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Foo JL, Kitano S, Susanto AV, Jin Z, Lin Y, Luo Z, Huang L, Liang Z, Mitchell LA, Yang K, Wong A, Cai Y, Cai J, Stracquadanio G, Bader JS, Boeke JD, Dai J, Chang MW. Establishing chromosomal design-build-test-learn through a synthetic chromosome and its combinatorial reconfiguration. Cell Genom 2023; 3:100435. [PMID: 38020970 PMCID: PMC10667554 DOI: 10.1016/j.xgen.2023.100435] [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] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 08/19/2023] [Accepted: 10/06/2023] [Indexed: 12/01/2023]
Abstract
Chromosome-level design-build-test-learn cycles (chrDBTLs) allow systematic combinatorial reconfiguration of chromosomes with ease. Here, we established chrDBTL with a redesigned synthetic Saccharomyces cerevisiae chromosome XV, synXV. We designed and built synXV to harbor strategically inserted features, modified elements, and synonymously recoded genes throughout the chromosome. Based on the recoded chromosome, we developed a method to enable chrDBTL: CRISPR-Cas9-mediated mitotic recombination with endoreduplication (CRIMiRE). CRIMiRE allowed the creation of customized wild-type/synthetic combinations, accelerating genotype-phenotype mapping and synthetic chromosome redesign. We also leveraged synXV as a "build-to-learn" model organism for translation studies by ribosome profiling. We conducted a locus-to-locus comparison of ribosome occupancy between synXV and the wild-type chromosome, providing insight into the effects of codon changes and redesigned features on translation dynamics in vivo. Overall, we established synXV as a versatile reconfigurable system that advances chrDBTL for understanding biological mechanisms and engineering strains.
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Affiliation(s)
- Jee Loon Foo
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, Singapore 117456, Singapore
- Synthetic Biology Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117456, Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597, Singapore
- Wilmar-NUS Corporate Laboratory (WIL@NUS), National University of Singapore, Singapore 117599, Singapore
| | - Shohei Kitano
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, Singapore 117456, Singapore
- Synthetic Biology Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117456, Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597, Singapore
- Wilmar-NUS Corporate Laboratory (WIL@NUS), National University of Singapore, Singapore 117599, Singapore
| | - Adelia Vicanatalita Susanto
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, Singapore 117456, Singapore
- Synthetic Biology Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117456, Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597, Singapore
- Wilmar-NUS Corporate Laboratory (WIL@NUS), National University of Singapore, Singapore 117599, Singapore
| | - Zhu Jin
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, Singapore 117456, Singapore
- Synthetic Biology Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117456, Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597, Singapore
- Wilmar-NUS Corporate Laboratory (WIL@NUS), National University of Singapore, Singapore 117599, Singapore
| | - Yicong Lin
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics and Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Zhouqing Luo
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics and Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Linsen Huang
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics and Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Zhenzhen Liang
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics and Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Leslie A. Mitchell
- Institute for Systems Genetics, NYU Langone Health, New York, NY 10016, USA
| | - Kun Yang
- Department of Biomedical Engineering, NYU Tandon School of Engineering, Brooklyn, NY 11201, USA
| | - Adison Wong
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, Singapore 117456, Singapore
- Singapore Institute of Technology, 10 Dover Drive, Singapore 138683, Singapore
| | - Yizhi Cai
- Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester M1 7DN, UK
| | - Jitong Cai
- High-Throughput Biological Center and Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Giovanni Stracquadanio
- High-Throughput Biological Center and Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21205, USA
- School of Biological Sciences, The University of Edinburgh, Edinburgh EH9 3BF, UK
| | - Joel S. Bader
- High-Throughput Biological Center and Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Jef D. Boeke
- Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY 10016, USA
- Institute for Systems Genetics, NYU Langone Health, New York, NY 10016, USA
- Department of Biomedical Engineering, NYU Tandon School of Engineering, Brooklyn, NY 11201, USA
| | - Junbiao Dai
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics and Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Matthew Wook Chang
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, Singapore 117456, Singapore
- Synthetic Biology Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117456, Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597, Singapore
- Wilmar-NUS Corporate Laboratory (WIL@NUS), National University of Singapore, Singapore 117599, Singapore
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Abstract
Since its inception, synthetic biology has overcome many technical barriers but is at a crossroads for high-precision biological design. Devising ways to fully utilize big biological data may be the key to achieving greater heights in synthetic biology.
