101
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Affiliation(s)
- Shuke Wu
- Department of Chemical and Biomolecular Engineering; National University of Singapore; 4 Engineering Drive 4 Singapore 117585 Singapore
| | - Zhi Li
- Department of Chemical and Biomolecular Engineering; National University of Singapore; 4 Engineering Drive 4 Singapore 117585 Singapore
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102
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Li S, Wang J, Xiang W, Yang K, Li Z, Wang W. An Autoregulated Fine-Tuning Strategy for Titer Improvement of Secondary Metabolites Using Native Promoters in Streptomyces. ACS Synth Biol 2018; 7:522-530. [PMID: 29087698 DOI: 10.1021/acssynbio.7b00318] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Streptomycetes are well-known producers of biologically active secondary metabolites. Various efforts have been made to increase productions of these metabolites, while few approaches could well coordinate the biosynthesis of secondary metabolites and other physiological events of their hosts. Here we develop a universal autoregulated strategy for fine-tuning the expression of secondary metabolites biosynthetic gene clusters (BGCs) in Streptomyces species. First, inducible promoters were used to control the expression of secondary metabolites BGCs. Then, the optimal induction condition was determined by response surface model in both dimensions of time and strength. Finally, native promoters with similar transcription profile to the inducible promoter under the optimal condition were identified based on time-course transcriptome analyses, and used to replace the inducible promoter following an elaborate replacement approach. The expression of actinorhodin (Act) and heterogeneous oxytetracycline (OTC) BGCs were optimized in Streptomyces coelicolor using this strategy. Compared to modulating the expression via constitutive promoters, our strategy could dramatically improve the titers of Act and OTC by 1.3- and 9.1-fold, respectively. The autoregulated fine-tuning strategy developed here opens a novel route for titer improvement of desired secondary metabolites in Streptomyces.
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Affiliation(s)
- Shanshan Li
- State
Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No.1 West Beichen Road, Chaoyang District, Beijing 100101, China
- State
Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute
of Plant Protection, Chinese Academy of Agricultural Sciences, No. 2 Yuanmingyuan West Road, Haidian District,
Beijing 100193, China
| | - Junyang Wang
- State
Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No.1 West Beichen Road, Chaoyang District, Beijing 100101, China
- University of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing 100049, China
| | - Wensheng Xiang
- State
Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute
of Plant Protection, Chinese Academy of Agricultural Sciences, No. 2 Yuanmingyuan West Road, Haidian District,
Beijing 100193, China
| | - Keqian Yang
- State
Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No.1 West Beichen Road, Chaoyang District, Beijing 100101, China
| | - Zilong Li
- State
Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No.1 West Beichen Road, Chaoyang District, Beijing 100101, China
| | - Weishan Wang
- State
Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No.1 West Beichen Road, Chaoyang District, Beijing 100101, China
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103
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Wu W, Maravelias CT. Synthesis and techno-economic assessment of microbial-based processes for terpenes production. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:294. [PMID: 30386431 PMCID: PMC6203976 DOI: 10.1186/s13068-018-1285-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Accepted: 10/09/2018] [Indexed: 05/03/2023]
Abstract
BACKGROUND Recent advances in metabolic engineering enable the production of chemicals from sugars through microbial bio-conversion. Terpenes have attracted substantial attention due to their relatively high prices and wide applications in different industries. To this end, we synthesize and assess processes for microbial production of terpenes. RESULTS To explain a counterintuitive experimental phenomenon where terpenes such as limonene (normal boiling point 176 °C) are often found to be 100% present in the vapor phase after bio-conversion (operating at only ~ 30 °C), we first analyze the vapor-liquid equilibrium for systems containing terpenes. Then, we propose alternative production configurations, which are further studied, using limonene as an example, in several case studies. Next, we perform economic assessment of the alternative processes and identify the major cost components. Finally, we extend the assessment to account for different process parameters, terpene products, ways to address terpene toxicity (microbial engineering vs. solvent use), and cellulosic biomass as a feedstock. We identify the key cost drivers to be (1) feed glucose concentration (wt%), (2) product yield (% of maximum theoretical yield) and (3) VVM (Volume of air per Volume of broth liquid per Minute, i.e., aeration rate in min-1). The production of limonene, based on current experimental data, is found to be economically infeasible (production cost ~ 465 $/kg vs. market selling price ~ 7 $/kg), but higher glucose concentration and yield can lower the cost. Among 12 terpenes studied, limonene appears to be the most reasonable short-term target because of its large market size (~ 160 million $/year in the US) and the relatively easier to achieve break-even yield (~ 30%, assuming a 14 wt% feed glucose concentration and 0.1 min-1 VVM). CONCLUSIONS The methods proposed in this work are applicable to a range of terpenes as well as other extracellular insoluble chemicals with density lower than that of water, such as fatty acids. The results provide guidance for future research in metabolic engineering toward terpenes production in terms of setting targets for key design parameters.
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Affiliation(s)
- Wenzhao Wu
- Dept. of Chemical and Biological Engineering and DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, 1415 Engineering Drive, Madison, WI 53706 USA
| | - Christos T. Maravelias
- Dept. of Chemical and Biological Engineering and DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, 1415 Engineering Drive, Madison, WI 53706 USA
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104
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Christ B, Hochstrasser R, Guyer L, Francisco R, Aubry S, Hörtensteiner S, Weng JK. Non-specific activities of the major herbicide-resistance gene BAR. NATURE PLANTS 2017; 3:937-945. [PMID: 29180815 PMCID: PMC6342461 DOI: 10.1038/s41477-017-0061-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2017] [Accepted: 10/23/2017] [Indexed: 05/20/2023]
Abstract
Bialaphos resistance (BAR) and phosphinothricin acetyltransferase (PAT) genes, which convey resistance to the broad-spectrum herbicide phosphinothricin (also known as glufosinate) via N-acetylation, have been globally used in basic plant research and genetically engineered crops 1-4 . Although early in vitro enzyme assays showed that recombinant BAR and PAT exhibit substrate preference toward phosphinothricin over the 20 proteinogenic amino acids 1 , indirect effects of BAR-containing transgenes in planta, including modified amino acid levels, have been seen but without the identification of their direct causes 5,6 . Combining metabolomics, plant genetics and biochemical approaches, we show that transgenic BAR indeed converts two plant endogenous amino acids, aminoadipate and tryptophan, to their respective N-acetylated products in several plant species. We report the crystal structures of BAR, and further delineate structural basis for its substrate selectivity and catalytic mechanism. Through structure-guided protein engineering, we generated several BAR variants that display significantly reduced non-specific activities compared with its wild-type counterpart in vivo. The transgenic expression of enzymes can result in unintended off-target metabolism arising from enzyme promiscuity. Understanding such phenomena at the mechanistic level can facilitate the design of maximally insulated systems featuring heterologously expressed enzymes.
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Affiliation(s)
- Bastien Christ
- Whitehead Institute for Biomedical Research, Cambridge, MA, 02142, USA
| | - Ramon Hochstrasser
- Department of Plant and Microbial Biology, University of Zurich, 8008, Zurich, Switzerland
- Institute of Medical Microbiology, University of Zurich, 8006, Zurich, Switzerland
| | - Luzia Guyer
- Department of Plant and Microbial Biology, University of Zurich, 8008, Zurich, Switzerland
| | - Rita Francisco
- Department of Plant and Microbial Biology, University of Zurich, 8008, Zurich, Switzerland
| | - Sylvain Aubry
- Department of Plant and Microbial Biology, University of Zurich, 8008, Zurich, Switzerland
| | - Stefan Hörtensteiner
- Department of Plant and Microbial Biology, University of Zurich, 8008, Zurich, Switzerland.
| | - Jing-Ke Weng
- Whitehead Institute for Biomedical Research, Cambridge, MA, 02142, USA.
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
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105
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Rodriguez A, Strucko T, Stahlhut SG, Kristensen M, Svenssen DK, Forster J, Nielsen J, Borodina I. Metabolic engineering of yeast for fermentative production of flavonoids. BIORESOURCE TECHNOLOGY 2017. [PMID: 28634125 DOI: 10.1016/j.biortech.2017.06.043] [Citation(s) in RCA: 78] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Yeast Saccharomyces cerevisiae was engineered for de novo production of six different flavonoids (naringenin, liquiritigenin, kaempferol, resokaempferol, quercetin, and fisetin) directly from glucose, without supplementation of expensive intermediates. This required reconstruction of long biosynthetic pathways, comprising up to eight heterologous genes from plants. The obtained titers of kaempferol 26.57±2.66mgL-1 and quercetin 20.38±2.57mgL-1 exceed the previously reported titers in yeast. This is also the first report of de novo biosynthesis of resokaempferol and fisetin in yeast. The work demonstrates the potential of flavonoid-producing yeast cell factories.
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Affiliation(s)
- Angelica Rodriguez
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet 220, 2800 Kgs Lyngby, Denmark
| | - Tomas Strucko
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet 220, 2800 Kgs Lyngby, Denmark
| | - Steen Gustav Stahlhut
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet 220, 2800 Kgs Lyngby, Denmark
| | - Mette Kristensen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet 220, 2800 Kgs Lyngby, Denmark
| | - Daniel Killerup Svenssen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet 220, 2800 Kgs Lyngby, Denmark
| | - Jochen Forster
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet 220, 2800 Kgs Lyngby, Denmark
| | - Jens Nielsen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet 220, 2800 Kgs Lyngby, Denmark; Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, SE412 96 Gothenburg, Sweden
| | - Irina Borodina
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet 220, 2800 Kgs Lyngby, Denmark.
