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Wang CH, Hou J, Deng HK, Wang LJ. Microbial Production of Mevalonate. J Biotechnol 2023; 370:1-11. [PMID: 37209831 DOI: 10.1016/j.jbiotec.2023.05.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 04/20/2023] [Accepted: 05/17/2023] [Indexed: 05/22/2023]
Abstract
Mevalonate, an important intermediate product of the mevalonate pathway, has a broad spectrum of applications. With the rapid growth of metabolic engineering and synthetic biology, mevalonate biosynthesis by microorganisms is feasible and holds great promise in the future. In this review, we summarize the applications of mevalonate and its derivatives and describe the biosynthesis pathways of mevalonate. The current status of mevalonate biosynthesis is also detailed with an emphasis on metabolic engineering strategies to enhance mevalonate production in typical industrial organisms, including Escherichia coli, Saccharomyces cerevisiae, and Pseudomonas putida, suggesting new insights for the efficient production of biosynthesized mevalonate.
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Affiliation(s)
- Cong-Han Wang
- School of Life Sciences and Medicine, Shandong University of Technology, Zibo, China
| | - Jie Hou
- School of Life Sciences and Medicine, Shandong University of Technology, Zibo, China
| | - Hong-Kuan Deng
- School of Life Sciences and Medicine, Shandong University of Technology, Zibo, China.
| | - Li-Juan Wang
- School of Life Sciences and Medicine, Shandong University of Technology, Zibo, China; College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, China.
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2
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Wu W, Meador TB, Könneke M, Elvert M, Wegener G, Hinrichs KU. Substrate-dependent incorporation of carbon and hydrogen for lipid biosynthesis by Methanosarcina barkeri. ENVIRONMENTAL MICROBIOLOGY REPORTS 2020; 12:555-567. [PMID: 32783290 DOI: 10.1111/1758-2229.12876] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Revised: 07/23/2020] [Accepted: 08/07/2020] [Indexed: 06/11/2023]
Abstract
Dual stable isotope probing has been used to infer rates of microbial biomass production and modes of carbon fixation. In order to validate this approach for assessing archaeal production, the methanogenic archaeon Methanosarcina barkeri was grown either with H2 , acetate or methanol with D2 O and 13 C-dissolved inorganic carbon (DIC). Our results revealed unexpectedly low D incorporation into lipids, with the net fraction of water-derived hydrogen amounting to 0.357 ± 0.042, 0.226 ± 0.003 and 0.393 ± 0.029 for growth on H2 /CO2 , acetate and methanol respectively. The variability in net water H assimilation into lipids during the growth of M. barkeri on different substrates is possibly attributed to different Gibbs free energy yields, such that higher energy yield promoted the exchange of hydrogen between medium water and lipids. Because NADPH likely serves as the portal for H transfer, increased NADPH production and/or turnover associated with high energy yield may explain the apparent differences in net water H assimilation into lipids. The variable DIC and water H incorporation into M. barkeri lipids imply systematic, metabolic patterns of isotope incorporation and suggest that the ratio of 13 C-DIC versus D2 O assimilation in environmental samples may serve as a proxy for microbial energetics in addition to microbial production and carbon assimilation pathways.
