratory, Berkeley, CA, USA; Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - John Gladden
- The Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA 94608, USA; Biomanufacturing and Biomaterials Department, Sandia National Laboratories, Livermore, CA, USA
| | - Blake A Simmons
- The Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA 94608, USA; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Jay D Keasling
- The Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA 94608, USA; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; QB3 Institute, University of California, Berkeley, 5885 Hollis Street, 4th Floor, Emeryville, CA 94608, USA; Department of Chemical & Biomolecular Engineering, University of California, Berkeley, Berkeley, CA 94720, USA; Department of Bioengineering, University of California, Berkeley, Berkeley, CA 94720, USA; Novo Nordisk Foundation Center for Biosustainability, Technical University Denmark, 2970 Horsholm, Denmark; Synthetic Biochemistry Center, Institute for Synthetic Biology, Shenzhen Institutes for Advanced Technologies, Shenzhen, China
| | - Christopher J Petzold
- The Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA 94608, USA; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Aindrila Mukhopadhyay
- The Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA 94608, USA; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
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Waldburger L, Thompson MG, Weisberg AJ, Lee N, Chang JH, Keasling JD, Shih PM. Transcriptome architecture of the three main lineages of agrobacteria. mSystems 2023; 8:e0033323. [PMID: 37477440 PMCID: PMC10469942 DOI: 10.1128/msystems.00333-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 06/15/2023] [Indexed: 07/22/2023] Open
Abstract
Agrobacteria are a diverse, polyphyletic group of prokaryotes with multipartite genomes capable of transferring DNA into the genomes of host plants, making them an essential tool in plant biotechnology. Despite their utility in plant transformation, genome-wide transcriptional regulation is not well understood across the three main lineages of agrobacteria. Transcription start sites (TSSs) are a necessary component of gene expression and regulation. In this study, we used differential RNA-seq and a TSS identification algorithm optimized on manually annotated TSS, then validated with existing TSS to identify thousands of TSS with nucleotide resolution for representatives of each lineage. We extend upon the 356 TSSs previously reported in Agrobacterium fabrum C58 by identifying 1,916 TSSs. In addition, we completed genomes and phenotyping of Rhizobium rhizogenes C16/80 and Allorhizobium vitis T60/94, identifying 2,650 and 2,432 TSSs, respectively. Parameter optimization was crucial for an accurate, high-resolution view of genome and transcriptional dynamics, highlighting the importance of algorithm optimization in genome-wide TSS identification and genomics at large. The optimized algorithm reduced the number of TSSs identified internal and antisense to the coding sequence on average by 90.5% and 91.9%, respectively. Comparison of TSS conservation between orthologs of the three lineages revealed differences in cell cycle regulation of ctrA as well as divergence of transcriptional regulation of chemotaxis-related genes when grown in conditions that simulate the plant environment. These results provide a framework to elucidate the mechanistic basis and evolution of pathology across the three main lineages of agrobacteria. IMPORTANCE Transcription start sites (TSSs) are fundamental for understanding gene expression and regulation. Agrobacteria, a group of prokaryotes with the ability to transfer DNA into the genomes of host plants, are widely used in plant biotechnology. However, the genome-wide transcriptional regulation of agrobacteria is not well understood, especially in less-studied lineages. Differential RNA-seq and an optimized algorithm enabled identification of thousands of TSSs with nucleotide resolution for representatives of each lineage. The results of this study provide a framework for elucidating the mechanistic basis and evolution of pathology across the three main lineages of agrobacteria. The optimized algorithm also highlights the importance of parameter optimization in genome-wide TSS identification and genomics at large.
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Affiliation(s)
- Lucas Waldburger
- Department of Bioengineering, University of California, Berkeley, California, USA
- Joint BioEnergy Institute, Emeryville, California, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Mitchell G. Thompson
- Joint BioEnergy Institute, Emeryville, California, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Alexandra J. Weisberg
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, USA
| | - Namil Lee
- Joint BioEnergy Institute, Emeryville, California, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California, USA
| | - Jeff H. Chang
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, USA
| | - Jay D. Keasling
- Joint BioEnergy Institute, Emeryville, California, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California, USA
- Institute for Quantitative Biosciences, University of California, Berkeley, California, USA
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
- Center for Synthetic Biochemistry, Institute for Synthetic Biology, Shenzhen Institutes for Advanced Technologies, Shenzhen, China
| | - Patrick M. Shih
- Joint BioEnergy Institute, Emeryville, California, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
- Department of Plant and Microbial Biology, University of California, Berkeley, California, USA
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29
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Englund E, Schmidt M, Nava AA, Klass S, Keiser L, Dan Q, Katz L, Yuzawa S, Keasling JD. Biosensor Guided Polyketide Synthases Engineering for Optimization of Domain Exchange Boundaries. Nat Commun 2023; 14:4871. [PMID: 37573440 PMCID: PMC10423236 DOI: 10.1038/s41467-023-40464-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 07/28/2023] [Indexed: 08/14/2023] Open
Abstract
Type I modular polyketide synthases (PKSs) are multi-domain enzymes functioning like assembly lines. Many engineering attempts have been made for the last three decades to replace, delete and insert new functional domains into PKSs to produce novel molecules. However, inserting heterologous domains often destabilize PKSs, causing loss of activity and protein misfolding. To address this challenge, here we develop a fluorescence-based solubility biosensor that can quickly identify engineered PKSs variants with minimal structural disruptions. Using this biosensor, we screen a library of acyltransferase (AT)-exchanged PKS hybrids with randomly assigned domain boundaries, and we identify variants that maintain wild type production levels. We then probe each position in the AT linker region to determine how domain boundaries influence structural integrity and identify a set of optimized domain boundaries. Overall, we have successfully developed an experimentally validated, high-throughput method for making hybrid PKSs that produce novel molecules.
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Affiliation(s)
- Elias Englund
- Joint BioEnergy Institute, Emeryville, CA, USA
- School of Engineering Sciences in Chemistry, Biotechnology and Health, Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Matthias Schmidt
- Joint BioEnergy Institute, Emeryville, CA, USA
- Institute of Applied Microbiology, Aachen Biology and Biotechnology (ABBt), RWTH Aachen University, Aachen, Germany
- Biological Systems and Engineering Division, Lawrence Berkeley National laboratory, Berkeley, CA, USA
| | - Alberto A Nava
- Joint BioEnergy Institute, Emeryville, CA, USA
- Department of Chemical & Biomolecular Engineering, University of California, Berkeley, Berkeley, CA, USA
| | - Sarah Klass
- Joint BioEnergy Institute, Emeryville, CA, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National laboratory, Berkeley, CA, USA
- Department of Chemical & Biomolecular Engineering, University of California, Berkeley, Berkeley, CA, USA
| | - Leah Keiser
- Joint BioEnergy Institute, Emeryville, CA, USA
- Department of Chemical & Biomolecular Engineering, University of California, Berkeley, Berkeley, CA, USA
| | - Qingyun Dan
- Joint BioEnergy Institute, Emeryville, CA, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National laboratory, Berkeley, CA, USA
| | - Leonard Katz
- Joint BioEnergy Institute, Emeryville, CA, USA
- QB3, University of California, Berkeley, Berkeley, CA, USA
| | - Satoshi Yuzawa
- Joint BioEnergy Institute, Emeryville, CA, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National laboratory, Berkeley, CA, USA
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, Japan
- Graduate school of Media and Governance, Keio University, Fujisawa, Kanagawa, Japan
| | - Jay D Keasling
- Joint BioEnergy Institute, Emeryville, CA, USA.
- Biological Systems and Engineering Division, Lawrence Berkeley National laboratory, Berkeley, CA, USA.
- Department of Chemical & Biomolecular Engineering, University of California, Berkeley, Berkeley, CA, USA.
- QB3, University of California, Berkeley, Berkeley, CA, USA.
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA.
- Center for Biosustainability, Danish Technical University, Lyngby, Denmark.
- Center for Synthetic biochemistry, Institute for Synthetic biology, Shenzhen Institute of Advanced Technology, Shenzhen, China.