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Affiliation(s)
- Shohei Kitano
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, Singapore
- Synthetic Biology Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Ciai Lin
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, Singapore
- Synthetic Biology Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Jee Loon Foo
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, Singapore
- Synthetic Biology Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Matthew Wook Chang
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, Singapore
- Synthetic Biology Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
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Aggarwal N, Liang Y, Foo JL, Ling H, Hwang IY, Chang MW. FELICX: A robust nucleic acid detection method using flap endonuclease and CRISPR-Cas12. Biosens Bioelectron 2023; 222:115002. [PMID: 36527830 DOI: 10.1016/j.bios.2022.115002] [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: 10/11/2022] [Revised: 11/26/2022] [Accepted: 12/07/2022] [Indexed: 12/13/2022]
Abstract
Nucleic acid detection is crucial for monitoring diseases for which rapid, sensitive, and easy-to-deploy diagnostic tools are needed. CRISPR-based technologies can potentially fulfill this need for nucleic acid detection. However, their widespread use has been restricted by the requirement of a protospacer adjacent motif in the target and extensive guide RNA optimization. In this study, we developed FELICX, a technique that can overcome these limitations and provide a useful alternative to existing technologies. FELICX comprises flap endonuclease, Taq ligase and CRISPR-Cas for diagnostics (X) and can be used for detecting nucleic acids and single-nucleotide polymorphisms. This method can be deployed as a point-of-care test, as only two temperatures are needed without thermocycling for its functionality, with the result generated on lateral flow strips. As a proof-of-concept, we showed that up to 0.6 copies/μL of DNA and RNA could be detected by FELICX in 60 min and 90 min, respectively, using simulated samples. Additionally, FELICX could be used to probe any base pair, unlike other CRISPR-based technologies. Finally, we demonstrated the versatility of FELICX by employing it for virus detection in infected human cells, the identification of antibiotic-resistant bacteria, and cancer diagnostics using simulated samples. Based on its unique advantages, we envision the use of FELICX as a next-generation CRISPR-based technology in nucleic acid diagnostics.
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Affiliation(s)
- Nikhil Aggarwal
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, Singapore; Synthetic Biology Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Yuanmei Liang
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, Singapore; Synthetic Biology Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore; Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Jee Loon Foo
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, Singapore; Synthetic Biology Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore; Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Hua Ling
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, Singapore; Synthetic Biology Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore; Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - In Young Hwang
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, Singapore; Synthetic Biology Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore; Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Matthew Wook Chang
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, Singapore; Synthetic Biology Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore; Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore.
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Miyake R, Ling H, Foo JL, Fugono N, Chang MW. Transporter-Driven Engineering of a Genetic Biosensor for the Detection and Production of Short-Branched Chain Fatty Acids in Saccharomyces cerevisiae. Front Bioeng Biotechnol 2022; 10:838732. [PMID: 35372305 PMCID: PMC8975619 DOI: 10.3389/fbioe.2022.838732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Accepted: 02/28/2022] [Indexed: 12/02/2022] Open
Abstract
Biosensors can be used for real-time monitoring of metabolites and high-throughput screening of producer strains. Use of biosensors has facilitated strain engineering to efficiently produce value-added compounds. Following our recent work on the production of short branched-chain fatty acids (SBCFAs) in engineered Saccharomyces cerevisiae, here we harnessed a weak organic acid transporter Pdr12p, engineered a whole-cell biosensor to detect exogenous and intracellular SBCFAs and optimized the biosensor’s performance by varying PDR12 expression. We firstly constructed the biosensor and evaluated its response to a range of short-chain carboxylic acids. Next, we optimized its sensitivity and operational range by deletion and overexpression of PDR12. We found that the biosensor responded to exogenous SBCFAs including isovaleric acid, isobutyric acid and 2-methylbutanoic acid. PDR12 deletion enhanced the biosensor’s sensitivity to isovaleric acid at a low concentration and PDR12 overexpression shifted the operational range towards a higher concentration. Lastly, the deletion of PDR12 improved the biosensor’s sensitivity to the SBCFAs produced in our previously engineered SBCFA-overproducing strain. To our knowledge, our work represents the first study on employing an ATP-binding-cassette transporter to engineer a transcription-factor-based genetic biosensor for sensing SBCFAs in S. cerevisiae. Our findings provide useful insights into SBCFA detection by a genetic biosensor that will facilitate the screening of SBCFA-overproducing strains.
