51
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Hu Y, Zhu Z, Nielsen J, Siewers V. Heterologous transporter expression for improved fatty alcohol secretion in yeast. Metab Eng 2018; 45:51-58. [DOI: 10.1016/j.ymben.2017.11.008] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Revised: 11/01/2017] [Accepted: 11/18/2017] [Indexed: 11/25/2022]
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52
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Ye L, Zhu X, Wu T, Wang W, Zhao D, Bi C, Zhang X. Optimizing the localization of astaxanthin enzymes for improved productivity. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:278. [PMID: 30337957 PMCID: PMC6180651 DOI: 10.1186/s13068-018-1270-1] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Accepted: 09/26/2018] [Indexed: 05/05/2023]
Abstract
BACKGROUND One important metabolic engineering strategy is to localize the enzymes close to their substrates for improved catalytic efficiency. However, localization configurations become more complex the greater the number of enzymes and substrates is involved. Indeed, optimizing synthetic pathways by localizing multiple enzymes remains a challenge. Terpenes are one of the most valuable and abundant natural product groups. Phytoene, lycopene and β-carotene serve as common intermediates for the synthesis of many carotenoids and derivative compounds, which are hydrophobic long-chain terpenoids, insoluble in water and usually accumulate in membrane compartments. RESULTS While β-ionone synthesis by β-carotene cleavage dioxygenase PhCCD1 and astaxanthin synthesis by β-carotene ketolase (CrtW) and β-carotene hydroxylase (CrtZ) differ in complexity (single and multiple step pathways), the productivity of both pathways benefited from controlling enzyme localization to the E. coli cell membrane via a GlpF protein fusion. Especially, the astaxanthin synthesis pathway comprises both CrtW and CrtZ, which perform four interchangeable reactions initiated from β-carotene. Up to four localization strategies of CrtW and CrtZ were exhaustively discussed in this work, and the optimal positioning strategy was achieved. CrtW and CrtZ were linked using a flexible linker and localized to the membrane via a GlpF protein fusion. Enzymes in the optimal localization configuration allowed a 215.4% astaxanthin production increase. CONCLUSIONS This work exploits a localization situation involving membrane-bound substrates, intermediates and multiple enzymes for the first time, and provides a workable positioning strategy to solve problems in similar circumstances.
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Affiliation(s)
- Lijun Ye
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 People’s Republic of China
- Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 People’s Republic of China
| | - Xinna Zhu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 People’s Republic of China
- Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 People’s Republic of China
| | - Tao Wu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 People’s Republic of China
- Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 People’s Republic of China
| | - Wen Wang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 People’s Republic of China
- Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 People’s Republic of China
| | - Dongdong Zhao
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 People’s Republic of China
- Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 People’s Republic of China
| | - Changhao Bi
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 People’s Republic of China
- Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 People’s Republic of China
| | - Xueli Zhang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 People’s Republic of China
- Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 People’s Republic of China
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53
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Performance and mechanism analysis of succinate production under different transporters in Escherichia coli. BIOTECHNOL BIOPROC E 2017. [DOI: 10.1007/s12257-017-0086-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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54
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Joshi C, Singhal RS. Zeaxanthin production by Paracoccus zeaxanthinifaciens ATCC 21588 in a lab-scale bubble column reactor: Artificial intelligence modelling for determination of optimal operational parameters and energy requirements. KOREAN J CHEM ENG 2017. [DOI: 10.1007/s11814-017-0253-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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55
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Wang C, Zada B, Wei G, Kim SW. Metabolic engineering and synthetic biology approaches driving isoprenoid production in Escherichia coli. BIORESOURCE TECHNOLOGY 2017; 241:430-438. [PMID: 28599221 DOI: 10.1016/j.biortech.2017.05.168] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Revised: 05/24/2017] [Accepted: 05/26/2017] [Indexed: 05/20/2023]
Abstract
Isoprenoids comprise the largest family of natural organic compounds with many useful applications in the pharmaceutical, nutraceutical, and industrial fields. Rapid developments in metabolic engineering and synthetic biology have facilitated the engineering of isoprenoid biosynthetic pathways in Escherichia coli to induce high levels of production of many different isoprenoids. In this review, the stem pathways for synthesizing isoprene units as well as the branch pathways deriving diverse isoprenoids from the isoprene units have been summarized. The review also highlights the metabolic engineering efforts made for the biosynthesis of hemiterpenoids, monoterpenoids, sesquiterpenoids, diterpenoids, carotenoids, retinoids, and coenzyme Q10 in E. coli. Perspectives and future directions for the synthesis of novel isoprenoids, decoration of isoprenoids using cytochrome P450 enzymes, and secretion or storage of isoprenoids in E. coli have also been included.
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Affiliation(s)
- Chonglong Wang
- School of Biology and Basic Medical Sciences, Soochow University, Suzhou, People's Republic of China
| | - Bakht Zada
- Division of Applied Life Science (BK21 Plus), PMBBRC, Institute of Agriculture and Life Sciences, Gyeongsang National University, Jinju, Republic of Korea
| | - Gongyuan Wei
- School of Biology and Basic Medical Sciences, Soochow University, Suzhou, People's Republic of China
| | - Seon-Won Kim
- Division of Applied Life Science (BK21 Plus), PMBBRC, Institute of Agriculture and Life Sciences, Gyeongsang National University, Jinju, Republic of Korea.