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30
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Zhan C, Lee N, Lan G, Dan Q, Cowan A, Wang Z, Baidoo EEK, Kakumanu R, Luckie B, Kuo RC, McCauley J, Liu Y, Valencia L, Haushalter RW, Keasling JD. Improved polyketide production in C. glutamicum by preventing propionate-induced growth inhibition. Nat Metab 2023; 5:1127-1140. [PMID: 37443355 DOI: 10.1038/s42255-023-00830-x] [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] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 05/25/2023] [Indexed: 07/15/2023]
Abstract
Corynebacterium glutamicum is a promising host for production of valuable polyketides. Propionate addition, a strategy known to increase polyketide production by increasing intracellular methylmalonyl-CoA availability, causes growth inhibition in C. glutamicum. The mechanism of this inhibition was unclear before our work. Here we provide evidence that accumulation of propionyl-CoA and methylmalonyl-CoA induces growth inhibition in C. glutamicum. We then show that growth inhibition can be relieved by introducing methylmalonyl-CoA-dependent polyketide synthases. With germicidin as an example, we used adaptive laboratory evolution to leverage the fitness advantage of polyketide production in the presence of propionate to evolve improved germicidin production. Whole-genome sequencing revealed mutations in germicidin synthase, which improved germicidin titer, as well as mutations in citrate synthase, which effectively evolved the native glyoxylate pathway to a new methylcitrate pathway. Together, our results show that C. glutamicum is a capable host for polyketide production and we can take advantage of propionate growth inhibition to drive titers higher using laboratory evolution or to screen for production of polyketides.
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Affiliation(s)
- Chunjun Zhan
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Departments of Chemical & Biomolecular Engineering and of Bioengineering, University of California, Berkeley, CA, USA
| | - Namil Lee
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Departments of Chemical & Biomolecular Engineering and of Bioengineering, University of California, Berkeley, CA, USA
| | - Guangxu Lan
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Qingyun Dan
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA, USA
| | - Aidan Cowan
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Zilong Wang
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, USA
- Departments of Chemical & Biomolecular Engineering and of Bioengineering, University of California, Berkeley, CA, USA
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA, USA
| | - Edward E K Baidoo
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Ramu Kakumanu
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Bridget Luckie
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Rita C Kuo
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Joshua McCauley
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Yuzhong Liu
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Luis Valencia
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Robert W Haushalter
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, USA.
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
| | - Jay D Keasling
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, USA.
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
- Departments of Chemical & Biomolecular Engineering and of Bioengineering, University of California, Berkeley, CA, USA.
- Center for Biosustainability, Danish Technical University, Lyngby, Denmark.
- Center for Synthetic Biochemistry, Shenzhen Institutes for Advanced Technologies, Shenzhen, China.
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31
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Pearson AN, Thompson MG, Kirkpatrick LD, Ho C, Vuu KM, Waldburger LM, Keasling JD, Shih PM. The pGinger Family of Expression Plasmids. Microbiol Spectr 2023; 11:e0037323. [PMID: 37212656 PMCID: PMC10269703 DOI: 10.1128/spectrum.00373-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Accepted: 05/09/2023] [Indexed: 05/23/2023] Open
Abstract
The pGinger suite of expression plasmids comprises 43 plasmids that will enable precise constitutive and inducible gene expression in a wide range of Gram-negative bacterial species. Constitutive vectors are composed of 16 synthetic constitutive promoters upstream of red fluorescent protein (RFP), with a broad-host-range BBR1 origin and a kanamycin resistance marker. The family also has seven inducible systems (Jungle Express, Psal/NahR, Pm/XylS, Prha/RhaS, LacO1/LacI, LacUV5/LacI, and Ptet/TetR) controlling RFP expression on BBR1/kanamycin plasmid backbones. For four of these inducible systems (Jungle Express, Psal/NahR, LacO1/LacI, and Ptet/TetR), we created variants that utilize the RK2 origin and spectinomycin or gentamicin selection. Relevant RFP expression and growth data have been collected in the model bacterium Escherichia coli as well as Pseudomonas putida. All pGinger vectors are available via the Joint BioEnergy Institute (JBEI) Public Registry. IMPORTANCE Metabolic engineering and synthetic biology are predicated on the precise control of gene expression. As synthetic biology expands beyond model organisms, more tools will be required that function robustly in a wide range of bacterial hosts. The pGinger family of plasmids constitutes 43 plasmids that will enable both constitutive and inducible gene expression in a wide range of nonmodel Proteobacteria.
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Affiliation(s)
- Allison N. Pearson
- Joint BioEnergy Institute, Emeryville, California, USA
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
- Department of Plant and Microbial Biology, University of California, Berkeley, California, USA
| | - Mitchell G. Thompson
- Joint BioEnergy Institute, Emeryville, California, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Liam D. Kirkpatrick
- Joint BioEnergy Institute, Emeryville, California, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Cindy Ho
- Joint BioEnergy Institute, Emeryville, California, USA
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Khanh M. Vuu
- Joint BioEnergy Institute, Emeryville, California, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Lucas M. Waldburger
- Joint BioEnergy Institute, Emeryville, California, USA
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
- Department of Bioengineering, University of California, Berkeley, California, USA
| | - Jay D. Keasling
- Joint BioEnergy Institute, Emeryville, California, USA
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California, USA
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
- Center for Synthetic Biochemistry, Institute for Synthetic Biology, Shenzhen Institutes for Advanced Technologies, Shenzhen, China
| | - Patrick M. Shih
- Joint BioEnergy Institute, Emeryville, California, USA
- Department of Plant and Microbial Biology, University of California, Berkeley, California, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
- Innovative Genomics Institute, University of California, Berkeley, California, USA
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32
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Van Cura D, Ng TL, Huang J, Hager H, Hartwig JF, Keasling JD, Balskus EP. Discovery of the Azaserine Biosynthetic Pathway Uncovers a Biological Route for α-Diazoester Production. Angew Chem Int Ed Engl 2023:e202304646. [PMID: 37151182 DOI: 10.1002/anie.202304646] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Revised: 05/04/2023] [Accepted: 05/05/2023] [Indexed: 05/09/2023]
Abstract
Azaserine is a bacterial metabolite containing a biologically unusual and synthetically enabling α-diazoester functional group. Here, we report the discovery of the azaserine (aza) biosynthetic gene cluster from Glycomyces harbinensis. Discovery of related gene clusters reveals previously unappreciated azaserine producers, and heterologous expression of the aza gene cluster confirms its role in azaserine assembly. Notably, this gene cluster encodes homologs of hydrazonoacetic acid (HYAA)-producing enzymes, implicating HYAA in α-diazoester biosynthesis. Isotope feeding and biochemical experiments support this hypothesis. These discoveries indicate that a 2-electron oxidation of a hydrazonoacetyl intermediate is required for α-diazoester formation, constituting a distinct logic for diazo biosynthesis. Uncovering this biological route for α-diazoester synthesis now enables the production of a highly versatile carbene precursor in cells, facilitating approaches for engineering complete carbene-mediated biosynthetic transformations in vivo.
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Affiliation(s)
- Devon Van Cura
- Harvard University, Chemistry and Chemical Biology, UNITED STATES
| | - Tai L Ng
- Harvard University, Chemistry and Chemical Biology, UNITED STATES
| | - Jing Huang
- Lawrence Berkeley Laboratory: E O Lawrence Berkeley National Laboratory, Biological Systems and Engineering Division, UNITED STATES
| | - Harry Hager
- Harvard University, Chemistry and Chemical Biology, UNITED STATES
| | - John F Hartwig
- University of California Berkeley, Chemistry, UNITED STATES
| | - Jay D Keasling
- Lawrence Berkeley Laboratory: E O Lawrence Berkeley National Laboratory, Biological Systems and Engineering Division, UNITED STATES
| | - Emily P Balskus
- Harvard University, Department of Chemistry and Chemical Biology, 12 Oxford St., Mallinckrodt 303N, 2138, Cambridge, UNITED STATES
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33
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Huang J, Quest A, Cruz-Morales P, Deng K, Pereira JH, Van Cura D, Kakumanu R, Baidoo EEK, Dan Q, Chen Y, Petzold CJ, Northen TR, Adams PD, Clark DS, Balskus EP, Hartwig JF, Mukhopadhyay A, Keasling JD. Complete integration of carbene-transfer chemistry into biosynthesis. Nature 2023; 617:403-408. [PMID: 37138074 DOI: 10.1038/s41586-023-06027-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 03/28/2023] [Indexed: 05/05/2023]
Abstract
Biosynthesis is an environmentally benign and renewable approach that can be used to produce a broad range of natural and, in some cases, new-to-nature products. However, biology lacks many of the reactions that are available to synthetic chemists, resulting in a narrower scope of accessible products when using biosynthesis rather than synthetic chemistry. A prime example of such chemistry is carbene-transfer reactions1. Although it was recently shown that carbene-transfer reactions can be performed in a cell and used for biosynthesis2,3, carbene donors and unnatural cofactors needed to be added exogenously and transported into cells to effect the desired reactions, precluding cost-effective scale-up of the biosynthesis process with these reactions. Here we report the access to a diazo ester carbene precursor by cellular metabolism and a microbial platform for introducing unnatural carbene-transfer reactions into biosynthesis. The α-diazoester azaserine was produced by expressing a biosynthetic gene cluster in Streptomyces albus. The intracellularly produced azaserine was used as a carbene donor to cyclopropanate another intracellularly produced molecule-styrene. The reaction was catalysed by engineered P450 mutants containing a native cofactor with excellent diastereoselectivity and a moderate yield. Our study establishes a scalable, microbial platform for conducting intracellular abiological carbene-transfer reactions to functionalize a range of natural and new-to-nature products and expands the scope of organic products that can be produced by cellular metabolism.
