1
|
Dooley D, Ryu S, Giannone RJ, Edwards J, Dien BS, Slininger PJ, Trinh CT. Expanded genome and proteome reallocation in a novel, robust Bacillus coagulans strain capable of utilizing pentose and hexose sugars. mSystems 2024:e0095224. [PMID: 39377583 DOI: 10.1128/msystems.00952-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2024] [Accepted: 09/06/2024] [Indexed: 10/09/2024] Open
Abstract
Bacillus coagulans, a Gram-positive thermophilic bacterium, is recognized for its probiotic properties and recent development as a microbial cell factory. Despite its importance for biotechnological applications, the current understanding of B. coagulans' robustness is limited, especially for undomesticated strains. To fill this knowledge gap, we characterized the metabolic capability and performed functional genomics and systems analysis of a novel, robust strain, B. coagulans B-768. Genome sequencing revealed that B-768 has the largest B. coagulans genome known to date (3.94 Mbp), about 0.63 Mbp larger than the average genome of sequenced B. coagulans strains, with expanded carbohydrate metabolism and mobilome. Functional genomics identified a well-equipped genetic portfolio for utilizing a wide range of C5 (xylose, arabinose), C6 (glucose, mannose, galactose), and C12 (cellobiose) sugars present in biomass hydrolysates, which was validated experimentally. For growth on individual xylose and glucose, the dominant sugars in biomass hydrolysates, B-768 exhibited distinct phenotypes and proteome profiles. Faster growth and glucose uptake rates resulted in lactate overflow metabolism, which makes B. coagulans a lactate overproducer; however, slower growth and xylose uptake diminished overflow metabolism due to the high energy demand for sugar assimilation. Carbohydrate Transport and Metabolism (COG-G), Translation (COG-J), and Energy Conversion and Production (COG-C) made up 60%-65% of the measured proteomes but were allocated differently when growing on xylose and glucose. The trade-off in proteome reallocation, with high investment in COG-C over COG-G, explains the xylose growth phenotype with significant upregulation of xylose metabolism, pyruvate metabolism, and tricarboxylic acid (TCA) cycle. Strain B-768 tolerates and effectively utilizes inhibitory biomass hydrolysates containing mixed sugars and exhibits hierarchical sugar utilization with glucose as the preferential substrate.IMPORTANCEThe robustness of B. coagulans makes it a valuable microorganism for biotechnology applications; yet, this phenotype is not well understood at the cellular level. Through phenotypic characterization and systems analysis, this study elucidates the functional genomics and robustness of a novel, undomesticated strain, B. coagulans B-768, capable of utilizing inhibitory switchgrass biomass hydrolysates. The genome of B-768, enriched with carbohydrate metabolism genes, demonstrates high regulatory capacity. The coordination of proteome reallocation in Carbohydrate Transport and Metabolism (COG-G), Translation (COG-J), and Energy Conversion and Production (COG-C) is critical for effective cell growth, sugar utilization, and lactate production via overflow metabolism. Overall, B-768 is a novel, robust, and promising B. coagulans strain that can be harnessed as a microbial biomanufacturing platform to produce chemicals and fuels from biomass hydrolysates.