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56
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Gong Z, Nielsen J, Zhou YJ. Engineering Robustness of Microbial Cell Factories. Biotechnol J 2017; 12. [DOI: 10.1002/biot.201700014] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2017] [Revised: 08/13/2017] [Indexed: 12/25/2022]
Affiliation(s)
- Zhiwei Gong
- Division of BiotechnologyDalian Institute of Chemical PhysicsCAS457 Zhongshan RoadDalian 116023P.R. China
- College of Chemistry and Chemical EngineeringWuhan University of Science and Technology947 Heping RoadWuhan 430081P.R. China
| | - Jens Nielsen
- Department of Biology and Biological EngineeringChalmers University of TechnologyKemivägen 10 Gothenburg SE‐41296Sweden
| | - Yongjin J. Zhou
- Division of BiotechnologyDalian Institute of Chemical PhysicsCAS457 Zhongshan RoadDalian 116023P.R. China
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57
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Hess SK, Lepetit B, Kroth PG, Mecking S. Production of chemicals from microalgae lipids - status and perspectives. EUR J LIPID SCI TECH 2017. [DOI: 10.1002/ejlt.201700152] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Sandra K. Hess
- Department of Chemistry; Chair of Chemical Materials Science; University of Konstanz; Konstanz Germany
| | - Bernard Lepetit
- Department of Biology; Plant Ecology; University of Konstanz; Konstanz Germany
| | - Peter G. Kroth
- Department of Biology; Plant Ecology; University of Konstanz; Konstanz Germany
| | - Stefan Mecking
- Department of Chemistry; Chair of Chemical Materials Science; University of Konstanz; Konstanz Germany
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58
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Joshi C, Singhal RS. Modelling and optimization of zeaxanthin production by Paracoccus zeaxanthinifaciens ATCC 21588 using hybrid genetic algorithm techniques. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2016. [DOI: 10.1016/j.bcab.2016.10.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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59
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Gustavsson M, Lee SY. Prospects of microbial cell factories developed through systems metabolic engineering. Microb Biotechnol 2016; 9:610-7. [PMID: 27435545 PMCID: PMC4993179 DOI: 10.1111/1751-7915.12385] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2016] [Accepted: 06/21/2016] [Indexed: 11/27/2022] Open
Abstract
While academic‐level studies on metabolic engineering of microorganisms for production of chemicals and fuels are ever growing, a significantly lower number of such production processes have reached commercial‐scale. In this work, we review the challenges associated with moving from laboratory‐scale demonstration of microbial chemical or fuel production to actual commercialization, focusing on key requirements on the production organism that need to be considered during the metabolic engineering process. Metabolic engineering strategies should take into account techno‐economic factors such as the choice of feedstock, the product yield, productivity and titre, and the cost effectiveness of midstream and downstream processes. Also, it is important to develop an industrial strain through metabolic engineering for pathway construction and flux optimization together with increasing tolerance to products and inhibitors present in the feedstock, and ensuring genetic stability and strain robustness under actual fermentation conditions.
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Affiliation(s)
- Martin Gustavsson
- Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering (BK21 Plus Program), BioProcess Engineering Research Center, Center for Systems and Synthetic Biotechnology, Institute for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Korea.,KTH Royal Institute of Technology, School of Biotechnology, Division of Industrial Biotechnology, AlbaNova University Center, 106 91, Stockholm, Sweden
| | - Sang Yup Lee
- Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering (BK21 Plus Program), BioProcess Engineering Research Center, Center for Systems and Synthetic Biotechnology, Institute for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Korea
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60
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Lyu Z, Jain R, Smith P, Fetchko T, Yan Y, Whitman WB. Engineering the Autotroph Methanococcus maripaludis for Geraniol Production. ACS Synth Biol 2016; 5:577-81. [PMID: 26886063 DOI: 10.1021/acssynbio.5b00267] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The rapid autotrophic growth of the methanogenic archaeon Methanococcus maripaludis on H2 and CO2 makes it an attractive microbial chassis to inexpensively produce biochemicals. To explore this potential, a synthetic gene encoding geraniol synthase (GES) derived from Ocimum basilicum was cloned into a M. maripaludis expression vector under selection for puromycin resistance. Recombinant expression of GES in M. maripaludis during autotrophic growth on H2/CO2 or formate yielded geraniol at 2.8 and 4.0 mg g(-1) of dry weight, respectively. The yield of geraniol decreased 2-3-fold when organic carbon sources were added to stimulate heterotrophic growth. In the absence of puromycin, geraniol production during autotrophic growth on formate increased to 4.6 mg g(-1) of dry weight. A conceptual model centered on the autotrophic acetyl coenzyme A biosynthetic pathway identified strategies to divert more autotrophic carbon flux to geraniol production.
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Affiliation(s)
- Zhe Lyu
- Department of Microbiology, ‡College of Engineering, and §Department of Biochemistry and Molecular
Biology, University of Georgia, Athens, Georgia 30602, United States
| | - Rachit Jain
- Department of Microbiology, ‡College of Engineering, and §Department of Biochemistry and Molecular
Biology, University of Georgia, Athens, Georgia 30602, United States
| | - Peyton Smith
- Department of Microbiology, ‡College of Engineering, and §Department of Biochemistry and Molecular
Biology, University of Georgia, Athens, Georgia 30602, United States
| | - Travis Fetchko
- Department of Microbiology, ‡College of Engineering, and §Department of Biochemistry and Molecular
Biology, University of Georgia, Athens, Georgia 30602, United States
| | - Yajun Yan
- Department of Microbiology, ‡College of Engineering, and §Department of Biochemistry and Molecular
Biology, University of Georgia, Athens, Georgia 30602, United States
| | - William B. Whitman
- Department of Microbiology, ‡College of Engineering, and §Department of Biochemistry and Molecular
Biology, University of Georgia, Athens, Georgia 30602, United States
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61
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Lv H, Li J, Wu Y, Garyali S, Wang Y. Transporter and its engineering for secondary metabolites. Appl Microbiol Biotechnol 2016; 100:6119-6130. [PMID: 27209041 DOI: 10.1007/s00253-016-7605-6] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Revised: 04/28/2016] [Accepted: 05/02/2016] [Indexed: 01/26/2023]
Abstract
Secondary metabolites possess a lot of biological activities, and to achieve their functions, transmembrane transportation is crucial. Elucidation of their transport mechanisms in the cell is critical for discovering ways to improve the production. Here, we have summarized the recent progresses for representative secondary metabolite transporters and also the strategies for uncovering the transporter systems in plants and microbes. We have also discussed the transporter engineering strategies being utilized for improving the heterologous natural product production, which exhibits promising future under the guide of synthetic biology.
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Affiliation(s)
- Huajun Lv
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Jianhua Li
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Yingying Wu
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Sanjog Garyali
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Yong Wang
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China.