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Affiliation(s)
- Ryoma Miyake
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, Singapore, Singapore
- Synthetic Biology Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Science & Innovation Center, Mitsubishi Chemical Corporation, Yokohama, Japan
| | - Hua Ling
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, Singapore, Singapore
- Synthetic Biology Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Jee Loon Foo
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, Singapore, Singapore
- Synthetic Biology Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Nobutake Fugono
- Science & Innovation Center, Mitsubishi Chemical Corporation, Yokohama, Japan
| | - Matthew Wook Chang
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, Singapore, Singapore
- Synthetic Biology Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- *Correspondence: Matthew Wook Chang,
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Zhu K, Kong J, Zhao B, Rong L, Liu S, Lu Z, Zhang C, Xiao D, Pushpanathan K, Foo JL, Wong A, Yu A. Metabolic engineering of microbes for monoterpenoid production. Biotechnol Adv 2021; 53:107837. [PMID: 34555428 DOI: 10.1016/j.biotechadv.2021.107837] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [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: 06/21/2021] [Revised: 09/07/2021] [Accepted: 09/14/2021] [Indexed: 12/29/2022]
Abstract
Monoterpenoids are an important class of natural products that are derived from the condensation of two five‑carbon isoprene subunits. They are widely used for flavouring, fragrances, colourants, cosmetics, fuels, chemicals, and pharmaceuticals in various industries. They can also serve as precursors for the production of many industrially important products. Currently, monoterpenoids are produced predominantly through extraction from plant sources. However, the small quantity of monoterpenoids in nature renders this method of isolation non-economically viable. Similarly impractical is the chemical synthesis of these compounds as they suffer from high energy consumption and pollutant discharge. Microbial biosynthesis, however, exists as a potential solution to these hindrances, but the transformation of cells into efficient factories remains a major impediment. Here, we critically review the recent advances in engineering microbes for monoterpenoid production, with an emphasis on categorized strategies, and discuss the challenges and perspectives to offer guidance for future engineering.
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Affiliation(s)
- Kun Zhu
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, No. 29 the 13th Street TEDA, Tianjin 300457, PR China.
| | - Jing Kong
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, No. 29 the 13th Street TEDA, Tianjin 300457, PR China.
| | - Baixiang Zhao
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, No. 29 the 13th Street TEDA, Tianjin 300457, PR China.
| | - Lanxin Rong
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, No. 29 the 13th Street TEDA, Tianjin 300457, PR China.
| | - Shiqi Liu
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, No. 29 the 13th Street TEDA, Tianjin 300457, PR China.
| | - Zhihui Lu
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, No. 29 the 13th Street TEDA, Tianjin 300457, PR China.
| | - Cuiying Zhang
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, No. 29 the 13th Street TEDA, Tianjin 300457, PR China.
| | - Dongguang Xiao
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, No. 29 the 13th Street TEDA, Tianjin 300457, PR China.
| | - Krithi Pushpanathan
- Chemical Engineering and Food Technology Cluster, Singapore Institute of Technology, Singapore 138683, Singapore.
| | - Jee Loon Foo
- Synthetic Biology Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228, Singapore; NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, Singapore 117456, Singapore; Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597, Singapore.
| | - Adison Wong
- Chemical Engineering and Food Technology Cluster, Singapore Institute of Technology, Singapore 138683, Singapore.
| | - Aiqun Yu
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, No. 29 the 13th Street TEDA, Tianjin 300457, PR China.
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Zhao Y, Liu S, Lu Z, Zhao B, Wang S, Zhang C, Xiao D, Foo JL, Yu A. Hybrid promoter engineering strategies in Yarrowia lipolytica: isoamyl alcohol production as a test study. Biotechnol Biofuels 2021; 14:149. [PMID: 34215293 PMCID: PMC8252286 DOI: 10.1186/s13068-021-02002-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 06/22/2021] [Indexed: 05/11/2023]
Abstract
BACKGROUND In biological cells, promoters drive gene expression by specific binding of RNA polymerase. They determine the starting position, timing and level of gene expression. Therefore, rational fine-tuning of promoters to regulate the expression levels of target genes for optimizing biosynthetic pathways in metabolic engineering has recently become an active area of research. RESULTS In this study, we systematically detected and characterized the common promoter elements in the unconventional yeast Yarrowia lipolytica, and constructed an artificial hybrid promoter library that covers a wide range of promoter strength. The results indicate that the hybrid promoter strength can be fine-tuned by promoter elements, namely, upstream activation sequences (UAS), TATA box and core promoter. Notably, the UASs of Saccharomyces cerevisiae promoters were reported for the first time to be functionally transferred to Y. lipolytica. Subsequently, using the production of a versatile platform chemical isoamyl alcohol as a test study, the hybrid promoter library was applied to optimize the biosynthesis pathway expression in Y. lipolytica. By expressing the key pathway gene, ScARO10, with the promoter library, 1.1-30.3 folds increase in the isoamyl alcohol titer over that of the control strain Y. lipolytica Po1g KU70∆ was achieved. Interestingly, the highest titer increase was attained with a weak promoter PUAS1B4-EXPm to express ScARO10. These results suggest that our hybrid promoter library can be a powerful toolkit for identifying optimum promoters for expressing metabolic pathways in Y. lipolytica. CONCLUSION We envision that this promoter engineering strategy and the rationally engineered promoters constructed in this study could also be extended to other non-model fungi for strain improvement.