Collapse
Affiliation(s)
- David Dooley
- Department of Chemical and Biomolecular Engineering, University of Tennessee Knoxville, Knoxville, Tennessee, USA
| | - Seunghyun Ryu
- Department of Chemical and Biomolecular Engineering, University of Tennessee Knoxville, Knoxville, Tennessee, USA
- Center for Bioenergy Innovation, Oak Ridge, Tennessee, USA
| | - Richard J Giannone
- Center for Bioenergy Innovation, Oak Ridge, Tennessee, USA
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Jackson Edwards
- United States Department of Agriculture (USDA), Agricultural Research Service (ARS), National Center for Agricultural Utilization Research (NCAUR), Bioenergy Research Unit, Peoria, Illinois, USA
| | - Bruce S Dien
- United States Department of Agriculture (USDA), Agricultural Research Service (ARS), National Center for Agricultural Utilization Research (NCAUR), Bioenergy Research Unit, Peoria, Illinois, USA
| | - Patricia J Slininger
- United States Department of Agriculture (USDA), Agricultural Research Service (ARS), National Center for Agricultural Utilization Research (NCAUR), Bioenergy Research Unit, Peoria, Illinois, USA
| | - Cong T Trinh
- Department of Chemical and Biomolecular Engineering, University of Tennessee Knoxville, Knoxville, Tennessee, USA
- Center for Bioenergy Innovation, Oak Ridge, Tennessee, USA
| |
Collapse
|
2
|
Sen O, Hinks J, Lin Q, Lin Q, Kjelleberg S, Rice SA, Seviour T. Escherichia coli displays a conserved membrane proteomic response to a range of alcohols. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2023; 16:147. [PMID: 37789404 PMCID: PMC10546733 DOI: 10.1186/s13068-023-02401-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 09/18/2023] [Indexed: 10/05/2023]
Abstract
BACKGROUND Alcohol is a good and environment-friendly fuel that can be microbially produced, capable of eliminating many of the limitations of the present-day fossil fuels. However, the inherent toxic nature of alcohols to the microbial cells leads to end-product inhibition that limits large-scale alcohol production by fermentation. Fundamental knowledge about the stress responses of microorganisms to alcohols would greatly facilitate to improve the microbial alcohol tolerance. The current study elucidates and compares the changes in the membrane proteome of Escherichia coli in response to a range of alcohols. RESULTS Although alcohol toxicity increased exponentially with alcohol chain length (2-6 carbon), similar stress responses were observed in the inner and outer membrane proteome of E. coli in the presence of 2-, 4- and 6-carbon alcohols at the MIC50. This pertains to: (1) increased levels of inner membrane transporters for uptake of energy-producing metabolites, (2) reduced levels of non-essential proteins, associated with anaerobic, carbon starvation and osmotic stress, for energy conservation, (3) increased levels of murein degrading enzymes (MltA, EmtA, MliC and DigH) promoting cell elongation and 4) reduced levels of most outer membrane β-barrel proteins (LptD, FadL, LamB, TolC and BamA). Major outer membrane β-barrel protein OmpC, which is known to contribute to ethanol tolerance and membrane integrity, was notably reduced by alcohol stress. While LPS is important for OmpC trimerisation, LPS release by EDTA did not lower OmpC levels. This suggests that LPS release, which is reported under alcohol stress, does not contribute to the reduced levels of OmpC in the presence of alcohol. CONCLUSIONS Since alcohol primarily targets the integrity of the membrane, maintenance of outer membrane OmpC levels in the presence of alcohol might help in the survival of E. coli to higher alcohol concentrations. The study provides important information about the membrane protein responses of E. coli to a range of alcohols, which can be used to develop targeted strategies for increased microbial alcohol tolerance and hence bioalcohol production.
Collapse
Affiliation(s)
- Oishi Sen
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Jamie Hinks
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Qifeng Lin
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore, Singapore
| | - Qingsong Lin
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore, Singapore
| | - Staffan Kjelleberg
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
- School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, 2052, Australia
| | - Scott A Rice
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
- The Australian Institute for Microbiology and Immunology, University of Technology Sydney, Sydney, 2007, Australia
- CSIRO, Agriculture and Food, Westmead and Microbiomes for One Systems Health, Sydney, Australia
| | - Thomas Seviour
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore.
- WATEC Aarhus University Centre for Water Technology, Universitetsbyen 36, Bldg 1783, 8000, Aarhus, Denmark.