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62
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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] [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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63
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Zhang C, Chen X, Stephanopoulos G, Too HP. Efflux transporter engineering markedly improves amorphadiene production inEscherichia coli. Biotechnol Bioeng 2016; 113:1755-63. [DOI: 10.1002/bit.25943] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Revised: 12/21/2015] [Accepted: 01/18/2016] [Indexed: 11/09/2022]
Affiliation(s)
- Congqiang Zhang
- Chemical and Pharmaceutical Engineering; Singapore-MIT Alliance; 4 Engineering Drive 3 Singapore Singapore
- Biotransformation Innovation Platform (BioTrans); Agency for Science, Technology and Research (A*STAR); Singapore Singapore
| | - Xixian Chen
- Chemical and Pharmaceutical Engineering; Singapore-MIT Alliance; 4 Engineering Drive 3 Singapore Singapore
- Biotransformation Innovation Platform (BioTrans); Agency for Science, Technology and Research (A*STAR); Singapore Singapore
| | - Gregory Stephanopoulos
- Chemical and Pharmaceutical Engineering; Singapore-MIT Alliance; 4 Engineering Drive 3 Singapore Singapore
- Department of Chemical Engineering; Massachusetts Institute of Technology; Cambridge Massachusetts
| | - Heng-Phon Too
- Chemical and Pharmaceutical Engineering; Singapore-MIT Alliance; 4 Engineering Drive 3 Singapore Singapore
- Biotransformation Innovation Platform (BioTrans); Agency for Science, Technology and Research (A*STAR); Singapore Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine; National University of Singapore, 8 Medical Drive; Blk MD7, Level 4 Singapore 117597 Singapore
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64
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Exporters for Production of Amino Acids and Other Small Molecules. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2016; 159:199-225. [PMID: 27832297 DOI: 10.1007/10_2016_32] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Microbes are talented catalysts to synthesize valuable small molecules in their cytosol. However, to make full use of their skills - and that of metabolic engineers - the export of intracellularly synthesized molecules to the culture medium has to be considered. This step is as essential as is each step for the synthesis of the favorite molecule of the metabolic engineer, but is frequently not taken into account. To export small molecules via the microbial cell envelope, a range of different types of carrier proteins is recognized to be involved, which are primary active carriers, secondary active carriers, or proteins increasing diffusion. Relevant export may require just one carrier as is the case with L-lysine export by Corynebacterium glutamicum or involve up to four carriers as known for L-cysteine excretion by Escherichia coli. Meanwhile carriers for a number of small molecules of biotechnological interest are recognized, like for production of peptides, nucleosides, diamines, organic acids, or biofuels. In addition to carriers involved in amino acid excretion, such carriers and their impact on product formation are described, as well as the relatedness of export carriers which may serve as a hint to identify further carriers required to improve product formation by engineering export.
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65
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Boyarskiy S, Davis López S, Kong N, Tullman-Ercek D. Transcriptional feedback regulation of efflux protein expression for increased tolerance to and production of n-butanol. Metab Eng 2015; 33:130-137. [PMID: 26656942 DOI: 10.1016/j.ymben.2015.11.005] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Revised: 10/28/2015] [Accepted: 11/23/2015] [Indexed: 01/11/2023]
Abstract
Microorganisms can be engineered to produce a variety of biofuels and commodity chemicals. The accumulation of these products, however, is often toxic to the cells and subsequently lowers production yields. Efflux pumps are a natural mechanism for alleviating toxicity through secretion of the product; unfortunately, pump overexpression also often inhibits growth. Tuning expression levels with inducible promoters is time-consuming and the reliance on small-molecule inducers is cost-prohibitive in industry. We design an expression regulation system utilizing a native Escherichia coli stress promoter, PgntK, to provide negative feedback to regulate transporter expression levels. We test the promoter in the context of the efflux pump AcrB and its butanol-secreting variant, AcrBv2. PgntK-driven AcrBv2 confers increased tolerance to n-butanol and increased titers of n-butanol in production. Furthermore, the system is responsive to stress from toxic overexpression of other membrane-associated proteins. Our results suggest a use for feedback regulation networks in membrane protein expression.
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Affiliation(s)
- Sergey Boyarskiy
- Joint Graduate Group in Bioengineering at UC Berkeley and UCSF, 306 Stanley Hall, Berkeley, CA 94720, United States
| | - Stephanie Davis López
- Department of Chemistry, University of California Berkeley, 201 Gilman Hall, Berkeley, CA 94720, United States
| | - Niwen Kong
- Department of Molecular and Cell Biology, University of California Berkeley, 142 LSA #3200, Berkeley, CA 94720, United States
| | - Danielle Tullman-Ercek
- Joint Graduate Group in Bioengineering at UC Berkeley and UCSF, 306 Stanley Hall, Berkeley, CA 94720, United States; Department of Chemistry, University of California Berkeley, 201 Gilman Hall, Berkeley, CA 94720, United States; Department of Chemical and Biomolecular Engineering, University of California Berkeley, 201 Gilman Hall, Berkeley, CA 94720, United States.
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66
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Ichikawa S, Karita S. Bacterial production and secretion of water-insoluble fuel compounds from cellulose without the supplementation of cellulases. FEMS Microbiol Lett 2015; 362:fnv202. [DOI: 10.1093/femsle/fnv202] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/18/2015] [Indexed: 01/15/2023] Open
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67
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Tomko TA, Dunlop MJ. Engineering improved bio-jet fuel tolerance in Escherichia coli using a transgenic library from the hydrocarbon-degrader Marinobacter aquaeolei. BIOTECHNOLOGY FOR BIOFUELS 2015; 8:165. [PMID: 26448785 PMCID: PMC4596283 DOI: 10.1186/s13068-015-0347-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Accepted: 09/22/2015] [Indexed: 06/05/2023]
Abstract
BACKGROUND Recent metabolic engineering efforts have generated microorganisms that can produce biofuels, including bio-jet fuels, however these fuels are often toxic to cells, limiting production yields. There are natural examples of microorganisms that have evolved mechanisms for tolerating hydrocarbon-rich environments, such as those that thrive near natural oil seeps and in oil-polluted waters. RESULTS Using genomic DNA from the hydrocarbon-degrading microbe Marinobacter aquaeolei, we constructed a transgenic library that we expressed in Escherichia coli. We exposed cells to inhibitory levels of pinene, a monoterpene that can serve as a jet fuel precursor with chemical properties similar to existing tactical fuels. Using a sequential strategy with a fosmid library followed by a plasmid library, we were able to isolate a region of DNA from the M. aquaeolei genome that conferred pinene tolerance when expressed in E. coli. We determined that a single gene, yceI, was responsible for the tolerance improvements. Overexpression of this gene placed no additional burden on the host. We also tested tolerance to other monoterpenes and showed that yceI selectively improves tolerance. CONCLUSIONS The genomes of hydrocarbon-tolerant microbes represent a rich resource for tolerance engineering. Using a transgenic library, we were able to identify a single gene that improves E. coli's tolerance to the bio-jet fuel precursor pinene.