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Affiliation(s)
- Jing Huang
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, USA
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA, USA
| | - Andrew Quest
- Department of Chemistry, University of California, Berkeley, CA, USA
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Pablo Cruz-Morales
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, USA
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Kai Deng
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, USA
- Department of Biomaterials and Biomanufacturing, Sandia National Laboratories, Livermore, CA, USA
| | - Jose Henrique Pereira
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Devon Van Cura
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Ramu Kakumanu
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, USA
| | - Edward E K Baidoo
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, USA
| | - Qingyun Dan
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, USA
| | - Yan Chen
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, USA
| | - Christopher J Petzold
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, USA
| | - Trent R Northen
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Paul D Adams
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department of Bioengineering, University of California, Berkeley, CA, USA
| | - Douglas S Clark
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA, USA.
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
| | - Emily P Balskus
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - John F Hartwig
- Department of Chemistry, University of California, Berkeley, CA, USA.
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
| | - Aindrila Mukhopadhyay
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, USA.
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
| | - Jay D Keasling
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, USA.
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA, USA.
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark.
- Department of Bioengineering, University of California, Berkeley, CA, USA.
- Synthetic Biochemistry Center, Institute for Synthetic Biology, Shenzhen Institutes for Advanced Technologies, Shenzhen, China.
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34
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Englund E, Schmidt M, Nava AA, Lechner A, Deng K, Jocic R, Lin Y, Roberts J, Benites VT, Kakumanu R, Gin JW, Chen Y, Liu Y, Petzold CJ, Baidoo EEK, Northen TR, Adams PD, Katz L, Yuzawa S, Keasling JD. Expanding Extender Substrate Selection for Unnatural Polyketide Biosynthesis by Acyltransferase Domain Exchange within a Modular Polyketide Synthase. J Am Chem Soc 2023; 145:8822-8832. [PMID: 37057992 PMCID: PMC10141241 DOI: 10.1021/jacs.2c11027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/15/2023]
Abstract
Modular polyketide synthases (PKSs) are polymerases that employ α-carboxyacyl-CoAs as extender substrates. This enzyme family contains several catalytic modules, where each module is responsible for a single round of polyketide chain extension. Although PKS modules typically use malonyl-CoA or methylmalonyl-CoA for chain elongation, many other malonyl-CoA analogues are used to diversify polyketide structures in nature. Previously, we developed a method to alter an extension substrate of a given module by exchanging an acyltransferase (AT) domain while maintaining protein folding. Here, we report in vitro polyketide biosynthesis by 13 PKSs (the wild-type PKS and 12 AT-exchanged PKSs with unusual ATs) and 14 extender substrates. Our ∼200 in vitro reactions resulted in 13 structurally different polyketides, including several polyketides that have not been reported. In some cases, AT-exchanged PKSs produced target polyketides by >100-fold compared to the wild-type PKS. These data also indicate that most unusual AT domains do not incorporate malonyl-CoA and methylmalonyl-CoA but incorporate various rare extender substrates that are equal to in size or slightly larger than natural substrates. We developed a computational workflow to predict the approximate AT substrate range based on active site volumes to support the selection of ATs. These results greatly enhance our understanding of rare AT domains and demonstrate the benefit of using the proposed PKS engineering strategy to produce novel chemicals in vitro.
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Affiliation(s)
- Elias Englund
- Joint BioEnergy Institute, Emeryville, California 94608, United States
- Science for Life Laboratory, KTH - Royal Institute of Technology, 17165 Stockholm, Sweden
| | - Matthias Schmidt
- Joint BioEnergy Institute, Emeryville, California 94608, United States
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- Institute of Applied Microbiology, Aachen Biology and Biotechnology, RWTH Aachen University, 52074 Aachen, Germany
| | - Alberto A Nava
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720, United States
| | - Anna Lechner
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720, United States
- Department of Bioengineering, University of California, Berkeley, California 94720, United States
| | - Kai Deng
- Joint BioEnergy Institute, Emeryville, California 94608, United States
- Department of Biomaterials and Biomanufacturing, Sandia National Laboratory, Livermore, California 94550, United States
| | - Renee Jocic
- Joint BioEnergy Institute, Emeryville, California 94608, United States
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Yingxin Lin
- Department of Molecular and Cell Biology, University of California, Berkeley, California 94720, United States
| | - Jacob Roberts
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- Department of Bioengineering, University of California, Berkeley, California 94720, United States
| | - Veronica T Benites
- Joint BioEnergy Institute, Emeryville, California 94608, United States
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Ramu Kakumanu
- Joint BioEnergy Institute, Emeryville, California 94608, United States
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Jennifer W Gin
- Joint BioEnergy Institute, Emeryville, California 94608, United States
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Yan Chen
- Joint BioEnergy Institute, Emeryville, California 94608, United States
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Yuzhong Liu
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720, United States
- Department of Bioengineering, University of California, Berkeley, California 94720, United States
| | - Christopher J Petzold
- Joint BioEnergy Institute, Emeryville, California 94608, United States
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Edward E K Baidoo
- Joint BioEnergy Institute, Emeryville, California 94608, United States
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Trent R Northen
- Joint BioEnergy Institute, Emeryville, California 94608, United States
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Paul D Adams
- Joint BioEnergy Institute, Emeryville, California 94608, United States
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- Department of Bioengineering, University of California, Berkeley, California 94720, United States
| | - Leonard Katz
- Joint BioEnergy Institute, Emeryville, California 94608, United States
- QB3 Institute, University of California, Berkeley, California 94720, United States
| | - Satoshi Yuzawa
- Joint BioEnergy Institute, Emeryville, California 94608, United States
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, Kanagawa 252-0882, Japan
- Institute of Advanced Biosciences, Keio University, Tsuruoka, Yamagata 997-0017, Japan
| | - Jay D Keasling
- Joint BioEnergy Institute, Emeryville, California 94608, United States
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720, United States
- Department of Bioengineering, University of California, Berkeley, California 94720, United States
- QB3 Institute, University of California, Berkeley, California 94720, United States
- Department of Biomaterials and Biomanufacturing, Sandia National Laboratory, Livermore, California 94550, United States
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby 2800, Denmark
- Center for Synthetic Biochemistry, Shenzhen Institutes of Advanced Technologies, Shenzhen, Guangdong 518055, China
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Yin K, Cruz-Morales P, Whitford CM, Keasling JD. Heterologous production of polycyclopropanated fatty acids and their methyl esters in Streptomyces. STAR Protoc 2023; 4:102190. [PMID: 36952335 PMCID: PMC10064271 DOI: 10.1016/j.xpro.2023.102190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 02/07/2023] [Accepted: 03/01/2023] [Indexed: 03/24/2023] Open
Abstract
Polycyclopropanated (POP) compounds show promise as fuels as their energy density can be greater than jet and rocket fuels in current use, but realizing their full potential requires significant development. This protocol guides the production of polycyclopropanated fatty acids in Streptomyces; POP production in another host remains to be demonstrated. This method can serve as a baseline for further development of POP as well as other polyketide products. For complete details on the use and execution of this protocol, please refer to Cruz-Morales et al. (2022).1.