| |
Collapse
|
3
|
Bao W, Li X, Liu J, Zheng R, Liu L, Zhang H. The Characterization of an Efficient Phenylpyruvate Decarboxylase KDC4427, Involved in 2-Phenylethanol and IAA Production from Bacterial Enterobacter sp. CGMCC 5087. Microbiol Spectr 2022; 10:e0266021. [PMID: 35377224 PMCID: PMC9045302 DOI: 10.1128/spectrum.02660-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 02/10/2022] [Indexed: 11/20/2022] Open
Abstract
Phenylpyruvate decarboxylase (PPDC) is a crucial enzyme that plays important roles in 2-phenylethanol (2-PE) biosynthesis. In our previous study, we screened a highly efficient PPDC KDC4427 from the novel 2-PE-producing strain Enterobacter sp. CGMCC 5087. Meanwhile, its decarboxylation activity of indolylpyruvate (IPyA) was also higher than other indolylpyruvate decarboxylases (IPDCs) reported so far. In this study, KDC4427 protein was purified and characterized, and its catalytic mechanisms were analyzed by biological methods. The optimum pH and temperature of KDC4427 was pH 6.5 and 35°C, respectively. The enzyme activity was relatively stable between pH 6 and 8 and over the range of temperatures from 25°C to 45°C. KDC4427 showed the highest catalytic efficiency on phenylpyruvic acid (PPA); meanwhile, it also showed high activity for IPyA and 2-ketobutanoic acid, and it was found that KDC4427 belongs to IPDCs by phylogenetic tree analysis. The coverage of the three-dimensional structure of KDC4427 and EcIPDC from Enterobacter cloacae was 96%. Leucine 542, one of the residues in the substrate-binding pocket, is replaced by isoleucine in KDC4427 compared with EcIPDC. Site-directed mutagenesis showed that the transition from leucine to isoleucine was unlikely to make KDC4427 have high catalytic activity for PPA and IPyA; the mutants at glutamate 468 almost completely lost catalytic activities for both PPA and IPyA, indicating that this glutamate was essential for the catalytic activity. Additionally, alanine 387 plays an important role in the substrate selectivity of KDC4427. IMPORTANCE Compared with the chemical synthesis of 2-phenylethanol (2-PE) by condensation of ethylene oxide and benzene, the biological synthesis of 2-PE is a potential method to replace the traditional process. This makes biotransformation gradually become the main way to produce high-quality 2-PE. Phenylpyruvate decarboxylase (PPDC) is the critical enzyme in 2-PE biosynthesis, and it is a momentous point of penetration to increase the production of 2-PE. In this regard, KDC4427 can catalyze phenylpyruvic acid (PPA) to phenylacetaldehyde more efficiently than any other PPDC previously reported. Moreover, it has high activity of indolepyruvate decarboxylases (IPDCs), which will be a great breakthrough in the synthesis of indole-3-acetic acid (IAA). With this study, we offer insights into the KDC4427 catalytic mechanism and significantly expand the toolbox of available α-ketoacid decarboxylases for application in biosynthesis.
Collapse
Affiliation(s)
- Wenzhi Bao
- Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
- Shandong Energy Institute, Qingdao, China
| | - Xing Li
- Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
- Shandong Energy Institute, Qingdao, China
| | - Jinfeng Liu
- Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
| | - Rong Zheng
- College of Life Science and Technology, Inner Mongolia Normal University, Hohhot, China
| | - Lijuan Liu
- Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
- Shandong Energy Institute, Qingdao, China
| | - Haibo Zhang
- Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
- Shandong Energy Institute, Qingdao, China
| |
Collapse
|
4
|
Microbial pathways for advanced biofuel production. Biochem Soc Trans 2022; 50:987-1001. [PMID: 35411379 PMCID: PMC9162456 DOI: 10.1042/bst20210764] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 03/14/2022] [Accepted: 03/25/2022] [Indexed: 01/16/2023]
Abstract
Decarbonisation of the transport sector is essential to mitigate anthropogenic climate change. Microbial metabolisms are already integral to the production of renewable, sustainable fuels and, building on that foundation, are being re-engineered to generate the advanced biofuels that will maintain mobility of people and goods during the energy transition. This review surveys the range of natural and engineered microbial systems for advanced biofuels production and summarises some of the techno-economic challenges associated with their implementation at industrial scales.
Collapse
|
5
|
Hillman ET, Li M, Hooker CA, Englaender JA, Wheeldon I, Solomon KV. Hydrolysis of lignocellulose by anaerobic fungi produces free sugars and organic acids for two-stage fine chemical production with Kluyveromyces marxianus. Biotechnol Prog 2021; 37:e3172. [PMID: 33960738 DOI: 10.1002/btpr.3172] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 04/06/2021] [Accepted: 05/03/2021] [Indexed: 12/12/2022]
Abstract
Development of the bioeconomy is driven by our ability to access the energy-rich carbon trapped in recalcitrant plant materials. Current strategies to release this carbon rely on expensive enzyme cocktails and physicochemical pretreatment, producing inhibitory compounds that hinder subsequent microbial bioproduction. Anaerobic fungi are an appealing solution as they hydrolyze crude, untreated biomass at ambient conditions into sugars that can be converted into value-added products by partner organisms. However, some carbon is lost to anaerobic fungal fermentation products. To improve efficiency and recapture this lost carbon, we built a two-stage bioprocessing system pairing the anaerobic fungus Piromyces indianae with the yeast Kluyveromyces marxianus, which grows on a wide range of sugars and fermentation products. In doing so we produce fine and commodity chemicals directly from untreated lignocellulose. P. indianae efficiently hydrolyzed substrates such as corn stover and poplar to generate sugars, fermentation acids, and ethanol, which K. marxianus consumed while producing 2.4 g/L ethyl acetate. An engineered strain of K. marxianus was also able to produce 550 mg/L 2-phenylethanol and 150 mg/L isoamyl alcohol from P. indianae hydrolyzed lignocellulosic biomass. Despite the use of crude untreated plant material, production yields were comparable to optimized rich yeast media due to the use of all available carbon including organic acids, which formed up to 97% of free carbon in the fungal hydrolysate. This work demonstrates that anaerobic fungal pretreatment of lignocellulose can sustain the production of fine chemicals at high efficiency by partnering organisms with broad substrate versatility.