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106
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Sarkari P, Marx H, Blumhoff ML, Mattanovich D, Sauer M, Steiger MG. An efficient tool for metabolic pathway construction and gene integration for Aspergillus niger. BIORESOURCE TECHNOLOGY 2017; 245:1327-1333. [PMID: 28533066 DOI: 10.1016/j.biortech.2017.05.004] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Revised: 04/28/2017] [Accepted: 05/01/2017] [Indexed: 06/07/2023]
Abstract
Metabolic engineering requires functional genetic tools for easy and quick generation of multiple pathway variants. A genetic engineering toolbox for A. niger is presented, which facilitates the generation of strains carrying heterologous expression cassettes at a defined genetic locus. The system is compatible with Golden Gate cloning, which facilitates the DNA construction process and provides high design flexibility. The integration process is mediated by a CRISPR/Cas9 strategy involving the cutting of both the genetic integration locus (pyrG) as well as the integrating plasmid. Only a transient expression of Cas9 is necessary and the carrying plasmid is readily lost using a size-reduced AMA1 variant. A high integration efficiency into the fungal genome of up to 100% can be achieved, thus reducing the screening process significantly. The feasibility of the approach was demonstrated by the integration of an expression cassette enabling the production of aconitic acid in A. niger.
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Affiliation(s)
- Parveen Sarkari
- ACIB GmbH, Muthgasse 18, 1190 Vienna, Austria; Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna (BOKU), Muthgasse 18, 1190 Vienna, Austria
| | - Hans Marx
- Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna (BOKU), Muthgasse 18, 1190 Vienna, Austria
| | - Marzena L Blumhoff
- Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna (BOKU), Muthgasse 18, 1190 Vienna, Austria; School of Bioengineering, University of Applied Sciences FH-Campus Wien, Vienna, Austria
| | - Diethard Mattanovich
- ACIB GmbH, Muthgasse 18, 1190 Vienna, Austria; Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna (BOKU), Muthgasse 18, 1190 Vienna, Austria
| | - Michael Sauer
- ACIB GmbH, Muthgasse 18, 1190 Vienna, Austria; Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna (BOKU), Muthgasse 18, 1190 Vienna, Austria.
| | - Matthias G Steiger
- ACIB GmbH, Muthgasse 18, 1190 Vienna, Austria; Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna (BOKU), Muthgasse 18, 1190 Vienna, Austria
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107
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Woolston BM, Roth T, Kohale I, Liu DR, Stephanopoulos G. Development of a formaldehyde biosensor with application to synthetic methylotrophy. Biotechnol Bioeng 2017; 115:206-215. [PMID: 28921510 DOI: 10.1002/bit.26455] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Revised: 09/01/2017] [Accepted: 09/14/2017] [Indexed: 02/03/2023]
Abstract
Formaldehyde is a prevalent environmental toxin and a key intermediate in single carbon metabolism. The ability to monitor formaldehyde concentration is, therefore, of interest for both environmental monitoring and for metabolic engineering of native and synthetic methylotrophs, but current methods suffer from low sensitivity, complex workflows, or require expensive analytical equipment. Here we develop a formaldehyde biosensor based on the FrmR repressor protein and cognate promoter of Escherichia coli. Optimization of the native repressor binding site and regulatory architecture enabled detection at levels as low as 1 µM. We then used the sensor to benchmark the in vivo activity of several NAD-dependent methanol dehydrogenase (Mdh) variants, the rate-limiting enzyme that catalyzes the first step of methanol assimilation. In order to use this biosensor to distinguish individuals in a mixed population of Mdh variants, we developed a strategy to prevent cross-talk by using glutathione as a formaldehyde sink to minimize intercellular formaldehyde diffusion. Finally, we applied this biosensor to balance expression of mdh and the formaldehyde assimilation enzymes hps and phi in an engineered E. coli strain to minimize formaldehyde build-up while also reducing the burden of heterologous expression. This biosensor offers a quick and simple method for sensitively detecting formaldehyde, and has the potential to be used as the basis for directed evolution of Mdh and dynamic formaldehyde control strategies for establishing synthetic methylotrophy.
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Affiliation(s)
| | - Timothy Roth
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA.,The Broad Institute of MIT and Harvard, Cambridge, MA 02141, USA.,Howard Hughes Medical Institute, Harvard University, Cambridge, MA 02138, USA
| | - Ishwar Kohale
- Department of Biological Engineering, MIT, Cambridge 02139, USA
| | - David R Liu
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA.,The Broad Institute of MIT and Harvard, Cambridge, MA 02141, USA.,Howard Hughes Medical Institute, Harvard University, Cambridge, MA 02138, USA
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108
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Zha J, Koffas MAG. Production of anthocyanins in metabolically engineered microorganisms: Current status and perspectives. Synth Syst Biotechnol 2017; 2:259-266. [PMID: 29552650 PMCID: PMC5851914 DOI: 10.1016/j.synbio.2017.10.005] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Revised: 09/24/2017] [Accepted: 10/26/2017] [Indexed: 11/17/2022] Open
Abstract
Microbial production of plant-derived natural products by engineered microorganisms has achieved great success thanks to large extend to metabolic engineering and synthetic biology. Anthocyanins, the water-soluble colored pigments found in terrestrial plants that are responsible for the red, blue and purple coloration of many flowers and fruits, are extensively used in food and cosmetics industry; however, their current supply heavily relies on complex extraction from plant-based materials. A promising alternative is their sustainable production in metabolically engineered microbes. Here, we review the recent progress on anthocyanin biosynthesis in engineered bacteria, with a special focus on the systematic engineering modifications such as selection and engineering of biosynthetic enzymes, engineering of transportation, regulation of UDP-glucose supply, as well as process optimization. These promising engineering strategies will facilitate successful microbial production of anthocyanins in industry in the near future.
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Key Words
- 4CL, 4-coumaroyl-CoA ligase
- ANS, anthocyanidin synthase
- Anthocyanin
- CHI, chalcone isomerase
- CHS, chalcone synthase
- DFR, dihydroflavonol 4-reductase
- DSSC, dye-sensitized solar cell
- Enzyme engineering
- F3GT, flavonoid 3-O-glucosyltransferase
- F3H, flavanone 3-hydroxylase
- F3′5′H, flavonoid 3′, 5′-hydroxylase
- F3′H, flavonoid 3′-hydroxylase
- FGT, flavonoid glucosyltransferase
- Metabolic engineering
- Microbial production
- UV, ultraviolet
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Affiliation(s)
- Jian Zha
- Department of Chemical and Biological Engineering, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, USA
| | - Mattheos A G Koffas
- Department of Chemical and Biological Engineering, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, USA.,Department of Biological Sciences, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, USA
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109
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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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110
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Hori Y, Kantak C, Murray RM, Abate AR. Cell-free extract based optimization of biomolecular circuits with droplet microfluidics. LAB ON A CHIP 2017; 17:3037-3042. [PMID: 28770936 DOI: 10.1039/c7lc00552k] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Engineering an efficient biomolecular circuit often requires time-consuming iterations of optimization. Cell-free protein expression systems allow rapid testing of biocircuits in vitro, speeding the design-build-test cycle of synthetic biology. In this paper, we combine this with droplet microfluidics to densely scan a transcription-translation biocircuit space. Our system assays millions of parameter combinations per hour, providing a detailed map of function. The ability to comprehensively map biocircuit parameter spaces allows accurate modeling to predict circuit function and identify optimal circuits and conditions.
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Affiliation(s)
- Yutaka Hori
- Department of Computing and Mathematical Sciences, California Institute of Technology, Pasadena, USA
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111
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Huang Z, Lee DY, Yoon S. Quantitative intracellular flux modeling and applications in biotherapeutic development and production using CHO cell cultures. Biotechnol Bioeng 2017; 114:2717-2728. [DOI: 10.1002/bit.26384] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2016] [Revised: 06/07/2017] [Accepted: 07/12/2017] [Indexed: 12/23/2022]
Affiliation(s)
- Zhuangrong Huang
- Department of Chemical Engineering, University of Massachusetts Lowell; One University Avenue; Lowell Massachusetts
| | - Dong-Yup Lee
- Department of Chemical and Biomolecular Engineering; National University of Singapore; Singapore Singapore
- Bioprocessing Technology Institute; Agency for Science, Technology and Research (A*STAR); Singapore Singapore
| | - Seongkyu Yoon
- Department of Chemical Engineering, University of Massachusetts Lowell; One University Avenue; Lowell Massachusetts
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112
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Jensen TØ, Pogrebnyakov I, Falkenberg KB, Redl S, Nielsen AT. Application of the thermostable β-galactosidase, BgaB, from Geobacillus stearothermophilus as a versatile reporter under anaerobic and aerobic conditions. AMB Express 2017; 7:169. [PMID: 28875485 PMCID: PMC5585113 DOI: 10.1186/s13568-017-0469-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Accepted: 08/29/2017] [Indexed: 11/10/2022] Open
Abstract
Use of thermophilic organisms has a range of advantages, but the significant lack of engineering tools limits their applications. Here we show that β-galactosidase from Geobacillus stearothermophilus (BgaB) can be applicable in a range of conditions, including different temperatures and oxygen concentrations. This protein functions both as a marker, promoting colony color development in the presence of a lactose analogue S-gal, and as a reporter enabling quantitative measurement by a simple colorimetric assay. Optimal performance was observed at 70 °C and pH 6.4. The gene was introduced into G. thermoglucosidans. The combination of BgaB expressed from promoters of varying strength with S-gal produced distinct black colonies in aerobic and anaerobic conditions at temperatures ranging from 37 to 60 °C. It showed an important advantage over the conventional β-galactosidase (LacZ) and substrate X-gal, which were inactive at high temperature and under anaerobic conditions. To demonstrate the versatility of the reporter, a promoter library was constructed by randomizing sequences around −35 and −10 regions in a wild type groES promoter from Geobacillus sp. GHH01. The library contained 28 promoter variants and encompassed fivefold variation. The experimental pipeline allowed construction and measurement of expression levels of the library in just 4 days. This β-galactosidase provides a promising tool for engineering of aerobic, anaerobic, and thermophilic production organisms such as Geobacillus species.