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Affiliation(s)
- Timothy A. Tomko
- School of Engineering, University of Vermont, 33 Colchester Ave, Burlington, VT 05405 USA
| | - Mary J. Dunlop
- School of Engineering, University of Vermont, 33 Colchester Ave, Burlington, VT 05405 USA
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68
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Efflux systems in bacteria and their metabolic engineering applications. Appl Microbiol Biotechnol 2015; 99:9381-93. [PMID: 26363557 DOI: 10.1007/s00253-015-6963-9] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Revised: 08/20/2015] [Accepted: 08/22/2015] [Indexed: 10/23/2022]
Abstract
The production of valuable chemicals from metabolically engineered microbes can be limited by excretion from the cell. Efflux is often overlooked as a bottleneck in metabolic pathways, despite its impact on alleviating feedback inhibition and product toxicity. In the past, it has been assumed that endogenous efflux pumps and membrane porins can accommodate product efflux rates; however, there are an increasing number of examples wherein overexpressing efflux systems is required to improve metabolite production. In this review, we highlight specific examples from the literature where metabolite export has been studied to identify unknown transporters, increase tolerance to metabolites, and improve the production capabilities of engineered bacteria. The review focuses on the export of a broad spectrum of valuable chemicals including amino acids, sugars, flavins, biofuels, and solvents. The combined set of examples supports the hypothesis that efflux systems can be identified and engineered to confer export capabilities on industrially relevant microbes.
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69
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Mukhopadhyay A. Tolerance engineering in bacteria for the production of advanced biofuels and chemicals. Trends Microbiol 2015; 23:498-508. [DOI: 10.1016/j.tim.2015.04.008] [Citation(s) in RCA: 163] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Revised: 04/17/2015] [Accepted: 04/23/2015] [Indexed: 02/06/2023]
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70
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Yang J, Xiong ZQ, Song SJ, Wang JF, Lv HJ, Wang Y. Improving heterologous polyketide production in Escherichia coli by transporter engineering. Appl Microbiol Biotechnol 2015; 99:8691-700. [DOI: 10.1007/s00253-015-6718-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2015] [Revised: 04/27/2015] [Accepted: 05/21/2015] [Indexed: 10/23/2022]
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71
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Volmer J, Schmid A, Bühler B. Guiding bioprocess design by microbial ecology. Curr Opin Microbiol 2015; 25:25-32. [DOI: 10.1016/j.mib.2015.02.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2014] [Revised: 02/26/2015] [Accepted: 02/26/2015] [Indexed: 12/20/2022]
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72
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Vinayak V, Manoylov KM, Gateau H, Blanckaert V, Hérault J, Pencréac'h G, Marchand J, Gordon R, Schoefs B. Diatom milking: a review and new approaches. Mar Drugs 2015; 13:2629-65. [PMID: 25939034 PMCID: PMC4446598 DOI: 10.3390/md13052629] [Citation(s) in RCA: 75] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2014] [Revised: 04/15/2015] [Accepted: 04/17/2015] [Indexed: 11/16/2022] Open
Abstract
The rise of human populations and the growth of cities contribute to the depletion of natural resources, increase their cost, and create potential climatic changes. To overcome difficulties in supplying populations and reducing the resource cost, a search for alternative pharmaceutical, nanotechnology, and energy sources has begun. Among the alternative sources, microalgae are the most promising because they use carbon dioxide (CO2) to produce biomass and/or valuable compounds. Once produced, the biomass is ordinarily harvested and processed (downstream program). Drying, grinding, and extraction steps are destructive to the microalgal biomass that then needs to be renewed. The extraction and purification processes generate organic wastes and require substantial energy inputs. Altogether, it is urgent to develop alternative downstream processes. Among the possibilities, milking invokes the concept that the extraction should not kill the algal cells. Therefore, it does not require growing the algae anew. In this review, we discuss research on milking of diatoms. The main themes are (a) development of alternative methods to extract and harvest high added value compounds; (b) design of photobioreactors;
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Affiliation(s)
- Vandana Vinayak
- Department of Criminology & Forensic Science, School of Applied Sciences, Dr. H.S. Gour University (Central University), Sagar Madhya Pradesh, India.
| | - Kalina M Manoylov
- Department of Biological & Environmental Sciences, Georgia College and State University, Milledgeville, GA 31061, USA.
| | - Hélène Gateau
- MicroMar, Mer Molécules Santé, IUML-FR 3473 CNRS, University of Le Mans, Faculté des Sciences et Techniques, Avenue Olivier Messiaen, 72085 Le Mans cedex 9, France.
| | - Vincent Blanckaert
- MicroMar, Mer Molécules Santé, IUML-FR 3473 CNRS, University of Le Mans, IUT de Laval, Rue des Drs Calmette et Guerin, 53020 Laval Cedex 9, France.
| | - Josiane Hérault
- ChimiMar, Mer Molécules Santé, IUML-FR 3473 CNRS, University of Le Mans, IUT de Laval, Rue des Drs Calmette et Guerin, 53020 Laval Cedex 9, France.
| | - Gaëlle Pencréac'h
- ChimiMar, Mer Molécules Santé, IUML-FR 3473 CNRS, University of Le Mans, IUT de Laval, Rue des Drs Calmette et Guerin, 53020 Laval Cedex 9, France.
| | - Justine Marchand
- MicroMar, Mer Molécules Santé, IUML-FR 3473 CNRS, University of Le Mans, Faculté des Sciences et Techniques, Avenue Olivier Messiaen, 72085 Le Mans cedex 9, France.
| | - Richard Gordon
- Gulf Specimen Aquarium & Marine Laboratory, Panacea, FL 32346, USA.
- Mott Center for Human Growth and Development, Department of Obstetrics & Gynecology, Wayne State University, 275 E. Hancock, Detroit, MI 48201, USA.
| | - Benoît Schoefs
- MicroMar, Mer Molécules Santé, IUML-FR 3473 CNRS, University of Le Mans, Faculté des Sciences et Techniques, Avenue Olivier Messiaen, 72085 Le Mans cedex 9, France.