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Affiliation(s)
- Kevin Yin
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA 94608, USA; Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA 94720, USA.
| | - Pablo Cruz-Morales
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA 94608, USA; Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; QB3 Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Christopher M Whitford
- The Novo Nordisk Foundation Center for Biosustainability, Technical University Denmark, Kemitorvet, Building 220, Kongens Lyngby 2800, Denmark
| | - Jay D Keasling
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA 94608, USA; Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; QB3 Institute, University of California, Berkeley, Berkeley, CA 94720, USA; Department of Chemical and Biomolecular Engineering and Department of Bioengineering, University of California, Berkeley, Berkeley, CA 94720, USA; Center for Synthetic Biochemistry, Shenzhen Institutes for Advanced Technologies, Shenzhen 518055, P.R. China; The Novo Nordisk Foundation Center for Biosustainability, Technical University Denmark, Kemitorvet, Building 220, Kongens Lyngby 2800, Denmark.
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36
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Zhao X, Wu Y, Feng T, Shen J, Lu H, Zhang Y, Chou HH, Luo X, Keasling JD. Dynamic upregulation of the rate-limiting enzyme for valerolactam biosynthesis in Corynebacterium glutamicum. Metab Eng 2023; 77:89-99. [PMID: 36933819 DOI: 10.1016/j.ymben.2023.02.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 01/26/2023] [Accepted: 02/13/2023] [Indexed: 03/18/2023]
Abstract
Valerolactam is a monomer used to manufacture high-value nylon-5 and nylon-6,5. However, the biological production of valerolactam has been limited by the inadequate efficiency of enzymes to cyclize 5-aminovaleric acid to produce valerolactam. In this study, we engineered Corynebacterium glutamicum with a valerolactam biosynthetic pathway consisting of DavAB from Pseudomonas putida to convert L-lysine to 5-aminovaleric acid and β-alanine CoA transferase (Act) from Clostridium propionicum to produce valerolactam from 5-aminovaleric acid. Most of the L-lysine was converted into 5-aminovaleric acid, but promoter optimization and increasing the copy number of Act were insufficient to significantly improve the titer of valerolactam. To eliminate the bottleneck at Act, we designed a dynamic upregulation system (a positive feedback loop based on the valerolactam biosensor ChnR/Pb). We used laboratory evolution to engineer ChnR/Pb to have higher sensitivity and a higher dynamic output range, and the engineered ChnR-B1/Pb-E1 system was used to overexpress the rate-limiting enzymes (Act/ORF26/CaiC) that cyclize 5-aminovaleric acid into valerolactam. In glucose fed-batch culture, we obtained 12.33 g/L valerolactam from the dynamic upregulation of Act, 11.88 g/L using ORF26, and 12.15 g/L using CaiC. Our engineered biosensor (ChnR-B1/Pb-E1 system) was also sensitive to 0.01-100 mM caprolactam, which suggests that this dynamic upregulation system can be used to enhance caprolactam biosynthesis in the future.
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Affiliation(s)
- Xixi Zhao
- Center for Synthetic Biochemistry, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China; CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Yanling Wu
- Center for Synthetic Biochemistry, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China; CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Tingye Feng
- Center for Synthetic Biochemistry, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China; CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Junfeng Shen
- Center for Synthetic Biochemistry, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China; CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Huan Lu
- Center for Synthetic Biochemistry, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China; CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Yunfeng Zhang
- Center for Synthetic Biochemistry, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China; CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Howard H Chou
- Center for Synthetic Biochemistry, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China; CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China; University of Chinese Academy of Sciences, Beijing, 100049, China; Shenzhen Key Laboratory for the Intelligent Microbial Manufacturing of Medicines, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Xiaozhou Luo
- Center for Synthetic Biochemistry, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China; CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China; University of Chinese Academy of Sciences, Beijing, 100049, China; Shenzhen Key Laboratory for the Intelligent Microbial Manufacturing of Medicines, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China.
| | - Jay D Keasling
- Center for Synthetic Biochemistry, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China; Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, 94608, USA; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA; QB3 Institute, University of California, Berkeley, CA, 94720, USA; Department of Chemical and Biomolecular Engineering and Department of Bioengineering, University of California, Berkeley, CA, 94720, USA; The Novo Nordisk Foundation Center for Biosustainability, Technical University Denmark, Kemitorvet, Building 220, Kongens Lyngby, 2800, Denmark
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37
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Lu X, Huang L, Scheller HV, Keasling JD. Medicinal terpenoid UDP-glycosyltransferases in plants: recent advances and research strategies. J Exp Bot 2023; 74:1343-1357. [PMID: 36573380 DOI: 10.1093/jxb/erac505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 12/17/2022] [Indexed: 06/18/2023]
Abstract
Terpenoid glycosides have significant curative effects on many kinds of diseases. Most of these compounds are derived from medicinal plants. Glycosylation is a key step in the biosynthesis of medicinal terpenoids. In plants, UDP-dependent glycosyltransferases comprise a large family of enzymes that catalyze the transfer of sugars from donor to acceptor to form various bioactive glycosides. In recent years, numerous terpenoid UDP-glycosyltransferases (UGTs) have been cloned and characterized in medicinal plants. We review the typical characteristics and evolution of terpenoid-related UGTs in plants and summarize the advances and research strategies of terpenoid UGTs in medicinal plants over the past 20 years. We provide a reference for the study of glycosylation of terpenoid skeletons and the biosynthetic pathways for medicinal terpenoids in plants.
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Affiliation(s)
- Xu Lu
- Department of Chemical & Biomolecular Engineering, University of California, Berkeley, CA 94720, USA
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 210009, China
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA 94608, USA
- Department of Bioengineering, University of California, Berkeley, CA 94720, USA
| | - Lijin Huang
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Henrik V Scheller
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA 94608, USA
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
| | - Jay D Keasling
- Department of Chemical & Biomolecular Engineering, University of California, Berkeley, CA 94720, USA
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA 94608, USA
- Department of Bioengineering, University of California, Berkeley, CA 94720, USA
- Center for Biosustainability, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark
- Center for Synthetic Biochemistry, Institute for Synthetic Biology, Shenzhen Institutes for Advanced Technologies, Shenzhen, China
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38
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Valencia LE, Incha MR, Schmidt M, Pearson AN, Thompson MG, Roberts JB, Mehling M, Yin K, Sun N, Oka A, Shih PM, Blank LM, Gladden J, Keasling JD. Engineering Pseudomonas putida KT2440 for chain length tailored free fatty acid and oleochemical production. Commun Biol 2022; 5:1363. [PMID: 36509863 PMCID: PMC9744835 DOI: 10.1038/s42003-022-04336-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 12/02/2022] [Indexed: 12/15/2022] Open
Abstract
Despite advances in understanding the metabolism of Pseudomonas putida KT2440, a promising bacterial host for producing valuable chemicals from plant-derived feedstocks, a strain capable of producing free fatty acid-derived chemicals has not been developed. Guided by functional genomics, we engineered P. putida to produce medium- and long-chain free fatty acids (FFAs) to titers of up to 670 mg/L. Additionally, by taking advantage of the varying substrate preferences of paralogous native fatty acyl-CoA ligases, we employed a strategy to control FFA chain length that resulted in a P. putida strain specialized in producing medium-chain FFAs. Finally, we demonstrate the production of oleochemicals in these strains by synthesizing medium-chain fatty acid methyl esters, compounds useful as biodiesel blending agents, in various media including sorghum hydrolysate at titers greater than 300 mg/L. This work paves the road to produce high-value oleochemicals and biofuels from cheap feedstocks, such as plant biomass, using this host.