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Affiliation(s)
- Yu Zhao
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, No. 29 the 13th Street TEDA, Tianjin, 300457 People’s Republic of China
| | - Shiqi Liu
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, No. 29 the 13th Street TEDA, Tianjin, 300457 People’s Republic of China
| | - Zhihui Lu
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, No. 29 the 13th Street TEDA, Tianjin, 300457 People’s Republic of China
| | - Baixiang Zhao
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, No. 29 the 13th Street TEDA, Tianjin, 300457 People’s Republic of China
| | - Shuhui Wang
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, No. 29 the 13th Street TEDA, Tianjin, 300457 People’s Republic of China
| | - Cuiying Zhang
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, No. 29 the 13th Street TEDA, Tianjin, 300457 People’s Republic of China
| | - Dongguang Xiao
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, No. 29 the 13th Street TEDA, Tianjin, 300457 People’s Republic of China
| | - Jee Loon Foo
- Synthetic Biology Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 119228 Singapore
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, Singapore, 117456 Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117597 Singapore
| | - Aiqun Yu
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, No. 29 the 13th Street TEDA, Tianjin, 300457 People’s Republic of China
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Li J, Zhu K, Miao L, Rong L, Zhao Y, Li S, Ma L, Li J, Zhang C, Xiao D, Foo JL, Yu A. Simultaneous Improvement of Limonene Production and Tolerance in Yarrowia lipolytica through Tolerance Engineering and Evolutionary Engineering. ACS Synth Biol 2021; 10:884-896. [PMID: 33715363 DOI: 10.1021/acssynbio.1c00052] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Limonene is an important plant natural product widely used in food and cosmetics production as well as in the pharmaceutical and chemical industries. However, low efficiency of plant extraction and high energy consumption in chemical synthesis limit the sustainability of industrial limonene production. Recently, the advancement of metabolic engineering and synthetic biology has facilitated the engineering of microbes into microbial cell factories for producing limonene. However, the deleterious effects on cellular activity by the toxicity of limonene is the major obstacle in achieving high-titer production of limonene in engineered microbes. In this study, by using transcriptomics, we identified 82 genes from the nonconventional yeast Yarrowia lipolytica that were up-regulated when exposed to limonene. When overexpressed, 8 of the gene candidates improved tolerance of this yeast to exogenously added limonene. To determine whether overexpression of these genes could also improve limonene production, we individually coexpressed the tolerance-enhancing genes with a limonene synthase gene. Indeed, expression of 5 of the 8 candidate genes enhanced limonene production in Y. lipolytica. Particularly, overexpressing YALI0F19492p led to an 8-fold improvement in product titer. Furthermore, through short-term adaptive laboratory evolution strategy, in combination with morphological and cytoplasmic membrane integrity analysis, we shed light on the underlying mechanism of limonene cytotoxicity to Y. lipolytica. This study demonstrated an effective strategy for improving limonene tolerance of Y. lipolytica and limonene titer in the host strain through the combinatorial use of tolerance engineering and evolutionary engineering.
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Affiliation(s)
- Jian Li
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, No. 29 13th Street TEDA, Tianjin 300457, PR China
| | - Kun Zhu
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, No. 29 13th Street TEDA, Tianjin 300457, PR China
| | - Lin Miao
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, No. 29 13th Street TEDA, Tianjin 300457, PR China
| | - Lanxin Rong
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, No. 29 13th Street TEDA, Tianjin 300457, PR China
| | - Yu Zhao
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, No. 29 13th Street TEDA, Tianjin 300457, PR China
| | - Shenglong Li
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, No. 29 13th Street TEDA, Tianjin 300457, PR China
| | - Lijuan Ma
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, No. 29 13th Street TEDA, Tianjin 300457, PR China
| | - Jianxun Li
- Agricultural Processing Institute, Chinese Academy of Agricultural Sciences, Beijing 100193, PR China
| | - Cuiying Zhang
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, No. 29 13th Street TEDA, Tianjin 300457, PR China
| | - Dongguang Xiao
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, No. 29 13th Street TEDA, Tianjin 300457, PR China
| | - Jee Loon Foo
- Synthetic Biology Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, 119228 Singapore
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, 117456 Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 117597 Singapore
| | - Aiqun Yu
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, No. 29 13th Street TEDA, Tianjin 300457, PR China