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Membrane transporter engineering in industrial biotechnology and whole cell biocatalysis. Trends Biotechnol 2015; 33:237-46. [DOI: 10.1016/j.tibtech.2015.02.001] [Citation(s) in RCA: 145] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2014] [Revised: 01/15/2015] [Accepted: 02/02/2015] [Indexed: 02/06/2023]
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Currin A, Swainston N, Day PJ, Kell DB. Synthetic biology for the directed evolution of protein biocatalysts: navigating sequence space intelligently. Chem Soc Rev 2015; 44:1172-239. [PMID: 25503938 PMCID: PMC4349129 DOI: 10.1039/c4cs00351a] [Citation(s) in RCA: 251] [Impact Index Per Article: 27.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Indexed: 12/21/2022]
Abstract
The amino acid sequence of a protein affects both its structure and its function. Thus, the ability to modify the sequence, and hence the structure and activity, of individual proteins in a systematic way, opens up many opportunities, both scientifically and (as we focus on here) for exploitation in biocatalysis. Modern methods of synthetic biology, whereby increasingly large sequences of DNA can be synthesised de novo, allow an unprecedented ability to engineer proteins with novel functions. However, the number of possible proteins is far too large to test individually, so we need means for navigating the 'search space' of possible protein sequences efficiently and reliably in order to find desirable activities and other properties. Enzymologists distinguish binding (Kd) and catalytic (kcat) steps. In a similar way, judicious strategies have blended design (for binding, specificity and active site modelling) with the more empirical methods of classical directed evolution (DE) for improving kcat (where natural evolution rarely seeks the highest values), especially with regard to residues distant from the active site and where the functional linkages underpinning enzyme dynamics are both unknown and hard to predict. Epistasis (where the 'best' amino acid at one site depends on that or those at others) is a notable feature of directed evolution. The aim of this review is to highlight some of the approaches that are being developed to allow us to use directed evolution to improve enzyme properties, often dramatically. We note that directed evolution differs in a number of ways from natural evolution, including in particular the available mechanisms and the likely selection pressures. Thus, we stress the opportunities afforded by techniques that enable one to map sequence to (structure and) activity in silico, as an effective means of modelling and exploring protein landscapes. Because known landscapes may be assessed and reasoned about as a whole, simultaneously, this offers opportunities for protein improvement not readily available to natural evolution on rapid timescales. Intelligent landscape navigation, informed by sequence-activity relationships and coupled to the emerging methods of synthetic biology, offers scope for the development of novel biocatalysts that are both highly active and robust.
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Affiliation(s)
- Andrew Currin
- Manchester Institute of Biotechnology , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK . ; http://dbkgroup.org/; @dbkell ; Tel: +44 (0)161 306 4492
- School of Chemistry , The University of Manchester , Manchester M13 9PL , UK
- Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM) , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK
| | - Neil Swainston
- Manchester Institute of Biotechnology , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK . ; http://dbkgroup.org/; @dbkell ; Tel: +44 (0)161 306 4492
- Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM) , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK
- School of Computer Science , The University of Manchester , Manchester M13 9PL , UK
| | - Philip J. Day
- Manchester Institute of Biotechnology , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK . ; http://dbkgroup.org/; @dbkell ; Tel: +44 (0)161 306 4492
- Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM) , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK
- Faculty of Medical and Human Sciences , The University of Manchester , Manchester M13 9PT , UK
| | - Douglas B. Kell
- Manchester Institute of Biotechnology , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK . ; http://dbkgroup.org/; @dbkell ; Tel: +44 (0)161 306 4492
- School of Chemistry , The University of Manchester , Manchester M13 9PL , UK
- Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM) , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK
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75
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Davies FK, Jinkerson RE, Posewitz MC. Toward a photosynthetic microbial platform for terpenoid engineering. PHOTOSYNTHESIS RESEARCH 2015; 123:265-84. [PMID: 24510550 DOI: 10.1007/s11120-014-9979-6] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2013] [Accepted: 01/23/2014] [Indexed: 05/20/2023]
Abstract
Plant terpenoids are among the most diverse group of naturally-occurring organic compounds known, and several are used in contemporary consumer products. Terpene synthase enzymes catalyze complex rearrangements of carbon skeleton precursors to yield thousands of unique chemical structures that range in size from the simplest five carbon isoprene unit to the long polymers of rubber. Such chemical diversity has established plant terpenoids as valuable commodity chemicals with applications in the pharmaceutical, neutraceutical, cosmetic, and food industries. More recently, terpenoids have received attention as a renewable alternative to petroleum-derived fuels and as the building blocks of synthetic biopolymers. However, the current plant- and petrochemical-based supplies of commodity terpenoids have major limitations. Photosynthetic microorganisms provide an opportunity to generate terpenoids in a renewable manner, employing a single consolidated host organism that is able to use solar energy, H2O and CO2 as the primary inputs for terpenoid biosynthesis. Advances in synthetic biology have seen important breakthroughs in microbial terpenoid engineering, traditionally via fermentative pathways in yeast and Escherichia coli. This review draws on the knowledge obtained from heterotrophic microbial engineering to propose strategies for the development of microbial photosynthetic platforms for industrial terpenoid production. The importance of utilizing the wealth of genetic information provided by nature to unravel the regulatory mechanisms of terpenoid biosynthesis is highlighted.
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Affiliation(s)
- Fiona K Davies
- Department of Chemistry and Geochemistry, Colorado School of Mines, Golden, CO, 80401, USA,
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Wang X, Ort DR, Yuan JS. Photosynthetic terpene hydrocarbon production for fuels and chemicals. PLANT BIOTECHNOLOGY JOURNAL 2015; 13:137-46. [PMID: 25626473 DOI: 10.1111/pbi.12343] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2014] [Revised: 12/10/2014] [Accepted: 12/12/2014] [Indexed: 05/19/2023]
Abstract
Photosynthetic hydrocarbon production bypasses the traditional biomass hydrolysis process and represents the most direct conversion of sunlight energy into the next-generation biofuels. As a major class of biologically derived hydrocarbons with diverse structures, terpenes are also valuable in producing a variety of fungible bioproducts in addition to the advanced 'drop-in' biofuels. However, it is highly challenging to achieve the efficient redirection of photosynthetic carbon and reductant into terpene biosynthesis. In this review, we discuss four major scientific and technical barriers for photosynthetic terpene production and recent advances to address these constraints. Collectively, photosynthetic terpene production needs to be optimized in a systematic fashion, in which the photosynthesis improvement, the optimization of terpene biosynthesis pathway, the improvement of key enzymes and the enhancement of sink effect through terpene storage or secretion are all important. New advances in synthetic biology also offer a suite of potential tools to design and engineer photosynthetic terpene platforms. The systemic integration of these solutions may lead to 'disruptive' technologies to enable biofuels and bioproducts with high efficiency, yield and infrastructure compatibility.