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Affiliation(s)
- Weichao Wu
- Organic Geochemistry Group, MARUM-Centre for Marine Environmental Sciences and Department of Geosciences, University of Bremen, Bremen, 28359, Germany
| | - Travis B Meador
- Organic Geochemistry Group, MARUM-Centre for Marine Environmental Sciences and Department of Geosciences, University of Bremen, Bremen, 28359, Germany
- Biology Centre Czech Academy of Sciences, Soil and Water Research Infrastructure, Ceske Budejovice, CZ-37005, Czechia
- Faculty of Science, Department Ecosystem Biology, University of South Bohemia, Ceske Budejovice, CZ-37005, Czechia
| | - Martin Könneke
- Organic Geochemistry Group, MARUM-Centre for Marine Environmental Sciences and Department of Geosciences, University of Bremen, Bremen, 28359, Germany
| | - Marcus Elvert
- Organic Geochemistry Group, MARUM-Centre for Marine Environmental Sciences and Department of Geosciences, University of Bremen, Bremen, 28359, Germany
| | - Gunter Wegener
- Organic Geochemistry Group, MARUM-Centre for Marine Environmental Sciences and Department of Geosciences, University of Bremen, Bremen, 28359, Germany
- Max Planck Institute for Marine Microbiology, Bremen, 28359, Germany
| | - Kai-Uwe Hinrichs
- Organic Geochemistry Group, MARUM-Centre for Marine Environmental Sciences and Department of Geosciences, University of Bremen, Bremen, 28359, Germany
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Daletos G, Katsimpouras C, Stephanopoulos G. Novel Strategies and Platforms for Industrial Isoprenoid Engineering. Trends Biotechnol 2020; 38:811-822. [DOI: 10.1016/j.tibtech.2020.03.009] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 03/16/2020] [Accepted: 03/17/2020] [Indexed: 12/13/2022]
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Dudley QM, Karim AS, Nash CJ, Jewett MC. In vitro prototyping of limonene biosynthesis using cell-free protein synthesis. Metab Eng 2020; 61:251-260. [PMID: 32464283 DOI: 10.1016/j.ymben.2020.05.006] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 05/13/2020] [Accepted: 05/17/2020] [Indexed: 01/03/2023]
Abstract
Metabolic engineering of microorganisms to produce sustainable chemicals has emerged as an important part of the global bioeconomy. Unfortunately, efforts to design and engineer microbial cell factories are challenging because design-build-test cycles, iterations of re-engineering organisms to test and optimize new sets of enzymes, are slow. To alleviate this challenge, we demonstrate a cell-free approach termed in vitro Prototyping and Rapid Optimization of Biosynthetic Enzymes (or iPROBE). In iPROBE, a large number of pathway combinations can be rapidly built and optimized. The key idea is to use cell-free protein synthesis (CFPS) to manufacture pathway enzymes in separate reactions that are then mixed to modularly assemble multiple, distinct biosynthetic pathways. As a model, we apply our approach to the 9-step heterologous enzyme pathway to limonene in extracts from Escherichia coli. In iterative cycles of design, we studied the impact of 54 enzyme homologs, multiple enzyme levels, and cofactor concentrations on pathway performance. In total, we screened over 150 unique sets of enzymes in 580 unique pathway conditions to increase limonene production in 24 h from 0.2 to 4.5 mM (23-610 mg/L). Finally, to demonstrate the modularity of this pathway, we also synthesized the biofuel precursors pinene and bisabolene. We anticipate that iPROBE will accelerate design-build-test cycles for metabolic engineering, enabling data-driven multiplexed cell-free methods for testing large combinations of biosynthetic enzymes to inform cellular design.
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Affiliation(s)
- Quentin M Dudley
- Department of Chemical and Biological Engineering and Center for Synthetic Biology, Northwestern University, Evanston, IL, 60208, USA
| | - Ashty S Karim
- Department of Chemical and Biological Engineering and Center for Synthetic Biology, Northwestern University, Evanston, IL, 60208, USA
| | - Connor J Nash
- Department of Chemical and Biological Engineering and Center for Synthetic Biology, Northwestern University, Evanston, IL, 60208, USA
| | - Michael C Jewett
- Department of Chemical and Biological Engineering and Center for Synthetic Biology, Northwestern University, Evanston, IL, 60208, USA.