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Li J, Rong L, Zhao Y, Li S, Zhang C, Xiao D, Foo JL, Yu A. Next-generation metabolic engineering of non-conventional microbial cell factories for carboxylic acid platform chemicals. Biotechnol Adv 2020; 43:107605. [DOI: 10.1016/j.biotechadv.2020.107605] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Revised: 06/30/2020] [Accepted: 07/27/2020] [Indexed: 01/21/2023]
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Foo JL, Rasouliha BH, Susanto AV, Leong SSJ, Chang MW. Engineering an Alcohol-Forming Fatty Acyl-CoA Reductase for Aldehyde and Hydrocarbon Biosynthesis in Saccharomyces cerevisiae. Front Bioeng Biotechnol 2020; 8:585935. [PMID: 33123518 PMCID: PMC7573125 DOI: 10.3389/fbioe.2020.585935] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [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: 07/22/2020] [Accepted: 09/08/2020] [Indexed: 11/19/2022] Open
Abstract
Aldehydes are a class of highly versatile chemicals that can undergo a wide range of chemical reactions and are in high demand as starting materials for chemical manufacturing. Biologically, fatty aldehydes can be produced from fatty acyl-CoA by the action of fatty acyl-CoA reductases. The aldehydes produced can be further converted enzymatically to other valuable derivatives. Thus, metabolic engineering of microorganisms for biosynthesizing aldehydes and their derivatives could provide an economical and sustainable platform for key aldehyde precursor production and subsequent conversion to various value-added chemicals. Saccharomyces cerevisiae is an excellent host for this purpose because it is a robust organism that has been used extensively for industrial biochemical production. However, fatty acyl-CoA-dependent aldehyde-forming enzymes expressed in S. cerevisiae thus far have extremely low activities, hence limiting direct utilization of fatty acyl-CoA as substrate for aldehyde biosynthesis. Toward overcoming this challenge, we successfully engineered an alcohol-forming fatty acyl-CoA reductase for aldehyde production through rational design. We further improved aldehyde production through strain engineering by deleting competing pathways and increasing substrate availability. Subsequently, we demonstrated alkane and alkene production as one of the many possible applications of the aldehyde-producing strain. Overall, by protein engineering of a fatty acyl-CoA reductase to alter its activity and metabolic engineering of S. cerevisiae, we generated strains with the highest reported cytosolic aliphatic aldehyde and alkane/alkene production to date in S. cerevisiae from fatty acyl-CoA.
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Affiliation(s)
- Jee Loon Foo
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, Singapore, Singapore
| | - Bahareh Haji Rasouliha
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, Singapore, Singapore
| | - Adelia Vicanatalita Susanto
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, Singapore, Singapore
| | - Susanna Su Jan Leong
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, Singapore, Singapore.,Singapore Institute of Technology, Singapore, Singapore
| | - Matthew Wook Chang
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, Singapore, Singapore
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Chen B, Foo JL, Ling H, Chang MW. Mechanism-Driven Metabolic Engineering for Bio-Based Production of Free R-Lipoic Acid in Saccharomyces cerevisiae Mitochondria. Front Bioeng Biotechnol 2020; 8:965. [PMID: 32974306 PMCID: PMC7468506 DOI: 10.3389/fbioe.2020.00965] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [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: 05/31/2020] [Accepted: 07/24/2020] [Indexed: 01/28/2023] Open
Abstract
Lipoic acid is a valuable organosulfur compound used as an antioxidant for dietary supplementation, and potentially anti-diabetic and anti-cancer. Currently, lipoic acid is obtained mainly through chemical synthesis, which requires toxic reagents and organic solvents, thus causing environmental issues. Moreover, chemically synthesized lipoic acid is conventionally a racemic mixture. To obtain enantiomerically pure R-lipoic acid, which has superior bioactivity than the S form, chiral resolution and asymmetric synthesis methods require additional reagents and solvents, and often lead to wastage of S-lipoic acid or precursors with undesired chirality. Toward sustainable production of R-lipoic acid, we aim to develop a synthetic biology-based method using engineered yeast. Here, we deepened mechanistic understanding of lipoic acid biosynthesis and protein lipoylation in the model yeast Saccharomyces cerevisiae to facilitate metabolic engineering of the microbe for producing free R-lipoic acid. In brief, we studied the biosynthesis and confirmed the availability of protein-bound lipoate in yeast cells through LC-MS/MS. We then characterized in vitro the activity of a lipoamidase from Enterococcus faecalis for releasing free R-lipoic acid from lipoate-modified yeast proteins. Overexpression of the lipoamidase in yeast mitochondria enabled de novo free R-lipoic acid production in vivo. By overexpressing pathway enzymes and regenerating the cofactor, the production titer was increased ∼2.9-fold. This study represents the first report of free R-lipoic acid biosynthesis in S. cerevisiae. We envision that these results could provide insights into lipoic acid biosynthesis in eukaryotic cells and drive development of sustainable R-lipoic acid production.