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Affiliation(s)
- Luis E. Valencia
- grid.451372.60000 0004 0407 8980Joint BioEnergy Institute, Emeryville, CA 94608 USA ,grid.184769.50000 0001 2231 4551Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA ,grid.47840.3f0000 0001 2181 7878Department of Bioengineering, University of California, Berkeley, CA 94720 USA
| | - Matthew R. Incha
- grid.451372.60000 0004 0407 8980Joint BioEnergy Institute, Emeryville, CA 94608 USA ,grid.184769.50000 0001 2231 4551Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA ,grid.47840.3f0000 0001 2181 7878Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720 USA
| | - Matthias Schmidt
- grid.451372.60000 0004 0407 8980Joint BioEnergy Institute, Emeryville, CA 94608 USA ,grid.184769.50000 0001 2231 4551Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA ,grid.1957.a0000 0001 0728 696XInstitute of Applied Microbiology (iAMB), Aachen Biology and Biotechnology (ABBt), RWTH Aachen University, Aachen, Germany
| | - Allison N. Pearson
- grid.451372.60000 0004 0407 8980Joint BioEnergy Institute, Emeryville, CA 94608 USA ,grid.184769.50000 0001 2231 4551Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA ,grid.47840.3f0000 0001 2181 7878Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720 USA
| | - Mitchell G. Thompson
- grid.451372.60000 0004 0407 8980Joint BioEnergy Institute, Emeryville, CA 94608 USA ,grid.184769.50000 0001 2231 4551Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA USA
| | - Jacob B. Roberts
- grid.451372.60000 0004 0407 8980Joint BioEnergy Institute, Emeryville, CA 94608 USA ,grid.184769.50000 0001 2231 4551Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA ,grid.47840.3f0000 0001 2181 7878Department of Bioengineering, University of California, Berkeley, CA 94720 USA
| | - Marina Mehling
- grid.451372.60000 0004 0407 8980Joint BioEnergy Institute, Emeryville, CA 94608 USA ,grid.184769.50000 0001 2231 4551Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
| | - Kevin Yin
- grid.451372.60000 0004 0407 8980Joint BioEnergy Institute, Emeryville, CA 94608 USA ,grid.184769.50000 0001 2231 4551Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA ,grid.47840.3f0000 0001 2181 7878Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720 USA
| | - Ning Sun
- grid.184769.50000 0001 2231 4551Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA ,Advanced Biofuels and Bioproducts Process Demonstration Unit, Emeryville, CA 94608 USA
| | - Asun Oka
- grid.184769.50000 0001 2231 4551Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA ,Advanced Biofuels and Bioproducts Process Demonstration Unit, Emeryville, CA 94608 USA
| | - Patrick M. Shih
- grid.451372.60000 0004 0407 8980Joint BioEnergy Institute, Emeryville, CA 94608 USA ,grid.184769.50000 0001 2231 4551Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA ,grid.47840.3f0000 0001 2181 7878Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720 USA ,grid.184769.50000 0001 2231 4551Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA USA
| | - Lars M. Blank
- grid.1957.a0000 0001 0728 696XInstitute of Applied Microbiology (iAMB), Aachen Biology and Biotechnology (ABBt), RWTH Aachen University, Aachen, Germany
| | - John Gladden
- grid.451372.60000 0004 0407 8980Joint BioEnergy Institute, Emeryville, CA 94608 USA ,grid.474523.30000000403888279Biomanufacturing and Biomaterials Department, Sandia National Laboratories, Livermore, CA 94550 USA
| | - Jay D. Keasling
- grid.451372.60000 0004 0407 8980Joint BioEnergy Institute, Emeryville, CA 94608 USA ,grid.184769.50000 0001 2231 4551Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA ,grid.47840.3f0000 0001 2181 7878Department of Bioengineering, University of California, Berkeley, CA 94720 USA ,grid.47840.3f0000 0001 2181 7878Department of Chemical & Biomolecular Engineering, University of California, Berkeley, CA 94720 USA ,grid.5170.30000 0001 2181 8870Center 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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39
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Otoupal PB, Geiselman GM, Oka AM, Barcelos CA, Choudhary H, Dinh D, Zhong W, Hwang H, Keasling JD, Mukhopadhyay A, Sundstrom E, Haushalter RW, Sun N, Simmons BA, Gladden JM. Advanced one-pot deconstruction and valorization of lignocellulosic biomass into triacetic acid lactone using Rhodosporidium toruloides. Microb Cell Fact 2022; 21:254. [PMID: 36482295 PMCID: PMC9733078 DOI: 10.1186/s12934-022-01977-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 11/19/2022] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Rhodosporidium toruloides is capable of co-utilization of complex carbon sources and robust growth from lignocellulosic hydrolysates. This oleaginous yeast is therefore an attractive host for heterologous production of valuable bioproducts at high titers from low-cost, deconstructed biomass in an economically and environmentally sustainable manner. Here we demonstrate this by engineering R. toruloides to produce the polyketide triacetic acid lactone (TAL) directly from unfiltered hydrolysate deconstructed from biomass with minimal unit process operations. RESULTS Introduction of the 2-pyrone synthase gene into R. toruloides enabled the organism to produce 2.4 g/L TAL from simple media or 2.0 g/L from hydrolysate produced from sorghum biomass. Both of these titers are on par with titers from other better-studied microbial hosts after they had been heavily engineered. We next demonstrate that filtered hydrolysates produced from ensiled sorghum are superior to those derived from dried sorghum for TAL production, likely due to the substantial organic acids produced during ensiling. We also demonstrate that the organic acids found in ensiled biomass can be used for direct synthesis of ionic liquids within the biomass pretreatment process, enabling consolidation of unit operations of in-situ ionic liquid synthesis, pretreatment, saccharification, and fermentation into a one-pot, separations-free process. Finally, we demonstrate this consolidation in a 2 L bioreactor using unfiltered hydrolysate, producing 3.9 g/L TAL. CONCLUSION Many steps involved in deconstructing biomass into fermentable substrate can be combined into a distinct operation, and directly fed to cultures of engineered R. toruloides cultures for subsequent valorization into gram per liter titers of TAL in a cost-effective manner.
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Affiliation(s)
- Peter B. Otoupal
- grid.474523.30000000403888279Biomanufacturing and Biomaterials Department, Sandia National Laboratories, Livermore, CA USA ,grid.184769.50000 0001 2231 4551DOE Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA USA ,Agile BioFoundry, Department of Energy, Emeryville, CA USA
| | - Gina M. Geiselman
- grid.474523.30000000403888279Biomanufacturing and Biomaterials Department, Sandia National Laboratories, Livermore, CA USA ,grid.184769.50000 0001 2231 4551DOE Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA USA ,Agile BioFoundry, Department of Energy, Emeryville, CA USA
| | - Asun M. Oka
- grid.184769.50000 0001 2231 4551Advanced Biofuels and Bioproducts Process Development Unit, Lawrence Berkeley National Laboratory, Emeryville, CA USA ,grid.184769.50000 0001 2231 4551Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA USA
| | - Carolina A. Barcelos
- grid.184769.50000 0001 2231 4551Advanced Biofuels and Bioproducts Process Development Unit, Lawrence Berkeley National Laboratory, Emeryville, CA USA ,grid.184769.50000 0001 2231 4551Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA USA
| | - Hemant Choudhary
- grid.474523.30000000403888279Biomanufacturing and Biomaterials Department, Sandia National Laboratories, Livermore, CA USA ,grid.184769.50000 0001 2231 4551DOE Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA USA
| | - Duy Dinh
- grid.184769.50000 0001 2231 4551Advanced Biofuels and Bioproducts Process Development Unit, Lawrence Berkeley National Laboratory, Emeryville, CA USA ,grid.184769.50000 0001 2231 4551Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA USA
| | - Wenqing Zhong
- grid.184769.50000 0001 2231 4551Advanced Biofuels and Bioproducts Process Development Unit, Lawrence Berkeley National Laboratory, Emeryville, CA USA ,grid.184769.50000 0001 2231 4551Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA USA
| | - HeeJin Hwang
- grid.474523.30000000403888279Biomanufacturing and Biomaterials Department, Sandia National Laboratories, Livermore, CA USA ,Agile BioFoundry, Department of Energy, Emeryville, CA USA