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Dudley QM, Nash CJ, Jewett MC. Cell-free biosynthesis of limonene using enzyme-enriched Escherichia coli lysates. Synth Biol (Oxf) 2019; 4:ysz003. [PMID: 30873438 PMCID: PMC6407499 DOI: 10.1093/synbio/ysz003] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 12/18/2018] [Accepted: 12/23/2018] [Indexed: 11/25/2022] Open
Abstract
Isoprenoids are an attractive class of metabolites for enzymatic synthesis from renewable substrates. However, metabolic engineering of microorganisms for monoterpenoid production is limited by the need for time-consuming, and often non-intuitive, combinatorial tuning of biosynthetic pathway variations to meet design criteria. Towards alleviating this limitation, the goal of this work was to build a modular, cell-free platform for construction and testing of monoterpenoid pathways, using the fragrance and flavoring molecule limonene as a model. In this platform, multiple Escherichia coli lysates, each enriched with a single overexpressed pathway enzyme, are mixed to construct the full biosynthetic pathway. First, we show the ability to synthesize limonene from six enriched lysates with mevalonate substrate, an adenosine triphosphate (ATP) source, and cofactors. Next, we extend the pathway to use glucose as a substrate, which relies on native metabolism in the extract to convert glucose to acetyl-CoA along with three additional enzymes to convert acetyl-CoA to mevalonate. We find that the native E. coli farnesyl diphosphate synthase (IspA) is active in the lysate and diverts flux from the pathway intermediate geranyl pyrophospahte to farnesyl pyrophsophate and the byproduct farnesol. By adjusting the relative levels of cofactors NAD+, ATP and CoA, the system can synthesize 0.66 mM (90.2 mg l-1) limonene over 24 h, a productivity of 3.8 mg l-1 h-1. Our results highlight the flexibility of crude lysates to sustain complex metabolism and, by activating a glucose-to-limonene pathway with 9 heterologous enzymes encompassing 20 biosynthetic steps, expands an approach of using enzyme-enriched lysates for constructing, characterizing and prototyping enzymatic pathways.
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Affiliation(s)
- Quentin M Dudley
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, USA
| | - Connor J Nash
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, USA
| | - Michael C Jewett
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, USA
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL, USA
- Center for Synthetic Biology, Northwestern University, Evanston, IL, USA
- Robert H. Lurie Comprehensive Cancer Center, Simpson Querrey Institute Northwestern University, Chicago, IL, USA
- Simpson Querrey Institute Northwestern University, Chicago, IL, USA
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Dirkmann M, Nowack J, Schulz F. An in Vitro Biosynthesis of Sesquiterpenes Starting from Acetic Acid. Chembiochem 2018; 19:2146-2151. [DOI: 10.1002/cbic.201800128] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Revised: 08/07/2018] [Indexed: 12/20/2022]
Affiliation(s)
- Michael Dirkmann
- Fakultät für Chemie und Biochemie; Organische Chemie I; Ruhr-Universität Bochum; Universitätsstrasse 150 44780 Bochum Germany
| | - Julia Nowack
- Fakultät für Chemie und Biochemie; Organische Chemie I; Ruhr-Universität Bochum; Universitätsstrasse 150 44780 Bochum Germany
| | - Frank Schulz
- Fakultät für Chemie und Biochemie; Organische Chemie I; Ruhr-Universität Bochum; Universitätsstrasse 150 44780 Bochum Germany
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Bu X, Sun L, Shang F, Yan G. Comparative metabolomics profiling of engineered Saccharomyces cerevisiae lead to a strategy that improving β-carotene production by acetate supplementation. PLoS One 2017; 12:e0188385. [PMID: 29161329 PMCID: PMC5697841 DOI: 10.1371/journal.pone.0188385] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Accepted: 11/06/2017] [Indexed: 12/14/2022] Open
Abstract
A comparative metabolomic analysis was conducted on recombinant Saccharomyces cerevisiae strain producing β-carotene and the parent strain cultivated with glucose as carbon source using gas chromatography-mass spectrometry (GC-MS), high performance liquid chromatography-mass spectrometry (HPLC-MS) and ultra-high performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS) based approach. The results showed that most of the central intermediates associated with amino acids, carbohydrates, glycolysis and TCA cycle intermediates (acetic acid, glycerol, citric acid, pyruvic acid and succinic acid), fatty acids, ergosterol and energy metabolites were produced in a lower amount in recombinant strain, as compared to the parent strain. To increase β-carotene production in recombinant strain, a strategy that exogenous addition of acetate (10 g/l) in exponential phase was developed, which could enhance most intracellular metabolites levels and result in 39.3% and 14.2% improvement of β-carotene concentration and production, respectively, which was accompanied by the enhancement of acetyl-CoA, fatty acids, ergosterol and ATP contents in cells. These results indicated that the amounts of intracellular metabolites in engineered strain are largely consumed by carotenoid formation. Therefore, maintaining intracellular metabolites pool at normal levels is essential for carotenoid biosynthesis. To relieve this limitation, rational supplementation of acetate could be a potential way because it can partially restore the levels of intracellular metabolites and improve the production of carotenoid compounds in recombinant S. cerevisiae.