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113
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Lopes H, Rocha I. Genome-scale modeling of yeast: chronology, applications and critical perspectives. FEMS Yeast Res 2017; 17:3950252. [PMID: 28899034 PMCID: PMC5812505 DOI: 10.1093/femsyr/fox050] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Accepted: 07/07/2017] [Indexed: 01/21/2023] Open
Abstract
Over the last 15 years, several genome-scale metabolic models (GSMMs) were developed for different yeast species, aiding both the elucidation of new biological processes and the shift toward a bio-based economy, through the design of in silico inspired cell factories. Here, an historical perspective of the GSMMs built over time for several yeast species is presented and the main inheritance patterns among the metabolic reconstructions are highlighted. We additionally provide a critical perspective on the overall genome-scale modeling procedure, underlining incomplete model validation and evaluation approaches and the quest for the integration of regulatory and kinetic information into yeast GSMMs. A summary of experimentally validated model-based metabolic engineering applications of yeast species is further emphasized, while the main challenges and future perspectives for the field are finally addressed.
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Affiliation(s)
- Helder Lopes
- CEB - Centre of Biological Engineering, University of Minho, 4710-057 Braga, Portugal
| | - Isabel Rocha
- CEB - Centre of Biological Engineering, University of Minho, 4710-057 Braga, Portugal
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114
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Kadisch M, Willrodt C, Hillen M, Bühler B, Schmid A. Maximizing the stability of metabolic engineering-derived whole-cell biocatalysts. Biotechnol J 2017; 12. [DOI: 10.1002/biot.201600170] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Revised: 05/22/2017] [Accepted: 06/08/2017] [Indexed: 12/20/2022]
Affiliation(s)
- Marvin Kadisch
- Department Solar Materials; Helmholtz Centre for Environmental Research - UFZ; Leipzig Germany
| | - Christian Willrodt
- Department Solar Materials; Helmholtz Centre for Environmental Research - UFZ; Leipzig Germany
| | - Michael Hillen
- Department Solar Materials; Helmholtz Centre for Environmental Research - UFZ; Leipzig Germany
| | - Bruno Bühler
- Department Solar Materials; Helmholtz Centre for Environmental Research - UFZ; Leipzig Germany
| | - Andreas Schmid
- Department Solar Materials; Helmholtz Centre for Environmental Research - UFZ; Leipzig Germany
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115
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In Vivo Synthesis of Polyhydroxylated Compounds from a “Hidden Reservoir” of Toxic Aldehyde Species. ChemCatChem 2017. [DOI: 10.1002/cctc.201700469] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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116
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117
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Yenkie KM, Wu W, Maravelias CT. Synthesis and analysis of separation networks for the recovery of intracellular chemicals generated from microbial-based conversions. BIOTECHNOLOGY FOR BIOFUELS 2017; 10:119. [PMID: 28503196 PMCID: PMC5422901 DOI: 10.1186/s13068-017-0804-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Accepted: 04/25/2017] [Indexed: 05/19/2023]
Abstract
BACKGROUND Bioseparations can contribute to more than 70% in the total production cost of a bio-based chemical, and if the desired chemical is localized intracellularly, there can be additional challenges associated with its recovery. Based on the properties of the desired chemical and other components in the stream, there can be multiple feasible options for product recovery. These options are composed of several alternative technologies, performing similar tasks. The suitability of a technology for a particular chemical depends on (1) its performance parameters, such as separation efficiency; (2) cost or amount of added separating agent; (3) properties of the bioreactor effluent (e.g., biomass titer, product content); and (4) final product specifications. Our goal is to first synthesize alternative separation options and then analyze how technology selection affects the overall process economics. To achieve this, we propose an optimization-based framework that helps in identifying the critical technologies and parameters. RESULTS We study the separation networks for two representative classes of chemicals based on their properties. The separation network is divided into three stages: cell and product isolation (stage I), product concentration (II), and product purification and refining (III). Each stage exploits differences in specific product properties for achieving the desired product quality. The cost contribution analysis for the two cases (intracellular insoluble and intracellular soluble) reveals that stage I is the key cost contributor (>70% of the overall cost). Further analysis suggests that changes in input conditions and technology performance parameters lead to new designs primarily in stage I. CONCLUSIONS The proposed framework provides significant insights for technology selection and assists in making informed decisions regarding technologies that should be used in combination for a given set of stream/product properties and final output specifications. Additionally, the parametric sensitivity provides an opportunity to make crucial design and selection decisions in a comprehensive and rational manner. This will prove valuable in the selection of chemicals to be produced using bioconversions (bioproducts) as well as in creating better bioseparation flow sheets for detailed economic assessment and process implementation on the commercial scale.
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Affiliation(s)
- Kirti M. Yenkie
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, 1415 Engineering Drive, Madison, WI 53706-1691 USA
| | - Wenzhao Wu
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, 1415 Engineering Drive, Madison, WI 53706-1691 USA
| | - Christos T. Maravelias
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, 1415 Engineering Drive, Madison, WI 53706-1691 USA
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, 1552 University Ave, Madison, WI 53726 USA
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118
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Chen X, Gao C, Guo L, Hu G, Luo Q, Liu J, Nielsen J, Chen J, Liu L. DCEO Biotechnology: Tools To Design, Construct, Evaluate, and Optimize the Metabolic Pathway for Biosynthesis of Chemicals. Chem Rev 2017; 118:4-72. [DOI: 10.1021/acs.chemrev.6b00804] [Citation(s) in RCA: 109] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Xiulai Chen
- State
Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- Key
Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Cong Gao
- State
Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- Key
Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Liang Guo
- State
Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- Key
Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Guipeng Hu
- State
Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- Key
Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Qiuling Luo
- State
Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- Key
Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Jia Liu
- State
Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- Key
Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Jens Nielsen
- Department
of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg SE-412 96, Sweden
- Novo
Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK2800 Lyngby, Denmark
| | - Jian Chen
- State
Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- Key
Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Liming Liu
- State
Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- Department
of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg SE-412 96, Sweden
- Key
Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
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119
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Ausländer S, Ausländer D, Fussenegger M. Synthetische Biologie - die Synthese der Biologie. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201609229] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- Simon Ausländer
- Department of Biosystems Science and Engineering; ETH Zürich; Mattenstrasse 26 4058 Basel Schweiz
| | - David Ausländer
- Department of Biosystems Science and Engineering; ETH Zürich; Mattenstrasse 26 4058 Basel Schweiz
| | - Martin Fussenegger
- Department of Biosystems Science and Engineering; ETH Zürich; Mattenstrasse 26 4058 Basel Schweiz
- Faculty of Science; Universität Basel; Mattenstrasse 26 4058 Basel Schweiz
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120
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Ausländer S, Ausländer D, Fussenegger M. Synthetic Biology-The Synthesis of Biology. Angew Chem Int Ed Engl 2017; 56:6396-6419. [PMID: 27943572 DOI: 10.1002/anie.201609229] [Citation(s) in RCA: 107] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Revised: 11/17/2016] [Indexed: 01/01/2023]
Abstract
Synthetic biology concerns the engineering of man-made living biomachines from standardized components that can perform predefined functions in a (self-)controlled manner. Different research strategies and interdisciplinary efforts are pursued to implement engineering principles to biology. The "top-down" strategy exploits nature's incredible diversity of existing, natural parts to construct synthetic compositions of genetic, metabolic, or signaling networks with predictable and controllable properties. This mainly application-driven approach results in living factories that produce drugs, biofuels, biomaterials, and fine chemicals, and results in living pills that are based on engineered cells with the capacity to autonomously detect and treat disease states in vivo. In contrast, the "bottom-up" strategy seeks to be independent of existing living systems by designing biological systems from scratch and synthesizing artificial biological entities not found in nature. This more knowledge-driven approach investigates the reconstruction of minimal biological systems that are capable of performing basic biological phenomena, such as self-organization, self-replication, and self-sustainability. Moreover, the syntheses of artificial biological units, such as synthetic nucleotides or amino acids, and their implementation into polymers inside living cells currently set the boundaries between natural and artificial biological systems. In particular, the in vitro design, synthesis, and transfer of complete genomes into host cells point to the future of synthetic biology: the creation of designer cells with tailored desirable properties for biomedicine and biotechnology.