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Affiliation(s)
- Binbin Chen
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, Singapore, Singapore
| | - Jee Loon Foo
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, Singapore, Singapore
| | - Hua Ling
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, Singapore, Singapore
| | - Matthew Wook Chang
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, Singapore, Singapore
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Xia P, Ling H, Foo JL, Chang MW. Synthetic Biology Toolkits for Metabolic Engineering of Cyanobacteria. Biotechnol J 2019; 14:e1800496. [DOI: 10.1002/biot.201800496] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 02/19/2019] [Indexed: 12/20/2022]
Affiliation(s)
- Peng‐Fei Xia
- Department of Biochemistry Yong Loo Lin School of MedicineNational University of Singapore8 Medical Drive Singapore 117597 Singapore
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI)National University of Singapore28 Medical Drive Singapore 117456 Singapore
| | - Hua Ling
- Department of Biochemistry Yong Loo Lin School of MedicineNational University of Singapore8 Medical Drive Singapore 117597 Singapore
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI)National University of Singapore28 Medical Drive Singapore 117456 Singapore
| | - Jee Loon Foo
- Department of Biochemistry Yong Loo Lin School of MedicineNational University of Singapore8 Medical Drive Singapore 117597 Singapore
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI)National University of Singapore28 Medical Drive Singapore 117456 Singapore
| | - Matthew Wook Chang
- Department of Biochemistry Yong Loo Lin School of MedicineNational University of Singapore8 Medical Drive Singapore 117597 Singapore
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI)National University of Singapore28 Medical Drive Singapore 117456 Singapore
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12
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Xia PF, Ling H, Foo JL, Chang MW. Synthetic genetic circuits for programmable biological functionalities. Biotechnol Adv 2019; 37:107393. [PMID: 31051208 DOI: 10.1016/j.biotechadv.2019.04.015] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [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: 12/15/2018] [Revised: 04/09/2019] [Accepted: 04/28/2019] [Indexed: 02/06/2023]
Abstract
Living organisms evolve complex genetic networks to interact with the environment. Due to the rapid development of synthetic biology, various modularized genetic parts and units have been identified from these networks. They have been employed to construct synthetic genetic circuits, including toggle switches, oscillators, feedback loops and Boolean logic gates. Building on these circuits, complex genetic machines with capabilities in programmable decision-making could be created. Consequently, these accomplishments have led to novel applications, such as dynamic and autonomous modulation of metabolic networks, directed evolution of biological units, remote and targeted diagnostics and therapies, as well as biological containment methods to prevent release of engineered microorganisms and genetic materials. Herein, we outline the principles in genetic circuit design that have initiated a new chapter in transforming concepts to realistic applications. The features of modularized building blocks and circuit architecture that facilitate realization of circuits for a variety of novel applications are discussed. Furthermore, recent advances and challenges in employing genetic circuits to impart microorganisms with distinct and programmable functionalities are highlighted. We envision that this review gives new insights into the design of synthetic genetic circuits and offers a guideline for the implementation of different circuits in various aspects of biotechnology and bioengineering.
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Affiliation(s)
- Peng-Fei Xia
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, Singapore 117597, Singapore; NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, 28 Medical Drive, Singapore 117456, Singapore
| | - Hua Ling
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, Singapore 117597, Singapore; NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, 28 Medical Drive, Singapore 117456, Singapore
| | - Jee Loon Foo
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, Singapore 117597, Singapore; NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, 28 Medical Drive, Singapore 117456, Singapore.
| | - Matthew Wook Chang
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, Singapore 117597, Singapore; NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, 28 Medical Drive, Singapore 117456, Singapore.
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Hossain GS, Nadarajan SP, Zhang L, Ng TK, Foo JL, Ling H, Choi WJ, Chang MW. Rewriting the Metabolic Blueprint: Advances in Pathway Diversification in Microorganisms. Front Microbiol 2018; 9:155. [PMID: 29483901 PMCID: PMC5816047 DOI: 10.3389/fmicb.2018.00155] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [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: 11/14/2017] [Accepted: 01/23/2018] [Indexed: 11/13/2022] Open
Abstract
Living organisms have evolved over millions of years to fine tune their metabolism to create efficient pathways for producing metabolites necessary for their survival. Advancement in the field of synthetic biology has enabled the exploitation of these metabolic pathways for the production of desired compounds by creating microbial cell factories through metabolic engineering, thus providing sustainable routes to obtain value-added chemicals. Following the past success in metabolic engineering, there is increasing interest in diversifying natural metabolic pathways to construct non-natural biosynthesis routes, thereby creating possibilities for producing novel valuable compounds that are non-natural or without elucidated biosynthesis pathways. Thus, the range of chemicals that can be produced by biological systems can be expanded to meet the demands of industries for compounds such as plastic precursors and new antibiotics, most of which can only be obtained through chemical synthesis currently. Herein, we review and discuss novel strategies that have been developed to rewrite natural metabolic blueprints in a bid to broaden the chemical repertoire achievable in microorganisms. This review aims to provide insights on recent approaches taken to open new avenues for achieving biochemical production that are beyond currently available inventions.