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Affiliation(s)
- Xin Wang
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, TX, USA; Synthetic and Systems Biology Innovation Hub, Texas A&M University, College Station, TX, USA; Institute for Plant Genomics and Biotechnology, Texas A&M University, College Station, TX, USA
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77
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Mingardon F, Clement C, Hirano K, Nhan M, Luning EG, Chanal A, Mukhopadhyay A. Improving olefin tolerance and production in E. coli using native and evolved AcrB. Biotechnol Bioeng 2015; 112:879-88. [PMID: 25450012 PMCID: PMC4406151 DOI: 10.1002/bit.25511] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2014] [Revised: 11/16/2014] [Accepted: 11/25/2014] [Indexed: 01/10/2023]
Abstract
Microorganisms can be engineered for the production of chemicals utilized in the polymer industry. However many such target compounds inhibit microbial growth and might correspondingly limit production levels. Here, we focus on compounds that are precursors to bioplastics, specifically styrene and representative alpha-olefins; 1-hexene, 1-octene, and 1-nonene. We evaluated the role of the Escherichia coli efflux pump, AcrAB-TolC, in enhancing tolerance towards these olefin compounds. AcrAB-TolC is involved in the tolerance towards all four compounds in E. coli. Both styrene and 1-hexene are highly toxic to E. coli. Styrene is a model plastics precursor with an established route for production in E. coli (McKenna and Nielsen, 2011). Though our data indicates that AcrAB-TolC is important for its optimal production, we observed a strong negative selection against the production of styrene in E. coli. Thus we used 1-hexene as a model compound to implement a directed evolution strategy to further improve the tolerance phenotype towards this alpha-olefin. We focused on optimization of AcrB, the inner membrane domain known to be responsible for substrate binding, and found several mutations (A279T, Q584R, F617L, L822P, F927S, and F1033Y) that resulted in improved tolerance. Several of these mutations could also be combined in a synergistic manner. Our study shows efflux pumps to be an important mechanism in host engineering for olefins, and one that can be further improved using strategies such as directed evolution, to increase tolerance and potentially production. Biotechnol. Bioeng. 2015;112: 879–888. © 2015 The Authors. Biotechnology and Bioengineering Published by John Wiley & Periodicals, Inc.
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78
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Zhou K, Qiao K, Edgar S, Stephanopoulos G. Distributing a metabolic pathway among a microbial consortium enhances production of natural products. Nat Biotechnol 2015; 33:377-83. [PMID: 25558867 PMCID: PMC4867547 DOI: 10.1038/nbt.3095] [Citation(s) in RCA: 438] [Impact Index Per Article: 48.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2014] [Accepted: 11/10/2014] [Indexed: 02/05/2023]
Abstract
Metabolic engineering of microorganisms such as Escherichia coli and Saccharomyces cerevisiae to produce high-value natural metabolites is often done through functional reconstitution of long metabolic pathways. Problems arise when parts of pathways require specialized environments or compartments for optimal function. Here we solve this problem through co-culture of engineered organisms, each of which contains the part of the pathway that it is best suited to hosting. In one example, we divided the synthetic pathway for the acetylated diol paclitaxel precursor into two modules, expressed in either S. cerevisiae or E. coli, neither of which can produce the paclitaxel precursor on their own. Stable co-culture in the same bioreactor was achieved by designing a mutualistic relationship between the two species in which a metabolic intermediate produced by E. coli was used and functionalized by yeast. This synthetic consortium produced 33 mg/L oxygenated taxanes, including a monoacetylated dioxygenated taxane. The same method was also used to produce tanshinone precursors and functionalized sesquiterpenes.
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Affiliation(s)
- Kang Zhou
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Kangjian Qiao
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Steven Edgar
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Gregory Stephanopoulos
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
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79
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Metabolic engineering of higher plants and algae for isoprenoid production. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2015; 148:161-99. [PMID: 25636485 DOI: 10.1007/10_2014_290] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Isoprenoids are a class of compounds derived from the five carbon precursors, dimethylallyl diphosphate, and isopentenyl diphosphate. These molecules present incredible natural chemical diversity, which can be valuable for humans in many aspects such as cosmetics, agriculture, and medicine. However, many terpenoids are only produced in small quantities by their natural hosts and can be difficult to generate synthetically. Therefore, much interest and effort has been directed toward capturing the genetic blueprint for their biochemistry and engineering it into alternative hosts such as plants and algae. These autotrophic organisms are attractive when compared to traditional microbial platforms because of their ability to utilize atmospheric CO2 as a carbon substrate instead of supplied carbon sources like glucose. This chapter will summarize important techniques and strategies for engineering the accumulation of isoprenoid metabolites into higher plants and algae by choosing the correct host, avoiding endogenous regulatory mechanisms, and optimizing potential flux into the target compound. Future endeavors will build on these efforts by fine-tuning product accumulation levels via the vast amount of available "-omic" data and devising metabolic engineering schemes that integrate this into a whole-organism approach. With the development of high-throughput transformation protocols and synthetic biology molecular tools, we have only begun to harness the power and utility of plant and algae metabolic engineering.
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80
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Akhtar MK, Dandapani H, Thiel K, Jones PR. Microbial production of 1-octanol: A naturally excreted biofuel with diesel-like properties. Metab Eng Commun 2014; 2:1-5. [PMID: 27066394 PMCID: PMC4802428 DOI: 10.1016/j.meteno.2014.11.001] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2014] [Revised: 09/09/2014] [Accepted: 11/03/2014] [Indexed: 11/29/2022] Open
Abstract
The development of sustainable, bio-based technologies to convert solar energy and carbon dioxide into fuels is a grand challenge. A core part of this challenge is to produce a fuel that is compatible with the existing transportation infrastructure. This task is further compounded by the commercial desire to separate the fuel from the biotechnological host. Based on its fuel characteristics, 1-octanol was identified as an attractive metabolic target with diesel-like properties. We therefore engineered a synthetic pathway specifically for the biosynthesis of 1-octanol in Escherichia coli BL21(DE3) by over-expression of three enzymes (thioesterase, carboxylic acid reductase and aldehyde reductase) and one maturation factor (phosphopantetheinyl transferase). Induction of this pathway in a shake flask resulted in 4.4 mg 1-octanol L-1 h-1 which exceeded the productivity of previously engineered strains. Furthermore, the majority (73%) of the fatty alcohol was localised within the media without the addition of detergent or solvent overlay. The deletion of acrA reduced the production and excretion of 1-octanol by 3-fold relative to the wild-type, suggesting that the AcrAB-TolC complex may be responsible for the majority of product efflux. This study presents 1-octanol as a potential fuel target that can be synthesised and naturally accumulated within the media using engineered microbes.