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Affiliation(s)
- Simon Ausländer
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, 4058, Basel, Switzerland
| | - David Ausländer
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, 4058, Basel, Switzerland
| | - Martin Fussenegger
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, 4058, Basel, Switzerland.,Faculty of Science, University of Basel, Mattenstrasse 26, 4058, Basel, Switzerland
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121
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Yang T, Rao Z, Zhang X, Xu M, Xu Z, Yang ST. Metabolic engineering strategies for acetoin and 2,3-butanediol production: advances and prospects. Crit Rev Biotechnol 2017; 37:990-1005. [DOI: 10.1080/07388551.2017.1299680] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Taowei Yang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
- Jiangnan University (Rugao) Food Biotechnology Research Institute, Rugao, Jiangsu Province, China
| | - Zhiming Rao
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
- Jiangnan University (Rugao) Food Biotechnology Research Institute, Rugao, Jiangsu Province, China
| | - Xian Zhang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Meijuan Xu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Zhenghong Xu
- Laboratory of Pharmaceutical Engineering, School of Pharmaceutical Science, Jiangnan University, Wuxi, China
| | - Shang-Tian Yang
- Department of Chemical and Biomolecular Engineering, Ohio State University, Columbus, OH, USA
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122
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Vranish JN, Ancona MG, Oh E, Susumu K, Medintz IL. Enhancing coupled enzymatic activity by conjugating one enzyme to a nanoparticle. NANOSCALE 2017; 9:5172-5187. [PMID: 28393943 DOI: 10.1039/c7nr00200a] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Enzymes have long been a prime research target for the commercial production of commodity and specialty chemicals, design of sensing devices, and the development of therapeutics and new chemical processes. Industrial applications for enzymes can potentially be enhanced by enzyme immobilization which often allows for increased enzyme stability, facile product purification, and minimized substrate diffusion times in multienzymatic cascades, but this is usually at the cost of a significant decrease in catalytic rates. Recently, enzyme immobilization has been advanced by the discovery that nanoparticle surfaces are frequently able to enhance the activity of the bound enzyme. Here we extend this observation to a multienzymatic coupled system using semiconductor quantum dots (QDs) as a model nanoparticle material and the prototypical enzyme pair of glucose oxidase (GOX) and horseradish peroxidase (HRP). We first demonstrate that HRP binding to QDs has a significant beneficial effect on enzymatic activity, producing a >2-fold improvement in kcat. We argue that this enhancement is due to affinity of the QD surface for the substrate. Furthermore, we demonstrate that when the ratio of GOX to HRP is adjusted to allow HRP to be the rate-limiting step of the pathway, the QD-induced rate enhancement of HRP can be maintained in a multi-enzyme cascade. Kinetic analysis shows that the underlying processes can be simulated numerically and provide insight into the governing mechanisms. The potential of nanoparticle-based catalytic enhancement is then discussed in the context of multienzyme cascades and synthetic biology.
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123
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de Carvalho CCCR. Whole cell biocatalysts: essential workers from Nature to the industry. Microb Biotechnol 2017; 10:250-263. [PMID: 27145540 PMCID: PMC5328830 DOI: 10.1111/1751-7915.12363] [Citation(s) in RCA: 140] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Revised: 03/28/2016] [Accepted: 03/31/2016] [Indexed: 11/30/2022] Open
Abstract
Microorganisms have been exposed to a myriad of substrates and environmental conditions throughout evolution resulting in countless metabolites and enzymatic activities. Although mankind have been using these properties for centuries, we have only recently learned to control their production, to develop new biocatalysts with high stability and productivity and to improve their yields under new operational conditions. However, microbial cells still provide the best known environment for enzymes, preventing conformational changes in the protein structure in non-conventional medium and under harsh reaction conditions, while being able to efficiently regenerate necessary cofactors and to carry out cascades of reactions. Besides, a still unknown microbe is probably already producing a compound that will cure cancer, Alzeihmer's disease or kill the most resistant pathogen. In this review, the latest developments in screening desirable activities and improving production yields are discussed.
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Affiliation(s)
- Carla C. C. R. de Carvalho
- iBB‐Institute for Bioengineering and BiosciencesDepartment of BioengineeringInstituto Superior TécnicoUniversidade de LisboaAv. Rovisco PaisLisbon1049‐001Portugal
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124
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Synthetic metabolism: metabolic engineering meets enzyme design. Curr Opin Chem Biol 2017; 37:56-62. [PMID: 28152442 DOI: 10.1016/j.cbpa.2016.12.023] [Citation(s) in RCA: 149] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Revised: 12/15/2016] [Accepted: 12/16/2016] [Indexed: 01/29/2023]
Abstract
Metabolic engineering aims at modifying the endogenous metabolic network of an organism to harness it for a useful biotechnological task, for example, production of a value-added compound. Several levels of metabolic engineering can be defined and are the topic of this review. Basic 'copy, paste and fine-tuning' approaches are limited to the structure of naturally existing pathways. 'Mix and match' approaches freely recombine the repertoire of existing enzymes to create synthetic metabolic networks that are able to outcompete naturally evolved pathways or redirect flux toward non-natural products. The space of possible metabolic solution can be further increased through approaches including 'new enzyme reactions', which are engineered on the basis of known enzyme mechanisms. Finally, by considering completely 'novel enzyme chemistries' with de novo enzyme design, the limits of nature can be breached to derive the most advanced form of synthetic pathways. We discuss the challenges and promises associated with these different metabolic engineering approaches and illuminate how enzyme engineering is expected to take a prime role in synthetic metabolic engineering for biotechnology, chemical industry and agriculture of the future.
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125
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Liu W, Zhang B, Jiang R. Improving acetyl-CoA biosynthesis in Saccharomyces cerevisiae via the overexpression of pantothenate kinase and PDH bypass. BIOTECHNOLOGY FOR BIOFUELS 2017; 10:41. [PMID: 28239413 PMCID: PMC5316175 DOI: 10.1186/s13068-017-0726-z] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Accepted: 02/09/2017] [Indexed: 05/09/2023]
Abstract
BACKGROUND Acetyl-CoA is an important precursor in Saccharomyces cerevisiae. Various approaches have been adopted to improve its cytosolic level previously with the emphasis on engineering the "acetyl-" part of acetyl-CoA. To the best of our knowledge, there have been no reports on engineering the "-CoA" part so far. RESULTS In this study, we had tried to engineer S. cerevisiae from both the "-CoA" part via pantothenate kinase overexpression (PanK from S. cerevisiae, the rate-limiting enzyme for CoA synthesis) and the "acetyl-"part through PDH bypass introduction (ALD6 from S. cerevisiae and SeAcsL641P from Salmonella enteric). A naringenin-producing reporter strain had been constructed to reflect cytosolic acetyl-CoA level as acetyl-CoA is the precursor of naringenin. It was found that PanK overexpression or PDH bypass introduction alone only led to a twofold or 6.74-fold increase in naringenin titer, but the combination of both (strain CENFPAA01) had resulted in 24.4-fold increase as compared to the control (strain CENF09) in the presence of 0.5 mM substrate p-coumaric acid. The supplement of PanK substrate pantothenate resulted in another 19% increase in naringenin production. CONCLUSIONS To greatly enhance acetyl-CoA level in yeast cytosol, it is feasible to engineer both the "acetyl-" part and the "-CoA" part simultaneously. Insufficient CoA supply might aggravate acetyl-CoA shortage and cause low yield of target product.
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Affiliation(s)
- Wenshan Liu
- School of Chemical & Biomedical Engineering, Nanyang Technological University, 62 Nanyang Drive, Singapore, 637459 Singapore
| | - Bo Zhang
- School of Chemical & Biomedical Engineering, Nanyang Technological University, 62 Nanyang Drive, Singapore, 637459 Singapore
| | - Rongrong Jiang
- School of Chemical & Biomedical Engineering, Nanyang Technological University, 62 Nanyang Drive, Singapore, 637459 Singapore
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126
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Wang J, Niyompanich S, Tai YS, Wang J, Bai W, Mahida P, Gao T, Zhang K. Engineering of a Highly Efficient Escherichia coli Strain for Mevalonate Fermentation through Chromosomal Integration. Appl Environ Microbiol 2016; 82:7176-7184. [PMID: 27736790 PMCID: PMC5118928 DOI: 10.1128/aem.02178-16] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Accepted: 09/30/2016] [Indexed: 01/09/2023] Open
Abstract
Chromosomal integration of heterologous metabolic pathways is optimal for industrially relevant fermentation, as plasmid-based fermentation causes extra metabolic burden and genetic instabilities. In this work, chromosomal integration was adapted for the production of mevalonate, which can be readily converted into β-methyl-δ-valerolactone, a monomer for the production of mechanically tunable polyesters. The mevalonate pathway, driven by a constitutive promoter, was integrated into the chromosome of Escherichia coli to replace the native fermentation gene adhE or ldhA The engineered strains (CMEV-1 and CMEV-2) did not require inducer or antibiotic and showed slightly higher maximal productivities (0.38 to ∼0.43 g/liter/h) and yields (67.8 to ∼71.4% of the maximum theoretical yield) than those of the plasmid-based fermentation. Since the glycolysis pathway is the first module for mevalonate synthesis, atpFH deletion was employed to improve the glycolytic rate and the production rate of mevalonate. Shake flask fermentation results showed that the deletion of atpFH in CMEV-1 resulted in a 2.1-fold increase in the maximum productivity. Furthermore, enhancement of the downstream pathway by integrating two copies of the mevalonate pathway genes into the chromosome further improved the mevalonate yield. Finally, our fed-batch fermentation showed that, with deletion of the atpFH and sucA genes and integration of two copies of the mevalonate pathway genes into the chromosome, the engineered strain CMEV-7 exhibited both high maximal productivity (∼1.01 g/liter/h) and high yield (86.1% of the maximum theoretical yield, 30 g/liter mevalonate from 61 g/liter glucose after 48 h in a shake flask). IMPORTANCE Metabolic engineering has succeeded in producing various chemicals. However, few of these chemicals are commercially competitive with the conventional petroleum-derived materials. In this work, chromosomal integration of the heterologous pathway and subsequent optimization strategies ensure stable and efficient (i.e., high-titer, high-yield, and high-productivity) production of mevalonate, which demonstrates the potential for scale-up fermentation. Among the optimization strategies, we demonstrated that enhancement of the glycolytic flux significantly improved the productivity. This result provides an example of how to tune the carbon flux for the optimal production of exogenous chemicals.