| | - Jay D. Keasling
- grid.184769.50000 0001 2231 4551DOE Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA USA ,grid.184769.50000 0001 2231 4551Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA USA ,grid.47840.3f0000 0001 2181 7878Department of Chemical & Biomolecular Engineering, University of California, Berkeley, Berkeley, CA USA ,grid.47840.3f0000 0001 2181 7878Department of Bioengineering, University of California, Berkeley, Berkeley, CA USA ,grid.5170.30000 0001 2181 8870Center for Biosustainability, Danish Technical University, Lyngby, Denmark ,grid.458489.c0000 0001 0483 7922Center for Synthetic Biochemistry, Institute for Synthetic Biology, Shenzhen Institute of Advanced Technology, Shenzhen, China
| | - Aindrila Mukhopadhyay
- grid.474523.30000000403888279Biomanufacturing and Biomaterials Department, Sandia National Laboratories, Livermore, CA USA ,grid.184769.50000 0001 2231 4551Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA USA ,grid.184769.50000 0001 2231 4551Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA USA
| | - Eric Sundstrom
- grid.184769.50000 0001 2231 4551Advanced Biofuels and Bioproducts Process Development Unit, Lawrence Berkeley National Laboratory, Emeryville, CA USA ,grid.184769.50000 0001 2231 4551Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA USA
| | - Robert W. Haushalter
- grid.184769.50000 0001 2231 4551DOE Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA USA ,grid.184769.50000 0001 2231 4551Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA USA
| | - Ning Sun
- grid.184769.50000 0001 2231 4551Advanced Biofuels and Bioproducts Process Development Unit, Lawrence Berkeley National Laboratory, Emeryville, CA USA ,grid.184769.50000 0001 2231 4551Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA USA
| | - Blake A. Simmons
- grid.184769.50000 0001 2231 4551DOE Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA USA ,Agile BioFoundry, Department of Energy, Emeryville, CA USA ,grid.184769.50000 0001 2231 4551Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA USA
| | - John M. Gladden
- grid.474523.30000000403888279Biomanufacturing and Biomaterials Department, Sandia National Laboratories, Livermore, CA USA ,grid.184769.50000 0001 2231 4551DOE Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA USA ,Agile BioFoundry, Department of Energy, Emeryville, CA USA
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Pang B, Graziani EI, Keasling JD. Acyltransferase Domain Swap in Modular Type I Polyketide Synthase to Adjust the Molecular Gluing Strength of Rapamycin. Tetrahedron Lett 2022. [DOI: 10.1016/j.tetlet.2022.154229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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41
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Li L, Zhang R, Chen L, Tian X, Li T, Pu B, Ma C, Ji X, Ba F, Xiong C, Shi Y, Mi X, Li J, Keasling JD, Zhang J, Liu Y. Permeability‐Engineered Compartmentalization Enables In Vitro Reconstitution of Sustained Synthetic Biology Systems. Adv Sci (Weinh) 2022; 9:e2203652. [PMID: 36180388 PMCID: PMC9731718 DOI: 10.1002/advs.202203652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 08/28/2022] [Indexed: 05/11/2023]
Abstract
In nature, biological compartments such as cells rely on dynamically controlled permeability for matter exchange and complex cellular activities. Likewise, the ability to engineer compartment permeability is crucial for in vitro systems to gain sustainability, robustness, and complexity. However, rendering in vitro compartments such a capability is challenging. Here, a facile strategy is presented to build permeability‐configurable compartments, and marked advantages of such compartmentalization are shown in reconstituting sustained synthetic biology systems in vitro. Through microfluidics, the strategy produces micrometer‐sized layered microgels whose shell layer serves as a sieving structure for biomolecules and particles. In this configuration, the transport of DNAs, proteins, and bacteriophages across the compartments can be controlled an guided by a physical model. Through permeability engineering, a compartmentalized cell‐free protein synthesis system sustains multicycle protein production; ≈100 000 compartments are repeatedly used in a five‐cycle synthesis, featuring a yield of 2.2 mg mL−1. Further, the engineered bacteria‐enclosing compartments possess near‐perfect phage resistance and enhanced environmental fitness. In a complex river silt environment, compartmentalized whole‐cell biosensors show maintained activity throughout the 32 h pollutant monitoring. It is anticipated that permeability‐engineered compartmentalization should pave the way for practical synthetic biology applications such as green bioproduction, environmental sensing, and bacteria‐based therapeutics.
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Affiliation(s)
- Luyao Li
- School of Physical Science and TechnologyShanghaiTech UniversityShanghai201210China
| | - Rong Zhang
- School of Physical Science and TechnologyShanghaiTech UniversityShanghai201210China
| | - Long Chen
- School of Physical Science and TechnologyShanghaiTech UniversityShanghai201210China
| | - Xintong Tian
- School of Physical Science and TechnologyShanghaiTech UniversityShanghai201210China
| | - Ting Li
- State Key Laboratory of Genetic EngineeringSchool of Life SciencesFudan UniversityShanghai200438China
| | - Bingchun Pu
- Department of Immunology and MicrobiologyShanghai Jiao Tong University School of MedicineShanghai200025China
| | - Conghui Ma
- School of Physical Science and TechnologyShanghaiTech UniversityShanghai201210China
| | - Xiangyang Ji
- School of Physical Science and TechnologyShanghaiTech UniversityShanghai201210China
| | - Fang Ba
- School of Physical Science and TechnologyShanghaiTech UniversityShanghai201210China
| | - Chenwei Xiong
- School of Physical Science and TechnologyShanghaiTech UniversityShanghai201210China
| | - Yunfeng Shi
- State Key Laboratory of Genetic EngineeringSchool of Life SciencesFudan UniversityShanghai200438China
| | - Xianqiang Mi
- Shanghai Institute of Microsystem and Information TechnologyChinese Academy of SciencesShanghai200050China
| | - Jian Li
- School of Physical Science and TechnologyShanghaiTech UniversityShanghai201210China
| | - Jay D. Keasling
- Joint BioEnergy InstituteEmeryvilleCA94608USA
- Biological Systems and Engineering DivisionLawrence Berkeley National LaboratoryBerkeleyCA94720USA
- Department of Chemical and Biomolecular Engineering & Department of BioengineeringUniversity of CaliforniaBerkeleyCA94720USA
| | - Jingwei Zhang
- State Key Laboratory of Genetic EngineeringSchool of Life SciencesFudan UniversityShanghai200438China
| | - Yifan Liu
- School of Physical Science and TechnologyShanghaiTech UniversityShanghai201210China
- Shanghai Clinical Research and Trial CenterShanghai201210China
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42
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Demarteau J, Epstein AR, Christensen PR, Abubekerov M, Wang H, Teat SJ, Seguin TJ, Chan CW, Scown CD, Russell TP, Keasling JD, Persson KA, Helms BA. Circularity in mixed-plastic chemical recycling enabled by variable rates of polydiketoenamine hydrolysis. Sci Adv 2022; 8:eabp8823. [PMID: 35857832 PMCID: PMC9299546 DOI: 10.1126/sciadv.abp8823] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 06/07/2022] [Indexed: 06/08/2023]
Abstract
Footwear, carpet, automotive interiors, and multilayer packaging are examples of products manufactured from several types of polymers whose inextricability poses substantial challenges for recycling at the end of life. Here, we show that chemical circularity in mixed-polymer recycling becomes possible by controlling the rates of depolymerization of polydiketoenamines (PDK) over several orders of magnitude through molecular engineering. Stepwise deconstruction of mixed-PDK composites, laminates, and assemblies is chemospecific, allowing a prescribed subset of monomers, fillers, and additives to be recovered under pristine condition at each stage of the recycling process. We provide a theoretical framework to understand PDK depolymerization via acid-catalyzed hydrolysis and experimentally validate trends predicted for the rate-limiting step. The control achieved by PDK resins in managing chemical and material entropy points to wide-ranging opportunities for pairing circular design with sustainable manufacturing.