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Affiliation(s)
- M Kalim Akhtar
- Department of Biochemistry, University of Turku, Tykistökatu 6B 4krs, 20520 Turku, Finland; Department of Biochemical Engineering, University College London, Torrington Place, London WC1E 7JE, UK
| | - Hariharan Dandapani
- Department of Biochemistry, University of Turku, Tykistökatu 6B 4krs, 20520 Turku, Finland
| | - Kati Thiel
- Department of Biochemistry, University of Turku, Tykistökatu 6B 4krs, 20520 Turku, Finland
| | - Patrik R Jones
- Department of Biochemistry, University of Turku, Tykistökatu 6B 4krs, 20520 Turku, Finland; Department of Life Sciences, Imperial College London, Sir Alexander Fleming Building, London SW7 2AZ, UK
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81
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Ledesma-Amaro R. Microbial oils: A customizable feedstock through metabolic engineering. EUR J LIPID SCI TECH 2014. [DOI: 10.1002/ejlt.201400181] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Rodrigo Ledesma-Amaro
- Departamento de Microbiología y Genética, Metabolic Engineering Group; Universidad de Salamanca; Salamanca Spain
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82
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Abstract
Engineering microbial hosts for the production of fungible fuels requires mitigation of limitations posed on the production capacity. One such limitation arises from the inherent toxicity of solvent-like biofuel compounds to production strains, such as Escherichia coli. Here we show the importance of host engineering for the production of short-chain alcohols by studying the overexpression of genes upregulated in response to exogenous isopentenol. Using systems biology data, we selected 40 genes that were upregulated following isopentenol exposure and subsequently overexpressed them in E. coli. Overexpression of several of these candidates improved tolerance to exogenously added isopentenol. Genes conferring isopentenol tolerance phenotypes belonged to diverse functional groups, such as oxidative stress response (soxS, fpr, and nrdH), general stress response (metR, yqhD, and gidB), heat shock-related response (ibpA), and transport (mdlB). To determine if these genes could also improve isopentenol production, we coexpressed the tolerance-enhancing genes individually with an isopentenol production pathway. Our data show that expression of 6 of the 8 candidates improved the production of isopentenol in E. coli, with the methionine biosynthesis regulator MetR improving the titer for isopentenol production by 55%. Additionally, expression of MdlB, an ABC transporter, facilitated a 12% improvement in isopentenol production. To our knowledge, MdlB is the first example of a transporter that can be used to improve production of a short-chain alcohol and provides a valuable new avenue for host engineering in biogasoline production. The use of microbial host platforms for the production of bulk commodities, such as chemicals and fuels, is now a focus of many biotechnology efforts. Many of these compounds are inherently toxic to the host microbe, which in turn places a limit on production despite efforts to optimize the bioconversion pathways. In order to achieve economically viable production levels, it is also necessary to engineer production strains with improved tolerance to these compounds. We demonstrate that microbial tolerance engineering using transcriptomics data can also identify targets that improve production. Our results include an exporter and a methionine biosynthesis regulator that improve isopentenol production, providing a starting point to further engineer the host for biogasoline production.
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83
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Kell DB, Oliver SG. How drugs get into cells: tested and testable predictions to help discriminate between transporter-mediated uptake and lipoidal bilayer diffusion. Front Pharmacol 2014; 5:231. [PMID: 25400580 PMCID: PMC4215795 DOI: 10.3389/fphar.2014.00231] [Citation(s) in RCA: 107] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2014] [Accepted: 09/29/2014] [Indexed: 12/12/2022] Open
Abstract
One approach to experimental science involves creating hypotheses, then testing them by varying one or more independent variables, and assessing the effects of this variation on the processes of interest. We use this strategy to compare the intellectual status and available evidence for two models or views of mechanisms of transmembrane drug transport into intact biological cells. One (BDII) asserts that lipoidal phospholipid Bilayer Diffusion Is Important, while a second (PBIN) proposes that in normal intact cells Phospholipid Bilayer diffusion Is Negligible (i.e., may be neglected quantitatively), because evolution selected against it, and with transmembrane drug transport being effected by genetically encoded proteinaceous carriers or pores, whose “natural” biological roles, and substrates are based in intermediary metabolism. Despite a recent review elsewhere, we can find no evidence able to support BDII as we can find no experiments in intact cells in which phospholipid bilayer diffusion was either varied independently or measured directly (although there are many papers where it was inferred by seeing a covariation of other dependent variables). By contrast, we find an abundance of evidence showing cases in which changes in the activities of named and genetically identified transporters led to measurable changes in the rate or extent of drug uptake. PBIN also has considerable predictive power, and accounts readily for the large differences in drug uptake between tissues, cells and species, in accounting for the metabolite-likeness of marketed drugs, in pharmacogenomics, and in providing a straightforward explanation for the late-stage appearance of toxicity and of lack of efficacy during drug discovery programmes despite macroscopically adequate pharmacokinetics. Consequently, the view that Phospholipid Bilayer diffusion Is Negligible (PBIN) provides a starting hypothesis for assessing cellular drug uptake that is much better supported by the available evidence, and is both more productive and more predictive.
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Affiliation(s)
- Douglas B Kell
- School of Chemistry, The University of Manchester Manchester, UK ; Manchester Institute of Biotechnology, The University of Manchester Manchester, UK
| | - Stephen G Oliver
- Department of Biochemistry, University of Cambridge Cambridge, UK ; Cambridge Systems Biology Centre, University of Cambridge Cambridge, UK
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84
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Identification of a novel ATP-binding cassette transporter involved in long-chain fatty acid import and its role in triacylglycerol accumulation in Rhodococcus jostii RHA1. Microbiology (Reading) 2014; 160:1523-1532. [DOI: 10.1099/mic.0.078477-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Members of the genus Rhodococcus are specialists in the biosynthesis and accumulation of triacylglycerols (TAGs). As no transport protein related to TAG metabolism has yet been characterized in these bacteria, we used the available genomic information of Rhodococcus jostii RHA1 to perform a broad survey of genes coding for putative lipid transporter proteins in this oleaginous micro-organism. Among the seven genes encoding putative lipid transporters, ro05645 (now called ltp1: lipid transporter protein) coding for an ATP-binding cassette protein was found clustered with others genes encoding enzymes catalysing the three putative acylation reactions of the Kennedy pathway for TAG synthesis. Overexpression of ltp1 in the RHA1 strain led to an increase of approximately sixfold and threefold in biomass and TAG production, respectively, when cells were cultivated on palmitic acid and oleic acid. Moreover, overexpression of ltp1 also promoted a significant increase in the uptake of a fluorescently labelled long-chain fatty acid (LCFA), as compared with the WT strain RHA1, and its further incorporation into the TAG fraction. Gluconate-grown cells showed increasing amounts of intracellular free fatty acids, but not of TAG, after overexpressing ltp1. Thus, for the first time to our knowledge, a transporter functionally related to TAG metabolism was identified in oleaginous rhodococci. Our results suggested that Ltp1 is an importer of LCFAs that plays a functional role in lipid homeostasis of R. jostii RHA1.