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Affiliation(s)
- Jilong Wang
- Department of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, Minnesota, USA
| | - Suthamat Niyompanich
- Department of Biology, Faculty of Science, Srinakharinwirot University, Bangkok, Thailand
| | - Yi-Shu Tai
- Department of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, Minnesota, USA
| | - Jingyu Wang
- Department of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, Minnesota, USA
| | - Wenqin Bai
- Department of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, Minnesota, USA
| | - Prithviraj Mahida
- Department of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, Minnesota, USA
| | - Tuo Gao
- Department of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, Minnesota, USA
| | - Kechun Zhang
- Department of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, Minnesota, USA
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127
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Williams TC, Peng B, Vickers CE, Nielsen LK. The Saccharomyces cerevisiae pheromone-response is a metabolically active stationary phase for bio-production. Metab Eng Commun 2016; 3:142-152. [PMID: 29468120 PMCID: PMC5779721 DOI: 10.1016/j.meteno.2016.05.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Revised: 05/02/2016] [Accepted: 05/10/2016] [Indexed: 11/04/2022] Open
Abstract
The growth characteristics and underlying metabolism of microbial production hosts are critical to the productivity of metabolically engineered pathways. Production in parallel with growth often leads to biomass/bio-product competition for carbon. The growth arrest phenotype associated with the Saccharomyces cerevisiae pheromone-response is potentially an attractive production phase because it offers the possibility of decoupling production from population growth. However, little is known about the metabolic phenotype associated with the pheromone-response, which has not been tested for suitability as a production phase. Analysis of extracellular metabolite fluxes, available transcriptomic data, and heterologous compound production (para-hydroxybenzoic acid) demonstrate that a highly active and distinct metabolism underlies the pheromone-response. These results indicate that the pheromone-response is a suitable production phase, and that it may be useful for informing synthetic biology design principles for engineering productive stationary phase phenotypes.
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Affiliation(s)
| | | | - Claudia E. Vickers
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, St. Lucia, QLD 4072, Australia
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128
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Gonzalez JE, Long CP, Antoniewicz MR. Comprehensive analysis of glucose and xylose metabolism in Escherichia coli under aerobic and anaerobic conditions by 13C metabolic flux analysis. Metab Eng 2016; 39:9-18. [PMID: 27840237 DOI: 10.1016/j.ymben.2016.11.003] [Citation(s) in RCA: 79] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2016] [Revised: 10/09/2016] [Accepted: 11/07/2016] [Indexed: 12/13/2022]
Abstract
Glucose and xylose are the two most abundant sugars derived from the breakdown of lignocellulosic biomass. While aerobic glucose metabolism is relatively well understood in E. coli, until now there have been only a handful of studies focused on anaerobic glucose metabolism and no 13C-flux studies on xylose metabolism. In the absence of experimentally validated flux maps, constraint-based approaches such as MOMA and RELATCH cannot be used to guide new metabolic engineering designs. In this work, we have addressed this critical gap in current understanding by performing comprehensive characterizations of glucose and xylose metabolism under aerobic and anaerobic conditions, using recent state-of-the-art techniques in 13C metabolic flux analysis (13C-MFA). Specifically, we quantified precise metabolic fluxes for each condition by performing parallel labeling experiments and analyzing the data through integrated 13C-MFA using the optimal tracers [1,2-13C]glucose, [1,6-13C]glucose, [1,2-13C]xylose and [5-13C]xylose. We also quantified changes in biomass composition and confirmed turnover of macromolecules by applying [U-13C]glucose and [U-13C]xylose tracers. We demonstrated that under anaerobic growth conditions there is significant turnover of lipids and that a significant portion of CO2 originates from biomass turnover. Using knockout strains, we also demonstrated that β-oxidation is critical for anaerobic growth on xylose. Quantitative analysis of co-factor balances (NADH/FADH2, NADPH, and ATP) for different growth conditions provided new insights regarding the interplay of energy and redox metabolism and the impact on E. coli cell physiology.
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Affiliation(s)
- Jacqueline E Gonzalez
- Department of Chemical and Biomolecular Engineering, Metabolic Engineering and Systems Biology Laboratory, University of Delaware, Newark, DE 19716, USA
| | - Christopher P Long
- Department of Chemical and Biomolecular Engineering, Metabolic Engineering and Systems Biology Laboratory, University of Delaware, Newark, DE 19716, USA
| | - Maciek R Antoniewicz
- Department of Chemical and Biomolecular Engineering, Metabolic Engineering and Systems Biology Laboratory, University of Delaware, Newark, DE 19716, USA.
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129
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Balagurunathan B, Jain VK, Tear CJY, Lim CY, Zhao H. In silico design of anaerobic growth-coupled product formation in Escherichia coli: experimental validation using a simple polyol, glycerol. Bioprocess Biosyst Eng 2016; 40:361-372. [PMID: 27796571 DOI: 10.1007/s00449-016-1703-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Accepted: 10/25/2016] [Indexed: 12/11/2022]
Abstract
Integrated approaches using in silico model-based design and advanced genetic tools have enabled efficient production of fuels, chemicals and functional ingredients using microbial cell factories. In this study, using a recently developed genome-scale metabolic model for Escherichia coli iJO1366, a mutant strain has been designed in silico for the anaerobic growth-coupled production of a simple polyol, glycerol. Computational complexity was significantly reduced by systematically reducing the target reactions used for knockout simulations. One promising penta knockout E. coli mutant (E. coli ΔadhE ΔldhA ΔfrdC ΔtpiA ΔmgsA) was selected from simulation study and was constructed experimentally by sequentially deleting five genes. The penta mutant E. coli bearing the Saccharomyces cerevisiae glycerol production pathway was able to grow anaerobically and produce glycerol as the major metabolite with up to 90% of theoretical yield along with stoichiometric quantities of acetate and formate. Using the penta mutant E. coli strain we have demonstrated that the ATP formation from the acetate pathway was essential for growth under anaerobic conditions. The general workflow developed can be easily applied to anaerobic production of other platform chemicals using E. coli as the cell factory.
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Affiliation(s)
- Balaji Balagurunathan
- Bioprocess Engineering Center, Institute of Chemical and Engineering Sciences, Agency for Science, Technology and Research (A*STAR), 1 Pesek Road, Jurong Island, 627833, Singapore
| | - Vishist Kumar Jain
- Industrial Biotechnology Division, Institute of Chemical and Engineering Sciences, Agency for Science, Technology and Research (A*STAR), 1 Pesek Road, Jurong Island, 627833, Singapore
| | - Crystal Jing Ying Tear
- Industrial Biotechnology Division, Institute of Chemical and Engineering Sciences, Agency for Science, Technology and Research (A*STAR), 1 Pesek Road, Jurong Island, 627833, Singapore
| | - Chan Yuen Lim
- Industrial Biotechnology Division, Institute of Chemical and Engineering Sciences, Agency for Science, Technology and Research (A*STAR), 1 Pesek Road, Jurong Island, 627833, Singapore
| | - Hua Zhao
- Industrial Biotechnology Division, Institute of Chemical and Engineering Sciences, Agency for Science, Technology and Research (A*STAR), 1 Pesek Road, Jurong Island, 627833, Singapore.
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130
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Takors R, de Lorenzo V. Editorial overview: Microbial systems biology: systems biology prepares the ground for successful synthetic biology. Curr Opin Microbiol 2016; 33:viii-x. [PMID: 27568258 DOI: 10.1016/j.mib.2016.08.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Ralf Takors
- Institute for Biochemical Engineering, University of Stuttgart, Allmandring 31, 50569 Stuttgart, Germany
| | - Víctor de Lorenzo
- Systems Biology Program, Centro Nacional de Biotecnología, CSIC, Campus de Cantoblanco Madrid 28049, Spain
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131
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Forward design of a complex enzyme cascade reaction. Nat Commun 2016; 7:12971. [PMID: 27677244 PMCID: PMC5052792 DOI: 10.1038/ncomms12971] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2016] [Accepted: 08/18/2016] [Indexed: 11/18/2022] Open
Abstract
Enzymatic reaction networks are unique in that one can operate a large number of reactions under the same set of conditions concomitantly in one pot, but the nonlinear kinetics of the enzymes and the resulting system complexity have so far defeated rational design processes for the construction of such complex cascade reactions. Here we demonstrate the forward design of an in vitro 10-membered system using enzymes from highly regulated biological processes such as glycolysis. For this, we adapt the characterization of the biochemical system to the needs of classical engineering systems theory: we combine online mass spectrometry and continuous system operation to apply standard system theory input functions and to use the detailed dynamic system responses to parameterize a model of sufficient quality for forward design. This allows the facile optimization of a 10-enzyme cascade reaction for fine chemical production purposes. Building multi-component enzymatic processes in one pot is challenged by the inherent complexity of each biochemical system. Here, the authors use online mass spectroscopy and engineering systems theory to achieve forward design of a ten-membered reaction cascade.