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Affiliation(s)
- Jeremy Demarteau
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Alexander R. Epstein
- Materials Sciences and Engineering, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Peter R. Christensen
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Mark Abubekerov
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Hai Wang
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Simon J. Teat
- Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Trevor J. Seguin
- Materials Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Christopher W. Chan
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Corinne D. Scown
- Joint BioEnergy Institute, Emeryville, CA 94608, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Energy Analysis and Environmental Impacts Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Energy and Biosciences Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Thomas P. Russell
- Materials Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Polymer Science and Engineering Department, University of Massachusetts, Amherst, MA 01003, USA
- Advanced Institute for Materials Research, Tohoku University, Sendai 980-8577, Japan
| | - Jay D. Keasling
- Joint BioEnergy Institute, Emeryville, CA 94608, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Department of Chemical and Biomolecular Engineering and Department of Bioengineering, University of California, Berkeley, Berkeley, CA 94720, USA
- Center for Synthetic Biochemistry, Institute for Synthetic Biology, Shenzhen Institutes of Advanced Technologies, Shenzhen 518055, China
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Kristin A. Persson
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Materials Sciences and Engineering, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Brett A. Helms
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Materials Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
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44
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Liu Z, Huang J, Gu Y, Clark DS, Mukhopadhyay A, Keasling JD, Hartwig JF. Assembly and Evolution of Artificial Metalloenzymes within E. coli Nissle 1917 for Enantioselective and Site-Selective Functionalization of C─H and C═C Bonds. J Am Chem Soc 2022; 144:883-890. [PMID: 34985270 DOI: 10.1021/jacs.1c10975] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The potential applications afforded by the generation and reactivity of artificial metalloenzymes (ArMs) in microorganisms are vast. We show that a non-pathogenic E. coli strain, Nissle 1917 (EcN), is a suitable host for the creation of ArMs from cytochrome P450s and artificial heme cofactors. An outer-membrane receptor in EcN transports an iridium porphyrin into the cell, and the Ir-CYP119 (CYP119 containing iridium porphyrin) assembled in vivo catalyzes carbene insertions into benzylic C-H bonds enantioselectively and site-selectively. The application of EcN as a whole-cell screening platform eliminates the need for laborious processing procedures, drastically increases the ease and throughput of screening, and accelerates the development of Ir-CYP119 with improved catalytic properties. Studies to identify the transport machinery suggest that a transporter different from the previously assumed ChuA receptor serves to usher the iridium porphyrin into the cytoplasm.
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Affiliation(s)
- Zhennan Liu
- Department of Chemistry, University of California, Berkeley, California 94720, United States.,Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Jing Huang
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States.,Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, California 94608, United States
| | - Yang Gu
- Department of Chemistry, University of California, Berkeley, California 94720, United States.,Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Douglas S Clark
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720, United States.,Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Aindrila Mukhopadhyay
- Department of Chemistry, University of California, Berkeley, California 94720, United States.,Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Jay D Keasling
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States.,Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, California 94608, United States.,Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720, United States.,Department of Bioengineering, University of California, Berkeley, California 94720, United States.,Synthetic Biochemistry Center, Institute for Synthetic Biology, Shenzhen Institutes for Advanced Technologies, Shenzhen 518055, China.,Center for Biosustainability, Danish Technical University, Lyngby 2800 Kgs, Denmark
| | - John F Hartwig
- Department of Chemistry, University of California, Berkeley, California 94720, United States.,Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
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45
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Jakočiūnas T, Jensen MK, Keasling JD. CasPER: A CRISPR/Cas9-Based Method for Directed Evolution in Genomic Loci in Saccharomyces cerevisiae. Methods Mol Biol 2022; 2513:23-37. [PMID: 35781198 DOI: 10.1007/978-1-0716-2399-2_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Here, in this chapter, we describe a detailed protocol for the method named Cas9-mediated protein evolution reaction or short CasPER. CasPER is based on the generation of large 300-600-bp mutagenized linear DNA fragments by error-prone PCR which are used as a donor for repair of double-strand break mediated by Cas9 and subsequently integrated to the genome. This method can be efficiently used for directed evolution of desired essential or nonessential genes in the genome and most importantly can be multiplexed. Altogether, the described method allows for heterogeneous DNA integration with successful transformation efficiencies of 98-100% for both single and multiplex targeting.
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Affiliation(s)
- Tadas Jakočiūnas
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Michael K Jensen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark.
| | - Jay D Keasling
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
- Joint BioEnergy Institute, Emeryville, CA, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department of Chemical and Biomolecular Engineering and Department of Bioengineering, University of California, Berkeley, CA, USA
- Center for Synthetic Biochemistry, Institute for Synthetic Biology, Shenzhen Institutes for Advanced Technologies, Shenzhen, China
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46
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Jensen ED, Ambri F, Bendtsen MB, Javanpour AA, Liu CC, Jensen MK, Keasling JD. Integrating continuous hypermutation with high-throughput screening for optimization of cis,cis-muconic acid production in yeast. Microb Biotechnol 2021; 14:2617-2626. [PMID: 33645919 PMCID: PMC8601171 DOI: 10.1111/1751-7915.13774] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 01/31/2021] [Accepted: 02/02/2021] [Indexed: 12/16/2022] Open
Abstract
Directed evolution is a powerful method to optimize proteins and metabolic reactions towards user-defined goals. It usually involves subjecting genes or pathways to iterative rounds of mutagenesis, selection and amplification. While powerful, systematic searches through large sequence-spaces is a labour-intensive task, and can be further limited by a priori knowledge about the optimal initial search space, and/or limits in terms of screening throughput. Here, we demonstrate an integrated directed evolution workflow for metabolic pathway enzymes that continuously generate enzyme variants using the recently developed orthogonal replication system, OrthoRep and screens for optimal performance in high-throughput using a transcription factor-based biosensor. We demonstrate the strengths of this workflow by evolving a rate-limiting enzymatic reaction of the biosynthetic pathway for cis,cis-muconic acid (CCM), a precursor used for bioplastic and coatings, in Saccharomyces cerevisiae. After two weeks of simply iterating between passaging of cells to generate variant enzymes via OrthoRep and high-throughput sorting of best-performing variants using a transcription factor-based biosensor for CCM, we ultimately identified variant enzymes improving CCM titers > 13-fold compared with reference enzymes. Taken together, the combination of synthetic biology tools as adopted in this study is an efficient approach to debottleneck repetitive workflows associated with directed evolution of metabolic enzymes.
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Affiliation(s)
- Emil D. Jensen
- Novo Nordisk Foundation Center for BiosustainabilityTechnical University of DenmarkKgs. LyngbyDenmark
| | - Francesca Ambri
- Novo Nordisk Foundation Center for BiosustainabilityTechnical University of DenmarkKgs. LyngbyDenmark
| | - Marie B. Bendtsen
- Novo Nordisk Foundation Center for BiosustainabilityTechnical University of DenmarkKgs. LyngbyDenmark
| | - Alex A. Javanpour
- Department of Biomedical EngineeringUniversity of California, IrvineIrvineCA92697USA
| | - Chang C. Liu
- Department of Biomedical EngineeringUniversity of California, IrvineIrvineCA92697USA
- Department of ChemistryUniversity of California, IrvineIrvineCA92697USA
- Department of Molecular Biology and BiochemistryUniversity of California, IrvineIrvineCA92697USA
| | - Michael K. Jensen
- Novo Nordisk Foundation Center for BiosustainabilityTechnical University of DenmarkKgs. LyngbyDenmark
| | - Jay D. Keasling
- Novo Nordisk Foundation Center for BiosustainabilityTechnical University of DenmarkKgs. LyngbyDenmark
- Joint BioEnergy InstituteEmeryvilleCAUSA
- Biological Systems and Engineering DivisionLawrence Berkeley National LaboratoryBerkeleyCAUSA
- Department of Chemical and Biomolecular EngineeringDepartment of BioengineeringUniversity of CaliforniaBerkeleyCAUSA
- Center for Synthetic BiochemistryInstitute for Synthetic BiologyShenzhen Institutes of Advanced TechnologiesShenzhenChina
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47
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Pang B, Li J, Eiben CB, Oksen E, Barcelos C, Chen R, Englund E, Sundstrom E, Keasling JD. Lepidopteran mevalonate pathway optimization in Escherichia coli efficiently produces isoprenol analogs for next-generation biofuels. Metab Eng 2021; 68:210-219. [PMID: 34673235 DOI: 10.1016/j.ymben.2021.10.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 10/12/2021] [Accepted: 10/16/2021] [Indexed: 12/31/2022]
Abstract
Terpenes constitute the largest class of natural products with over 55,000 compounds with versatile applications including drugs and biofuels. Introducing structural modifications to terpenes through metabolic engineering is an efficient and sustainable way to improve their properties. Here, we report the optimization of the lepidopteran mevalonate (LMVA) pathway towards the efficient production of isopentenyl pyrophosphate (IPP) analogs as terpene precursors. First, we linked the LMVA pathway to NudB, a promiscuous phosphatase, resulting in the production of the six-carbon analog of 3-methyl-3-buten-1-ol (isoprenol), 3-ethyl-3-buten-1-ol (C6-isoprenol). Using C6-isoprenol as the final product, we then engineered the LMVA pathway by redirecting its upstream portion from a thiolase-dependent pathway to a beta-oxidation pathway. The beta-oxidation LMVA pathway transforms valeric acid, a platform chemical that can be produced from biomass, into C6-isoprenol at a titer of 110.3 mg/L, improved from 5.5 mg/L by the thiolase LMVA pathway, which used propionic acid as a feedstock. Knockout of the E. coli endogenous thiolase genes further improved the C6-isoprenol titer to 390 mg/L, implying efficient production of homo isopentenyl pyrophosphate (HIPP). The beta-oxidation LMVA-NudB pathway also converts butanoic acid and hexanoic acid into isoprenol and isoprenol's seven-carbon analog, 3-propyl-3-buten-1-ol (C7-isoprenol), respectively, suggesting the beta-oxidation LMVA pathway produces IPP and C7-IPP from the corresponding fatty acids. Fuel property tests revealed the longer chain isoprenol analogs have lower water solubilities, similar or higher energy densities, and comparable research octane number (RON) boosting effects to isopentenols. This work not only optimizes the LMVA pathway, setting the basis for homoterpene biosynthesis to expand terpene chemical space, but provides an efficient pathway to produce isoprenol analogs as next-generation biofuels from sustainable feedstocks.