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Affiliation(s)
- Xiao Bu
- Center for Viticulture and Enology, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, P.R., China
- Key Laboratory of Viticulture and Enology, Ministry of Agriculture, Beijing, P.R., China
| | - Liang Sun
- Center for Viticulture and Enology, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, P.R., China
- Key Laboratory of Viticulture and Enology, Ministry of Agriculture, Beijing, P.R., China
| | - Fei Shang
- Beijing Key Laboratory of Bioprocess, Beijing University of Chemical Technology, Beijing, P.R., China
| | - Guoliang Yan
- Center for Viticulture and Enology, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, P.R., China
- Key Laboratory of Viticulture and Enology, Ministry of Agriculture, Beijing, P.R., China
- * E-mail:
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Dudley QM, Anderson KC, Jewett MC. Cell-Free Mixing of Escherichia coli Crude Extracts to Prototype and Rationally Engineer High-Titer Mevalonate Synthesis. ACS Synth Biol 2016; 5:1578-1588. [PMID: 27476989 DOI: 10.1021/acssynbio.6b00154] [Citation(s) in RCA: 97] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Cell-free metabolic engineering (CFME) is advancing a powerful paradigm for accelerating the design and synthesis of biosynthetic pathways. However, as most cell-free biomolecule synthesis systems to date use purified enzymes, energy and cofactor balance can be limiting. To address this challenge, we report a new CFME framework for building biosynthetic pathways by mixing multiple crude lysates, or extracts. In our modular approach, cell-free lysates, each selectively enriched with an overexpressed enzyme, are generated in parallel and then combinatorically mixed to construct a full biosynthetic pathway. Endogenous enzymes in the cell-free extract fuel high-level energy and cofactor regeneration. As a model, we apply our framework to synthesize mevalonate, an intermediate in isoprenoid synthesis. We use our approach to rapidly screen enzyme variants, optimize enzyme ratios, and explore cofactor landscapes for improving pathway performance. Further, we show that genomic deletions in the source strain redirect metabolic flux in resultant lysates. In an optimized system, mevalonate was synthesized at 17.6 g·L-1 (119 mM) over 20 h, resulting in a volumetric productivity of 0.88 g·L-1·hr-1. We also demonstrate that this system can be lyophilized and retain biosynthesis capability. Our system catalyzes ∼1250 turnover events for the cofactor NAD+ and demonstrates the ability to rapidly prototype and debug enzymatic pathways in vitro for compelling metabolic engineering and synthetic biology applications.
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Affiliation(s)
- Quentin M. Dudley
- Department of Chemical and Biological
Engineering, ‡Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois 60208, United States
- Robert H. Lurie Comprehensive
Cancer Center, ∥Simpson Querrey Institute, Northwestern University, Chicago, Illinois 60611, United States
| | - Kim C. Anderson
- Department of Chemical and Biological
Engineering, ‡Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois 60208, United States
- Robert H. Lurie Comprehensive
Cancer Center, ∥Simpson Querrey Institute, Northwestern University, Chicago, Illinois 60611, United States
| | - Michael C. Jewett
- Department of Chemical and Biological
Engineering, ‡Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois 60208, United States
- Robert H. Lurie Comprehensive
Cancer Center, ∥Simpson Querrey Institute, Northwestern University, Chicago, Illinois 60611, United States
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Zhang YHP. Production of biofuels and biochemicals by in vitro synthetic biosystems: Opportunities and challenges. Biotechnol Adv 2015; 33:1467-83. [DOI: 10.1016/j.biotechadv.2014.10.009] [Citation(s) in RCA: 116] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2014] [Revised: 10/09/2014] [Accepted: 10/19/2014] [Indexed: 12/20/2022]
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