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Affiliation(s)
- Gazi Sakir Hossain
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), Life Sciences Institute, National University of Singapore, Singapore, Singapore
| | - Saravanan Prabhu Nadarajan
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), Life Sciences Institute, National University of Singapore, Singapore, Singapore
| | - Lei Zhang
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), Life Sciences Institute, National University of Singapore, Singapore, Singapore
| | - Tee-Kheang Ng
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), Life Sciences Institute, National University of Singapore, Singapore, Singapore
| | - Jee Loon Foo
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), Life Sciences Institute, National University of Singapore, Singapore, Singapore
| | - Hua Ling
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), Life Sciences Institute, National University of Singapore, Singapore, Singapore
| | - Won Jae Choi
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), Life Sciences Institute, National University of Singapore, Singapore, Singapore
- Agency for Science, Technology and Research (ASTAR), Institute of Chemical and Engineering Sciences, Singapore, Singapore
| | - Matthew Wook Chang
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), Life Sciences Institute, National University of Singapore, Singapore, Singapore
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Foo JL, Ling H, Lee YS, Chang MW. Microbiome engineering: Current applications and its future. Biotechnol J 2017; 12. [PMID: 28133942 DOI: 10.1002/biot.201600099] [Citation(s) in RCA: 75] [Impact Index Per Article: 10.7] [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: 09/10/2016] [Revised: 12/12/2016] [Accepted: 12/19/2016] [Indexed: 01/07/2023]
Abstract
Microbiomes exist in all ecosystems and are composed of diverse microbial communities. Perturbation to microbiomes brings about undesirable phenotypes in the hosts, resulting in diseases and disorders, and disturbs the balance of the associated ecosystems. Engineering of microbiomes can be used to modify structures of the microbiota and restore ecological balance. Consequently, microbiome engineering has been employed for improving human health and agricultural productivity. The importance and current applications of microbiome engineering, particularly in humans, animals, plants and soil is reviewed. Furthermore, we explore the challenges in engineering microbiome and the future of this field, thus providing perspectives and outlook of microbiome engineering.
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Affiliation(s)
- Jee Loon Foo
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore.,NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), Life Sciences Institute, National University of Singapore, Singapore
| | - Hua Ling
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore.,NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), Life Sciences Institute, National University of Singapore, Singapore
| | - Yung Seng Lee
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), Life Sciences Institute, National University of Singapore, Singapore.,Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Matthew Wook Chang
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore.,NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), Life Sciences Institute, National University of Singapore, Singapore
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Yu AQ, Pratomo Juwono NK, Foo JL, Leong SSJ, Chang MW. Metabolic engineering of Saccharomyces cerevisiae for the overproduction of short branched-chain fatty acids. Metab Eng 2016; 34:36-43. [DOI: 10.1016/j.ymben.2015.12.005] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Revised: 11/14/2015] [Accepted: 12/14/2015] [Indexed: 10/22/2022]
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Foo JL, Susanto AV, Keasling JD, Leong SSJ, Chang MW. Whole-cell biocatalytic and de novo production of alkanes from free fatty acids in Saccharomyces cerevisiae. Biotechnol Bioeng 2016; 114:232-237. [PMID: 26717118 PMCID: PMC5132040 DOI: 10.1002/bit.25920] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [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: 10/27/2015] [Revised: 12/15/2015] [Accepted: 12/29/2015] [Indexed: 12/17/2022]
Abstract
Rapid global industrialization in the past decades has led to extensive utilization of fossil fuels, which resulted in pressing environmental problems due to excessive carbon emission. This prompted increasing interest in developing advanced biofuels with higher energy density to substitute fossil fuels and bio‐alkane has gained attention as an ideal drop‐in fuel candidate. Production of alkanes in bacteria has been widely studied but studies on the utilization of the robust yeast host, Saccharomyces cerevisiae, for alkane biosynthesis have been lacking. In this proof‐of‐principle study, we present the unprecedented engineering of S. cerevisiae for conversion of free fatty acids to alkanes. A fatty acid α‐dioxygenase from Oryza sativa (rice) was expressed in S. cerevisiae to transform C12–18 free fatty acids to C11–17 aldehydes. Co‐expression of a cyanobacterial aldehyde deformylating oxygenase converted the aldehydes to the desired alkanes. We demonstrated the versatility of the pathway by performing whole‐cell biocatalytic conversion of exogenous free fatty acid feedstocks into alkanes as well as introducing the pathway into a free fatty acid overproducer for de novo production of alkanes from simple sugar. The results from this work are anticipated to advance the development of yeast hosts for alkane production. Biotechnol. Bioeng. 2017;114: 232–237. © 2016 The Authors. Biotechnology and Bioengineering Published by Wiley Periodicals, Inc.