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Affiliation(s)
- Bo Pang
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, 94608, United States; Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, United States; Department of Chemical & Biomolecular Engineering, University of California, Berkeley, CA, 94720, United States
| | - Jia Li
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, 94608, United States; State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, School of Life Sciences, Hubei University, Wuhan, Hubei, 430062, PR China; Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, United States
| | - Christopher B Eiben
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, 94608, United States; Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, United States
| | - Ethan Oksen
- Advanced Biofuels & Bioproducts Process Development Unit, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, United States; Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, United States
| | - Carolina Barcelos
- Advanced Biofuels & Bioproducts Process Development Unit, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, United States; Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, United States
| | - Rong Chen
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, 94608, United States; Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, United States; School of Public Health, Hangzhou Normal University, Hangzhou, Zhejiang, 311121, PR China
| | - Elias Englund
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, 94608, United States; Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, United States
| | - Eric Sundstrom
- Advanced Biofuels & Bioproducts Process Development Unit, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, United States; Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, United States
| | - Jay D Keasling
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, 94608, United States; Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, United States; Department of Chemical & Biomolecular Engineering, University of California, Berkeley, CA, 94720, United States; Novo Nordisk Foundation Center for Biosustainability, Technical University Denmark, DK 2970 Horsholm, Denmark; Center for Synthetic Biochemistry, Shenzhen Institutes for Advanced Technologies, Shenzhen, Guangdong, 518055, PR China.
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48
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Deng J, Wu Y, Zheng Z, Chen N, Luo X, Tang H, Keasling JD. A synthetic promoter system for well-controlled protein expression with different carbon sources in Saccharomyces cerevisiae. Microb Cell Fact 2021; 20:202. [PMID: 34663323 PMCID: PMC8522093 DOI: 10.1186/s12934-021-01691-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 09/27/2021] [Indexed: 11/24/2022] Open
Abstract
Background Saccharomyces cerevisiae is an important synthetic biology chassis for microbial production of valuable molecules. Promoter engineering has been frequently applied to generate more synthetic promoters with a variety of defined characteristics in order to achieve a well-regulated genetic network for high production efficiency. Galactose-inducible (GAL) expression systems, composed of GAL promoters and multiple GAL regulators, have been widely used for protein overexpression and pathway construction in S. cerevisiae. However, the function of each element in synthetic promoters and how they interact with GAL regulators are not well known. Results Here, a library of synthetic GAL promoters demonstrate that upstream activating sequences (UASs) and core promoters have a synergistic relationship that determines the performance of each promoter under different carbon sources. We found that the strengths of synthetic GAL promoters could be fine-tuned by manipulating the sequence, number, and substitution of UASs. Core promoter replacement generated synthetic promoters with a twofold strength improvement compared with the GAL1 promoter under multiple different carbon sources in a strain with GAL1 and GAL80 engineering. These results represent an expansion of the classic GAL expression system with an increased dynamic range and a good tolerance of different carbon sources. Conclusions In this study, the effect of each element on synthetic GAL promoters has been evaluated and a series of well-controlled synthetic promoters are constructed. By studying the interaction of synthetic promoters and GAL regulators, synthetic promoters with an increased dynamic range under different carbon sources are created. Supplementary Information The online version contains supplementary material available at 10.1186/s12934-021-01691-3.
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Affiliation(s)
- Jiliang Deng
- Center for Synthetic Biochemistry, Shenzhen Institute of Synthetic Biology, Shenzhen Institute for Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China.,State Key Laboratory of Hybrid Rice, Department of Plant Science, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Yanling Wu
- Center for Synthetic Biochemistry, Shenzhen Institute of Synthetic Biology, Shenzhen Institute for Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Zhaohui Zheng
- Center for Synthetic Biochemistry, Shenzhen Institute of Synthetic Biology, Shenzhen Institute for Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Nanzhu Chen
- Center for Synthetic Biochemistry, Shenzhen Institute of Synthetic Biology, Shenzhen Institute for Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Xiaozhou Luo
- Center for Synthetic Biochemistry, Shenzhen Institute of Synthetic Biology, Shenzhen Institute for Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China.
| | - Hongting Tang
- Center for Synthetic Biochemistry, Shenzhen Institute of Synthetic Biology, Shenzhen Institute for Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China.
| | - Jay D Keasling
- Center for Synthetic Biochemistry, Shenzhen Institute of Synthetic Biology, Shenzhen Institute for Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China.,Joint BioEnergy Institute, Emeryville, CA, 94608, USA.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.,Department of Chemical and Biomolecular Engineering & Department of Bioengineering, University of California, Berkeley, CA, 94720, USA.,Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kgs. Lyngby, Denmark
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49
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Qin J, Krivoruchko A, Ji B, Chen Y, Kristensen M, Özdemir E, Keasling JD, Jensen MK, Nielsen J. Engineering yeast metabolism for the discovery and production of polyamines and polyamine analogues. Nat Catal 2021. [DOI: 10.1038/s41929-021-00631-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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Vora N, Christensen PR, Demarteau J, Baral NR, Keasling JD, Helms BA, Scown CD. Leveling the cost and carbon footprint of circular polymers that are chemically recycled to monomer. Sci Adv 2021; 7:7/15/eabf0187. [PMID: 33837082 PMCID: PMC8034859 DOI: 10.1126/sciadv.abf0187] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 02/19/2021] [Indexed: 05/27/2023]
Abstract
Mechanical recycling of polymers downgrades them such that they are unusable after a few cycles. Alternatively, chemical recycling to monomer offers a means to recover the embodied chemical feedstocks for remanufacturing. However, only a limited number of commodity polymers may be chemically recycled, and the processes remain resource intensive. We use systems analysis to quantify the costs and life-cycle carbon footprints of virgin and chemically recycled polydiketoenamines (PDKs), next-generation polymers that depolymerize under ambient conditions in strong acid. The cost of producing virgin PDK resin using unoptimized processes is ~30-fold higher than recycling them, and the cost of recycled PDK resin ($1.5 kg-1) is on par with PET and HDPE, and below that of polyurethanes. Virgin resin production is carbon intensive (86 kg CO2e kg-1), while chemical recycling emits only 2 kg CO2e kg-1 This cost and emissions disparity provides a strong incentive to recover and recycle future polymer waste.
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Affiliation(s)
- Nemi Vora
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Advanced Systems Analysis Group, International Institute for Applied Systems Analysis, Schlossplatz 1, A-2361 Laxenburg, Austria
| | - Peter R Christensen
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Jérémy Demarteau
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Nawa Raj Baral
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Life-Cycle, Economics, and Agronomy Division, Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, CA 94608, USA
| | - Jay D Keasling
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, CA 94720, USA
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
- Center for Synthetic Biochemistry, Institute for Synthetic Biology, Shenzhen Institutes for Advanced Technologies, Shenzhen, China
- Biofuels and Bioproducts Division, Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, CA 94608, USA
| | - Brett A Helms
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Materials Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Corinne D Scown
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
- Life-Cycle, Economics, and Agronomy Division, Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, CA 94608, USA
- Energy Analysis and Environmental Impacts Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Energy & Biosciences Institute, University of California, Berkeley, Berkeley, CA 94720, USA
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