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85
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Wang BL, Ghaderi A, Zhou H, Agresti J, Weitz DA, Fink GR, Stephanopoulos G. Microfluidic high-throughput culturing of single cells for selection based on extracellular metabolite production or consumption. Nat Biotechnol 2014; 32:473-8. [PMID: 24705516 PMCID: PMC4412259 DOI: 10.1038/nbt.2857] [Citation(s) in RCA: 234] [Impact Index Per Article: 23.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2013] [Accepted: 02/21/2014] [Indexed: 11/09/2022]
Abstract
Phenotyping single cells based on the products they secrete or consume is a key bottleneck in many biotechnology applications, such as combinatorial metabolic engineering for the overproduction of secreted metabolites. Here we present a flexible high-throughput approach that uses microfluidics to compartmentalize individual cells for growth and analysis in monodisperse nanoliter aqueous droplets surrounded by an immiscible fluorinated oil phase. We use this system to identify xylose-overconsuming Saccharomyces cerevisiae cells from a population containing one such cell per 10(4) cells and to screen a genomic library to identify multiple copies of the xylose isomerase gene as a genomic change contributing to high xylose consumption, a trait important for lignocellulosic feedstock utilization. We also enriched L-lactate-producing Escherichia coli clones 5,800× from a population containing one L-lactate producer per 10(4) D-lactate producers. Our approach has broad applications for single-cell analyses, such as in strain selection for the overproduction of fuels, chemicals and pharmaceuticals.
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Affiliation(s)
- Benjamin L Wang
- 1] Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA. [2]
| | - Adel Ghaderi
- 1] Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA. [2]
| | - Hang Zhou
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Jeremy Agresti
- Department of Physics and School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts, USA
| | - David A Weitz
- Department of Physics and School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts, USA
| | - Gerald R Fink
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts, USA
| | - Gregory Stephanopoulos
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
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86
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Gillet JN. Ultrafast molecular dynamics of biofuel extraction for microalgae and bacteria milking: blocking membrane folding pathways to damaged lipid-bilayer conformations with nanomicelles. J Biomol Struct Dyn 2014; 33:690-705. [DOI: 10.1080/07391102.2014.907544] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Jean-Numa Gillet
- Jawaharlal Nehru University (JNU), School of Computational and Integrative Sciences, Centre for Computational Biology and Bioinformatics, New Delhi 110067, India
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87
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Engineering biofuel tolerance in non-native producing microorganisms. Biotechnol Adv 2014; 32:541-8. [PMID: 24530635 DOI: 10.1016/j.biotechadv.2014.02.001] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2013] [Revised: 01/19/2014] [Accepted: 02/08/2014] [Indexed: 01/17/2023]
Abstract
Large-scale production of renewable biofuels through microbiological processes has drawn significant attention in recent years, mostly due to the increasing concerns on the petroleum fuel shortages and the environmental consequences of the over-utilization of petroleum-based fuels. In addition to native biofuel-producing microbes that have been employed for biofuel production for decades, recent advances in metabolic engineering and synthetic biology have made it possible to produce biofuels in several non-native biofuel-producing microorganisms. Compared to native producers, these non-native systems carry the advantages of fast growth, simple nutrient requirements, readiness for genetic modifications, and even the capability to assimilate CO2 and solar energy, making them competitive alternative systems to further decrease the biofuel production cost. However, the tolerance of these non-native microorganisms to toxic biofuels is naturally low, which has restricted the potentials of their application for high-efficiency biofuel production. To address the issues, researches have been recently conducted to explore the biofuel tolerance mechanisms and to construct robust high-tolerance strains for non-native biofuel-producing microorganisms. In this review, we critically summarize the recent progress in this area, focusing on three popular non-native biofuel-producing systems, i.e. Escherichia coli, Lactobacillus and photosynthetic cyanobacteria.
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88
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Fisher MA, Boyarskiy S, Yamada MR, Kong N, Bauer S, Tullman-Ercek D. Enhancing tolerance to short-chain alcohols by engineering the Escherichia coli AcrB efflux pump to secrete the non-native substrate n-butanol. ACS Synth Biol 2014; 3:30-40. [PMID: 23991711 DOI: 10.1021/sb400065q] [Citation(s) in RCA: 82] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The microbial conversion of sugars to fuels is a promising technology, but the byproducts of biomass pretreatment processes and the fuels themselves are often toxic at industrially relevant levels. One promising solution to these problems is to engineer efflux pumps to secrete fuels and inhibitory chemicals from the cell, increasing microbial tolerance and enabling higher fuel titer. Toward that end, we used a directed evolution strategy to generate variants of the Escherichia coli AcrB efflux pump that act on the non-native substrate n-butanol, enhancing growth rates of E. coli in the presence of this biofuel by up to 25%. Furthermore, these variants confer improved tolerance to isobutanol and straight-chain alcohols up to n-heptanol. Single amino acid changes in AcrB responsible for this phenotype were identified. We have also shown that both the chemical and genetic inactivation of pump activity eliminate the tolerance conferred by AcrB pump variants, supporting our assertion that the variants secrete the non-native substrates. This strategy can be applied to create an array of efflux pumps that modulate the intracellular concentrations of small molecules of interest to microbial fuel and chemical production.
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Affiliation(s)
- Michael A. Fisher
- Energy Biosciences
Institute, University of California Berkeley, 2151 Berkeley Way, Berkeley, California 94704, United States
| | - Sergey Boyarskiy
- Energy Biosciences
Institute, University of California Berkeley, 2151 Berkeley Way, Berkeley, California 94704, United States
- Department
of Bioengineering, University of California Berkeley, 306 Stanley
Hall MC #1762, Berkeley, California 94720, United States
| | - Masaki R. Yamada
- Department
of Chemical and Biomolecular Engineering, University of California Berkeley, 201 Gilman Hall, Berkeley, California 94720, United States
| | - Niwen Kong
- Department
of Molecular and Cell Biology, University of California Berkeley, 142 LSA #3200, Berkeley, California 94720, United States
| | - Stefan Bauer
- Energy Biosciences
Institute, University of California Berkeley, 2151 Berkeley Way, Berkeley, California 94704, United States
| | - Danielle Tullman-Ercek
- Energy Biosciences
Institute, University of California Berkeley, 2151 Berkeley Way, Berkeley, California 94704, United States
- Department
of Chemical and Biomolecular Engineering, University of California Berkeley, 201 Gilman Hall, Berkeley, California 94720, United States
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