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Affiliation(s)
- Jee Loon Foo
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore.,NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), Life Sciences Institute, National University of Singapore, Singapore
| | - Adelia Vicanatalita Susanto
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore.,NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), Life Sciences Institute, National University of Singapore, Singapore
| | - Jay D Keasling
- Joint BioEnergy Institute, Emeryville, California.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California.,Department of Chemical and Biomolecular Engineering and Department of Bioengineering, University of California, Berkeley, California
| | - Susanna Su Jan Leong
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore.,NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), Life Sciences Institute, National University of Singapore, Singapore.,Singapore Institute of Technology, Singapore
| | - Matthew Wook Chang
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore.,NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), Life Sciences Institute, National University of Singapore, Singapore
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Jin Z, Wong A, Foo JL, Ng J, Cao Y, Chang MW, Yuan Y. Engineering
Saccharomyces cerevisiae
to produce odd chain‐length fatty alcohols. Biotechnol Bioeng 2015; 113:842-51. [DOI: 10.1002/bit.25856] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2015] [Revised: 09/15/2015] [Accepted: 10/08/2015] [Indexed: 01/12/2023]
Affiliation(s)
- Zhu Jin
- Key Laboratory of Systems Bioengineering (Ministry of Education)Tianjin UniversityTianjin300072PR China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and EngineeringSchool of Chemical Engineering and Technology, Tianjin UniversityTianjin300072PR China
- Department of BiochemistryYong Loo Lin School of MedicineNational University of Singapore14 Medical Drive117599Singapore
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI)Life Sciences InstituteNational University of Singapore, 28 Medical Drive117456Singapore
| | - Adison Wong
- Department of BiochemistryYong Loo Lin School of MedicineNational University of Singapore14 Medical Drive117599Singapore
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI)Life Sciences InstituteNational University of Singapore, 28 Medical Drive117456Singapore
| | - Jee Loon Foo
- Department of BiochemistryYong Loo Lin School of MedicineNational University of Singapore14 Medical Drive117599Singapore
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI)Life Sciences InstituteNational University of Singapore, 28 Medical Drive117456Singapore
| | - Joey Ng
- Department of BiochemistryYong Loo Lin School of MedicineNational University of Singapore14 Medical Drive117599Singapore
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI)Life Sciences InstituteNational University of Singapore, 28 Medical Drive117456Singapore
| | - Ying‐Xiu Cao
- Key Laboratory of Systems Bioengineering (Ministry of Education)Tianjin UniversityTianjin300072PR China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and EngineeringSchool of Chemical Engineering and Technology, Tianjin UniversityTianjin300072PR China
| | - Matthew Wook Chang
- Department of BiochemistryYong Loo Lin School of MedicineNational University of Singapore14 Medical Drive117599Singapore
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI)Life Sciences InstituteNational University of Singapore, 28 Medical Drive117456Singapore
| | - Ying‐Jin Yuan
- Key Laboratory of Systems Bioengineering (Ministry of Education)Tianjin UniversityTianjin300072PR China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and EngineeringSchool of Chemical Engineering and Technology, Tianjin UniversityTianjin300072PR China
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Foo JL, Leong SSJ. Directed evolution of an E. coli inner membrane transporter for improved efflux of biofuel molecules. Biotechnol Biofuels 2013; 6:81. [PMID: 23693002 PMCID: PMC3680313 DOI: 10.1186/1754-6834-6-81] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2012] [Accepted: 05/16/2013] [Indexed: 05/04/2023]
Abstract
BACKGROUND The depletion of fossil fuels and the rising need to meet global energy demands have led to a growing interest in microbial biofuel synthesis, particularly in Escherichia coli, due to its tractable characteristics. Besides engineering more efficient metabolic pathways for synthesizing biofuels, efforts to improve production yield by engineering efflux systems to overcome toxicity problems is also crucial. This study aims to enhance hydrocarbon efflux capability in E. coli by engineering a native inner membrane transporter, AcrB, using the directed evolution approach. RESULTS We developed a selection platform based on competitive growth using a toxic substrate surrogate, which allowed rapid selection of AcrB variants showing enhanced efflux of linear and cyclic fuel molecule candidates, n-octane and α-pinene. Two mutants exhibiting increased efflux efficiency for n-octane and α-pinene by up to 47% and 400%, respectively, were isolated. Single-site mutants based on the mutations found in the isolated variants were synthesized and the amino acid substitutions N189H, T678S, Q737L and M844L were identified to have conferred improvement in efflux efficiency. The locations of beneficial mutations in AcrB suggest their contributions in widening the substrate channel, altering the dynamics of substrate efflux and promoting the assembly of AcrB with the outer membrane channel protein TolC for more efficient substrate export. It is interesting to note that three of the four beneficial mutations were located relatively distant from the known substrate channels, thus exemplifying the advantage of directed evolution over rational design. CONCLUSIONS Using directed evolution, we have isolated AcrB mutants with improved efflux efficiency for n-octane and α-pinene. The utilization of such optimized native efflux pumps will increase productivity of biofuels synthesis and alleviate toxicity and difficulties in production scale-up in current microbial platforms.
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Affiliation(s)
- Jee Loon Foo
- School of Chemical and Biomedical Engineering, Nanyang Technological University, 62 Nanyang Drive, Singapore 637459, Singapore
| | - Susanna Su Jan Leong
- School of Chemical and Biomedical Engineering, Nanyang Technological University, 62 Nanyang Drive, Singapore 637459, Singapore
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