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132
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Isoprenoid-Based Biofuels: Homologous Expression and Heterologous Expression in Prokaryotes. Appl Environ Microbiol 2016; 82:5730-40. [PMID: 27422837 DOI: 10.1128/aem.01192-16] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Enthusiasm for mining advanced biofuels from microbial hosts has increased remarkably in recent years. Isoprenoids are one of the highly diverse groups of secondary metabolites and are foreseen as an alternative to petroleum-based fuels. Most of the prokaryotes synthesize their isoprenoid backbone via the deoxyxylulose-5-phosphate pathway from glyceraldehyde-3-phosphate and pyruvate, whereas eukaryotes synthesize isoprenoids via the mevalonate pathway from acetyl coenzyme A (acetyl-CoA). Microorganisms do not accumulate isoprenoids in large quantities naturally, which restricts their application for fuel purposes. Various metabolic engineering efforts have been utilized to overcome the limitations associated with their natural and nonnatural production. The introduction of heterologous pathways/genes and overexpression of endogenous/homologous genes have shown a remarkable increase in isoprenoid yield and substrate utilization in microbial hosts. Such modifications in the hosts' genomes have enabled researchers to develop commercially competent microbial strains for isoprenoid-based biofuel production utilizing a vast array of substrates. The present minireview briefly discusses the recent advancement in metabolic engineering efforts in prokaryotic hosts for the production of isoprenoid-based biofuels, with an emphasis on endogenous, homologous, and heterologous expression strategies.
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133
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Zhou Y, Wu S, Li Z. Cascade Biocatalysis for Sustainable Asymmetric Synthesis: From Biobased l-Phenylalanine to High-Value Chiral Chemicals. Angew Chem Int Ed Engl 2016; 55:11647-50. [PMID: 27512928 DOI: 10.1002/anie.201606235] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Indexed: 11/08/2022]
Abstract
Sustainable synthesis of useful and valuable chiral fine chemicals from renewable feedstocks is highly desirable but remains challenging. Reported herein is a designed and engineered set of unique non-natural biocatalytic cascades to achieve the asymmetric synthesis of chiral epoxide, diols, hydroxy acid, and amino acid in high yield and with excellent ee values from the easily available biobased l-phenylalanine. Each of the cascades was efficiently performed in one pot by using the cells of a single recombinant strain over-expressing 4-10 different enzymes. The cascade biocatalysis approach is promising for upgrading biobased bulk chemicals to high-value chiral chemicals. In addition, combining the non-natural enzyme cascades with the natural metabolic pathway of the host strain enabled the fermentative production of the chiral fine chemicals from glucose.
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Affiliation(s)
- Yi Zhou
- Synthetic Biology for Clinical and Technological Innovation (SynCTI), Life Sciences Institute, National University of Singapore, 28 Medical Drive, Singapore, 117456, Singapore
| | - Shuke Wu
- Synthetic Biology for Clinical and Technological Innovation (SynCTI), Life Sciences Institute, National University of Singapore, 28 Medical Drive, Singapore, 117456, Singapore.,Department of Chemical and Biomolecular Engineering, National University of Singapore, 4 Engineering Drive 4, Singapore, 117585, Singapore
| | - Zhi Li
- Synthetic Biology for Clinical and Technological Innovation (SynCTI), Life Sciences Institute, National University of Singapore, 28 Medical Drive, Singapore, 117456, Singapore. .,Department of Chemical and Biomolecular Engineering, National University of Singapore, 4 Engineering Drive 4, Singapore, 117585, Singapore.
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134
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Zhou Y, Wu S, Li Z. Cascade Biocatalysis for Sustainable Asymmetric Synthesis: From Biobasedl-Phenylalanine to High-Value Chiral Chemicals. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201606235] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Yi Zhou
- Synthetic Biology for Clinical and Technological Innovation (SynCTI); Life Sciences Institute; National University of Singapore; 28 Medical Drive Singapore 117456 Singapore
| | - Shuke Wu
- Synthetic Biology for Clinical and Technological Innovation (SynCTI); Life Sciences Institute; National University of Singapore; 28 Medical Drive Singapore 117456 Singapore
- Department of Chemical and Biomolecular Engineering; National University of Singapore; 4 Engineering Drive 4 Singapore 117585 Singapore
| | - Zhi Li
- Synthetic Biology for Clinical and Technological Innovation (SynCTI); Life Sciences Institute; National University of Singapore; 28 Medical Drive Singapore 117456 Singapore
- Department of Chemical and Biomolecular Engineering; National University of Singapore; 4 Engineering Drive 4 Singapore 117585 Singapore
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135
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Wu G, Yan Q, Jones JA, Tang YJ, Fong SS, Koffas MA. Metabolic Burden: Cornerstones in Synthetic Biology and Metabolic Engineering Applications. Trends Biotechnol 2016; 34:652-664. [DOI: 10.1016/j.tibtech.2016.02.010] [Citation(s) in RCA: 365] [Impact Index Per Article: 45.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Revised: 02/18/2016] [Accepted: 02/19/2016] [Indexed: 01/23/2023]
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136
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Liu Y, Link H, Liu L, Du G, Chen J, Sauer U. A dynamic pathway analysis approach reveals a limiting futile cycle in N-acetylglucosamine overproducing Bacillus subtilis. Nat Commun 2016; 7:11933. [PMID: 27324299 PMCID: PMC5512609 DOI: 10.1038/ncomms11933] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Accepted: 05/13/2016] [Indexed: 01/24/2023] Open
Abstract
Recent advances in genome engineering have further widened the gap between our ability to implement essentially any genetic change and understanding the impact of these changes on cellular function. We lack efficient methods to diagnose limiting steps in engineered pathways. Here, we develop a generally applicable approach to reveal limiting steps within a synthetic pathway. It is based on monitoring metabolite dynamics and simplified kinetic modelling to differentiate between putative causes of limiting product synthesis during the start-up phase of the pathway with near-maximal rates. We examine the synthetic N-acetylglucosamine (GlcNAc) pathway in Bacillus subtilis and find none of the acetyl-, amine- or glucose-moiety precursors to limit synthesis. Our dynamic metabolomics approach predicts an energy-dissipating futile cycle between GlcNAc6P and GlcNAc as the primary problem in the pathway. Deletion of the responsible glucokinase more than doubles GlcNAc productivity by restoring healthy growth of the overproducing strain. Rate-limiting steps in synthetic metabolic pathways are difficult to identify. Here, the authors monitor metabolite dynamics and apply kinetic modelling during the start-up phase of the Bacillus subtilis GlcNAc pathway to discover a futile cycle, allowing them to identify a more productive strain.
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Affiliation(s)
- Yanfeng Liu
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Lihu Road 1800, Wuxi 214122, China.,Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Lihu Road 1800, Wuxi 214122, China.,Institute of Molecular Systems Biology, ETH Zurich, Zurich 8093, Switzerland
| | - Hannes Link
- Max Planck Institute for terrestrial Microbiology, Marburg 35043, Germany
| | - Long Liu
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Lihu Road 1800, Wuxi 214122, China.,Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Lihu Road 1800, Wuxi 214122, China
| | - Guocheng Du
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Lihu Road 1800, Wuxi 214122, China.,Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Lihu Road 1800, Wuxi 214122, China
| | - Jian Chen
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Lihu Road 1800, Wuxi 214122, China.,Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Lihu Road 1800, Wuxi 214122, China
| | - Uwe Sauer
- Institute of Molecular Systems Biology, ETH Zurich, Zurich 8093, Switzerland
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137
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Roehner N, Beal J, Clancy K, Bartley B, Misirli G, Grünberg R, Oberortner E, Pocock M, Bissell M, Madsen C, Nguyen T, Zhang M, Zhang Z, Zundel Z, Densmore D, Gennari JH, Wipat A, Sauro HM, Myers CJ. Sharing Structure and Function in Biological Design with SBOL 2.0. ACS Synth Biol 2016; 5:498-506. [PMID: 27111421 DOI: 10.1021/acssynbio.5b00215] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The Synthetic Biology Open Language (SBOL) is a standard that enables collaborative engineering of biological systems across different institutions and tools. SBOL is developed through careful consideration of recent synthetic biology trends, real use cases, and consensus among leading researchers in the field and members of commercial biotechnology enterprises. We demonstrate and discuss how a set of SBOL-enabled software tools can form an integrated, cross-organizational workflow to recapitulate the design of one of the largest published genetic circuits to date, a 4-input AND sensor. This design encompasses the structural components of the system, such as its DNA, RNA, small molecules, and proteins, as well as the interactions between these components that determine the system's behavior/function. The demonstrated workflow and resulting circuit design illustrate the utility of SBOL 2.0 in automating the exchange of structural and functional specifications for genetic parts, devices, and the biological systems in which they operate.
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Affiliation(s)
- Nicholas Roehner
- Department
of Electrical and Computer Engineering, Boston University, Boston, Massachusetts 02215, United States
| | - Jacob Beal
- Raytheon BBN Technologies, Cambridge, Massachusetts 02138, United States
| | - Kevin Clancy
- Thermo Fisher Scientific, Carlsbad, California 92008, United States
| | - Bryan Bartley
- Department
of Bioengineering, University of Washington, Seattle, Washington 98195, United States
| | - Goksel Misirli
- School
of Computing Science, Newcastle University, Newcastle upon Tyne NE1
7RU, U.K
| | - Raik Grünberg
- Institute
for Research in Immunology and Cancer, University of Montreal, Montreal, Quebec H3T 1J4, Canada
| | - Ernst Oberortner
- U.S. Department of Energy Joint Genome Institute, Walnut Creek, California 94598, United States
| | - Matthew Pocock
- Turing Ate My Hamster, Ltd., Newcastle
upon Tyne NE27 0RT, U.K
| | | | - Curtis Madsen
- School
of Computing Science, Newcastle University, Newcastle upon Tyne NE1
7RU, U.K
| | - Tramy Nguyen
- Department
of Electrical and Computer Engineering, University of Utah, Salt Lake
City, Utah 84112, United States
| | - Michael Zhang
- Department
of Electrical and Computer Engineering, University of Utah, Salt Lake
City, Utah 84112, United States
| | - Zhen Zhang
- Department
of Electrical and Computer Engineering, University of Utah, Salt Lake
City, Utah 84112, United States
| | - Zach Zundel
- Department
of Bioengineering, University of Utah, Salt Lake City, Utah 84112, United States
| | - Douglas Densmore
- Department
of Electrical and Computer Engineering, Boston University, Boston, Massachusetts 02215, United States
| | - John H. Gennari
- Department
of Biomedical Informatics and Medical Education, University of Washington, Seattle, Washington 98195, United States
| | - Anil Wipat
- School
of Computing Science, Newcastle University, Newcastle upon Tyne NE1
7RU, U.K
| | - Herbert M. Sauro
- Department
of Bioengineering, University of Washington, Seattle, Washington 98195, United States
| | - Chris J. Myers
- Department
of Electrical and Computer Engineering, University of Utah, Salt Lake
City, Utah 84112, United States
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138
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Zhang H, Wang X. Modular co-culture engineering, a new approach for metabolic engineering. Metab Eng 2016; 37:114-121. [PMID: 27242132 DOI: 10.1016/j.ymben.2016.05.007] [Citation(s) in RCA: 172] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Revised: 05/13/2016] [Accepted: 05/26/2016] [Indexed: 10/21/2022]
Abstract
With the development of metabolic engineering, employment of a selected microbial host for accommodation of a designed biosynthetic pathway to produce a target compound has achieved tremendous success in the past several decades. Yet, increasing requirements for sophisticated microbial biosynthesis call for establishment and application of more advanced metabolic engineering methodologies. Recently, important progress has been made towards employing more than one engineered microbial strains to constitute synthetic co-cultures and modularizing the biosynthetic labor between the co-culture members in order to improve bioproduction performance. This emerging approach, referred to as modular co-culture engineering in this review, presents a valuable opportunity for expanding the scope of the broad field of metabolic engineering. We highlight representative research accomplishments using this approach, especially those utilizing metabolic engineering tools for microbial co-culture manipulation. Key benefits and major challenges associated with modular co-culture engineering are also presented and discussed.
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Affiliation(s)
- Haoran Zhang
- Department of Chemical and Biochemical Engineering, Rutgers, The State University of New Jersey, 98 Brett Rd, Piscataway, NJ 08854, USA.
| | - Xiaonan Wang
- Department of Chemical and Biochemical Engineering, Rutgers, The State University of New Jersey, 98 Brett Rd, Piscataway, NJ 08854, USA
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139
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Jang S, Lee B, Jeong HH, Jin SH, Jang S, Kim SG, Jung GY, Lee CS. On-chip analysis, indexing and screening for chemical producing bacteria in a microfluidic static droplet array. LAB ON A CHIP 2016; 16:1909-16. [PMID: 27102263 DOI: 10.1039/c6lc00118a] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Economic production of chemicals from microbes necessitates development of high-producing strains and an efficient screening technology is crucial to maximize the effect of the most popular strain improvement method, the combinatorial approach. However, high-throughput screening has been limited for assessment of diverse intracellular metabolites at the single-cell level. Herein, we established a screening platform that couples a microfluidic static droplet array (SDA) and an artificial riboswitch to analyse intracellular metabolite concentration from single microbial cells. Using this system, we entrapped single Escherichia coli cells in SDA to measure intracellular l-tryptophan concentrations. It was validated that intracellular l-tryptophan concentration can be evaluated by the fluorescence from the riboswitch. Moreover, high-producing strains were successfully screened from a mutagenized library, exhibiting up to 145% productivity compared to its parental strain. This platform will be widely applicable to strain improvement for diverse metabolites by developing new artificial riboswitches.
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Affiliation(s)
- Sungho Jang
- Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-ro, Nam-gu, Pohang, Gyeongbuk 790-784, Korea.
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140
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Page AF, Cseke LJ, Minocha R, Turlapati SA, Podila GK, Ulanov A, Li Z, Minocha SC. Genetic manipulation of putrescine biosynthesis reprograms the cellular transcriptome and the metabolome. BMC PLANT BIOLOGY 2016; 16:113. [PMID: 27188293 PMCID: PMC4870780 DOI: 10.1186/s12870-016-0796-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2016] [Accepted: 04/29/2016] [Indexed: 05/23/2023]
Abstract
BACKGROUND With the increasing interest in metabolic engineering of plants using genetic manipulation and gene editing technologies to enhance growth, nutritional value and environmental adaptation, a major concern is the potential of undesirable broad and distant effects of manipulating the target gene or metabolic step in the resulting plant. A comprehensive transcriptomic and metabolomic analysis of the product may shed some useful light in this regard. The present study used these two techniques with plant cell cultures to analyze the effects of genetic manipulation of a single step in the biosynthesis of polyamines because of their well-known roles in plant growth, development and stress responses. RESULTS The transcriptomes and metabolomes of a control and a high putrescine (HP) producing cell line of poplar (Populus nigra x maximowiczii) were compared using microarrays and GC/MS. The HP cells expressed an ornithine decarboxylase transgene and accumulated several-fold higher concentrations of putrescine, with only small changes in spermidine and spermine. The results show that up-regulation of a single step in the polyamine biosynthetic pathway (i.e. ornithine → putrescine) altered the expression of a broad spectrum of genes; many of which were involved in transcription, translation, membrane transport, osmoregulation, shock/stress/wounding, and cell wall metabolism. More than half of the 200 detected metabolites were significantly altered (p ≤ 0.05) in the HP cells irrespective of sampling date. The most noteworthy differences were in organic acids, carbohydrates and nitrogen-containing metabolites. CONCLUSIONS The results provide valuable information about the role of polyamines in regulating nitrogen and carbon use pathways in cell cultures of high putrescine producing transgenic cells of poplar vs. their low putrescine counterparts. The results underscore the complexity of cellular responses to genetic perturbation of a single metabolic step related to nitrogen metabolism in plants. Combined with recent studies from our lab, where we showed that higher putrescine production caused an increased flux of glutamate into ornithine concurrent with enhancement in glutamate production via additional nitrogen and carbon assimilation, the results from this study provide guidance in designing transgenic plants with increased nitrogen use efficiency, especially in plants intended for non-food/feed applications (e.g. increased biomass production for biofuels).
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Affiliation(s)
- Andrew F Page
- Department of Biological Sciences, University of New Hampshire, Durham, NH, 03824, USA
| | - Leland J Cseke
- Department of Biological Sciences, University of Alabama in Huntsville, Huntsville, AL, 35899, USA
| | - Rakesh Minocha
- USDA Forest Service, Northern Research Station, Durham, NH, 03824, USA
| | - Swathi A Turlapati
- Department of Biological Sciences, University of New Hampshire, Durham, NH, 03824, USA
- USDA Forest Service, Northern Research Station, Durham, NH, 03824, USA
| | - Gopi K Podila
- Department of Biological Sciences, University of Alabama in Huntsville, Huntsville, AL, 35899, USA
| | - Alexander Ulanov
- Metabolomics Center, Roy J. Carver Biotechnology Center, University of Illinois at Urbana-Champaign, Champaign, IL, 61801, USA
| | - Zhong Li
- Metabolomics Center, Roy J. Carver Biotechnology Center, University of Illinois at Urbana-Champaign, Champaign, IL, 61801, USA
| | - Subhash C Minocha
- Department of Biological Sciences, University of New Hampshire, Durham, NH, 03824, USA.
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141
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Synthetic Evolution of Metabolic Productivity Using Biosensors. Trends Biotechnol 2016; 34:371-381. [DOI: 10.1016/j.tibtech.2016.02.002] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2015] [Revised: 02/01/2016] [Accepted: 02/01/2016] [Indexed: 11/23/2022]
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142
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Mehrotra P. Biosensors and their applications - A review. J Oral Biol Craniofac Res 2016; 6:153-9. [PMID: 27195214 PMCID: PMC4862100 DOI: 10.1016/j.jobcr.2015.12.002] [Citation(s) in RCA: 503] [Impact Index Per Article: 62.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Accepted: 12/05/2015] [Indexed: 10/22/2022] Open
Abstract
The various types of biosensors such as enzyme-based, tissue-based, immunosensors, DNA biosensors, thermal and piezoelectric biosensors have been deliberated here to highlight their indispensable applications in multitudinous fields. Some of the popular fields implementing the use of biosensors are food industry to keep a check on its quality and safety, to help distinguish between the natural and artificial; in the fermentation industry and in the saccharification process to detect precise glucose concentrations; in metabolic engineering to enable in vivo monitoring of cellular metabolism. Biosensors and their role in medical science including early stage detection of human interleukin-10 causing heart diseases, rapid detection of human papilloma virus, etc. are important aspects. Fluorescent biosensors play a vital role in drug discovery and in cancer. Biosensor applications are prevalent in the plant biology sector to find out the missing links required in metabolic processes. Other applications are involved in defence, clinical sector, and for marine applications.
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143
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Kim S, Bae SJ, Hahn JS. Redirection of pyruvate flux toward desired metabolic pathways through substrate channeling between pyruvate kinase and pyruvate-converting enzymes in Saccharomyces cerevisiae. Sci Rep 2016; 6:24145. [PMID: 27052099 PMCID: PMC4823786 DOI: 10.1038/srep24145] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Accepted: 03/21/2016] [Indexed: 11/08/2022] Open
Abstract
Spatial organization of metabolic enzymes allows substrate channeling, which accelerates processing of intermediates. Here, we investigated the effect of substrate channeling on the flux partitioning at a metabolic branch point, focusing on pyruvate metabolism in Saccharomyces cerevisiae. As a platform strain for the channeling of pyruvate flux, PYK1-Coh-Myc strain was constructed in which PYK1 gene encoding pyruvate kinase is tagged with cohesin domain. By using high-affinity cohesin-dockerin interaction, the pyruvate-forming enzyme Pyk1 was tethered to heterologous pyruvate-converting enzymes, lactate dehydrogenase and α-acetolactate synthase, to produce lactic acid and 2,3-butanediol, respectively. Pyruvate flux was successfully redirected toward desired pathways, with a concomitant decrease in ethanol production even without genetic attenuation of the ethanol-producing pathway. This pyruvate channeling strategy led to an improvement of 2,3-butanediol production by 38%, while showing a limitation in improving lactic acid production due to a reduced activity of lactate dehydrogenase by dockerin tagging.
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Affiliation(s)
- Sujin Kim
- School of Chemical and Biological Engineering, Seoul National University, Institute of Chemical Processes, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea
| | - Sang-Jeong Bae
- School of Chemical and Biological Engineering, Seoul National University, Institute of Chemical Processes, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea
| | - Ji-Sook Hahn
- School of Chemical and Biological Engineering, Seoul National University, Institute of Chemical Processes, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea
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144
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Xiao Y, Bowen CH, Liu D, Zhang F. Exploiting nongenetic cell-to-cell variation for enhanced biosynthesis. Nat Chem Biol 2016; 12:339-44. [DOI: 10.1038/nchembio.2046] [Citation(s) in RCA: 167] [Impact Index Per Article: 20.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Accepted: 01/11/2016] [Indexed: 12/18/2022]
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145
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Freedman BG, Zu TNK, Wallace RS, Senger RS. Raman spectroscopy detects phenotypic differences among
Escherichia coli
enriched for 1‐butanol tolerance using a metagenomic DNA library. Biotechnol J 2016; 11:877-89. [DOI: 10.1002/biot.201500144] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2015] [Revised: 10/22/2015] [Accepted: 01/26/2016] [Indexed: 11/11/2022]
Affiliation(s)
- Benjamin G. Freedman
- Department of Biological Systems Engineering; Virginia Tech Blacksburg Virginia USA
| | - Theresah N. K. Zu
- Department of Biological Systems Engineering; Virginia Tech Blacksburg Virginia USA
| | - Robert S. Wallace
- Department of Biological Systems Engineering; Virginia Tech Blacksburg Virginia USA
| | - Ryan S. Senger
- Department of Biological Systems Engineering; Virginia Tech Blacksburg Virginia USA
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146
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Lee MJ, Brown IR, Juodeikis R, Frank S, Warren MJ. Employing bacterial microcompartment technology to engineer a shell-free enzyme-aggregate for enhanced 1,2-propanediol production in Escherichia coli. Metab Eng 2016; 36:48-56. [PMID: 26969252 PMCID: PMC4909751 DOI: 10.1016/j.ymben.2016.02.007] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Revised: 02/05/2016] [Accepted: 02/22/2016] [Indexed: 01/01/2023]
Abstract
Bacterial microcompartments (BMCs) enhance the breakdown of metabolites such as 1,2-propanediol (1,2-PD) to propionic acid. The encapsulation of proteins within the BMC is mediated by the presence of targeting sequences. In an attempt to redesign the Pdu BMC into a 1,2-PD synthesising factory using glycerol as the starting material we added N-terminal targeting peptides to glycerol dehydrogenase, dihydroxyacetone kinase, methylglyoxal synthase and 1,2-propanediol oxidoreductase to allow their inclusion into an empty BMC. 1,2-PD producing strains containing the fused enzymes exhibit a 245% increase in product formation in comparison to un-tagged enzymes, irrespective of the presence of BMCs. Tagging of enzymes with targeting peptides results in the formation of dense protein aggregates within the cell that are shown by immuno-labelling to contain the vast majority of tagged proteins. It can therefore be concluded that these protein inclusions are metabolically active and facilitate the significant increase in product formation. Fusion of BMC targeting peptides to enzymes has a variable effect on activity. Tagged enzymes for 1,2-propanediol synthesis are localised to a BMC. BMC-targeted proteins localised within the BMC are protected from proteases. TEM reveals tagged enzymes form large intracellular protein aggregates. Strains with enzyme aggregates are shown to have enhanced 1,2-propanediol production.
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Affiliation(s)
- Matthew J Lee
- School of Biosciences, University of Kent, Giles Lane, Canterbury, Kent CT2 7NJ, UK
| | - Ian R Brown
- School of Biosciences, University of Kent, Giles Lane, Canterbury, Kent CT2 7NJ, UK
| | - Rokas Juodeikis
- School of Biosciences, University of Kent, Giles Lane, Canterbury, Kent CT2 7NJ, UK
| | - Stefanie Frank
- School of Biosciences, University of Kent, Giles Lane, Canterbury, Kent CT2 7NJ, UK.
| | - Martin J Warren
- School of Biosciences, University of Kent, Giles Lane, Canterbury, Kent CT2 7NJ, UK.
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147
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Overcoming heterologous protein interdependency to optimize P450-mediated Taxol precursor synthesis in Escherichia coli. Proc Natl Acad Sci U S A 2016; 113:3209-14. [PMID: 26951651 DOI: 10.1073/pnas.1515826113] [Citation(s) in RCA: 155] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Recent advances in metabolic engineering have demonstrated the potential to exploit biological chemistry for the synthesis of complex molecules. Much of the progress to date has leveraged increasingly precise genetic tools to control the transcription and translation of enzymes for superior biosynthetic pathway performance. However, applying these approaches and principles to the synthesis of more complex natural products will require a new set of tools for enabling various classes of metabolic chemistries (i.e., cyclization, oxygenation, glycosylation, and halogenation) in vivo. Of these diverse chemistries, oxygenation is one of the most challenging and pivotal for the synthesis of complex natural products. Here, using Taxol as a model system, we use nature's favored oxygenase, the cytochrome P450, to perform high-level oxygenation chemistry in Escherichia coli. An unexpected coupling of P450 expression and the expression of upstream pathway enzymes was discovered and identified as a key obstacle for functional oxidative chemistry. By optimizing P450 expression, reductase partner interactions, and N-terminal modifications, we achieved the highest reported titer of oxygenated taxanes (∼570 ± 45 mg/L) in E. coli. Altogether, this study establishes E. coli as a tractable host for P450 chemistry, highlights the potential magnitude of protein interdependency in the context of synthetic biology and metabolic engineering, and points to a promising future for the microbial synthesis of complex chemical entities.
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148
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Wu SG, Shimizu K, Tang JKH, Tang YJ. Facilitate Collaborations among Synthetic Biology, Metabolic Engineering and Machine Learning. CHEMBIOENG REVIEWS 2016. [DOI: 10.1002/cben.201500024] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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149
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Abstract
A central challenge in the field of metabolic engineering is the efficient identification of a metabolic pathway genotype that maximizes specific productivity over a robust range of process conditions. Here we review current methods for optimizing specific productivity of metabolic pathways in living cells. New tools for library generation, computational analysis of pathway sequence-flux space, and high-throughput screening and selection techniques are discussed.
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Affiliation(s)
- Justin R Klesmith
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Timothy A Whitehead
- Department of Chemical Engineering and Materials Science, Michigan State University, East Lansing, MI 48824, USA; Department of Biosystems and Agricultural Engineering, Michigan State University, East Lansing, MI 48824, USA
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150
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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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