Collapse
Affiliation(s)
- Ethan T Hillman
- Department of Agricultural & Biological Engineering, Purdue University, West Lafayette, Indiana, USA.,Purdue University Interdisciplinary Life Sciences (PULSe) Program, Purdue University, West Lafayette, Indiana, USA
| | - Mengwan Li
- Department of Chemical & Environmental Engineering, University of California Riverside, Riverside, California, USA
| | - Casey A Hooker
- Department of Agricultural & Biological Engineering, Purdue University, West Lafayette, Indiana, USA.,Laboratory of Renewable Resources Engineering (LORRE), Purdue University, West Lafayette, Indiana, USA
| | - Jacob A Englaender
- Department of Agricultural & Biological Engineering, Purdue University, West Lafayette, Indiana, USA
| | - Ian Wheeldon
- Department of Chemical & Environmental Engineering, University of California Riverside, Riverside, California, USA
| | - Kevin V Solomon
- Department of Agricultural & Biological Engineering, Purdue University, West Lafayette, Indiana, USA.,Purdue University Interdisciplinary Life Sciences (PULSe) Program, Purdue University, West Lafayette, Indiana, USA.,Laboratory of Renewable Resources Engineering (LORRE), Purdue University, West Lafayette, Indiana, USA
| |
Collapse
|
6
|
Awad G, Garnier A. Maximization of saturated fatty acids through the production of P450BM3 monooxygenase in the engineered Escherichia coli. FOOD AND BIOPRODUCTS PROCESSING 2021. [DOI: 10.1016/j.fbp.2021.01.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
|
7
|
Li M, Lang X, Moran Cabrera M, De Keyser S, Sun X, Da Silva N, Wheeldon I. CRISPR-mediated multigene integration enables Shikimate pathway refactoring for enhanced 2-phenylethanol biosynthesis in Kluyveromyces marxianus. BIOTECHNOLOGY FOR BIOFUELS 2021; 14:3. [PMID: 33407831 PMCID: PMC7788952 DOI: 10.1186/s13068-020-01852-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 12/09/2020] [Indexed: 05/08/2023]
Abstract
BACKGROUND 2-phenylethanol (2-PE) is a rose-scented flavor and fragrance compound that is used in food, beverages, and personal care products. Compatibility with gasoline also makes it a potential biofuel or fuel additive. A biochemical process converting glucose or other fermentable sugars to 2-PE can potentially provide a more sustainable and economical production route than current methods that use chemical synthesis and/or isolation from plant material. RESULTS We work toward this goal by engineering the Shikimate and Ehrlich pathways in the stress-tolerant yeast Kluyveromyces marxianus. First, we develop a multigene integration tool that uses CRISPR-Cas9 induced breaks on the genome as a selection for the one-step integration of an insert that encodes one, two, or three gene expression cassettes. Integration of a 5-kbp insert containing three overexpression cassettes successfully occurs with an efficiency of 51 ± 9% at the ABZ1 locus and was used to create a library of K. marxianus CBS 6556 strains with refactored Shikimate pathway genes. The 33-factorial library includes all combinations of KmARO4, KmARO7, and KmPHA2, each driven by three different promoters that span a wide expression range. Analysis of the refactored pathway library reveals that high expression of the tyrosine-deregulated KmARO4K221L and native KmPHA2, with the medium expression of feedback insensitive KmARO7G141S, results in the highest increase in 2-PE biosynthesis, producing 684 ± 73 mg/L. Ehrlich pathway engineering by overexpression of KmARO10 and disruption of KmEAT1 further increases 2-PE production to 766 ± 6 mg/L. The best strain achieves 1943 ± 63 mg/L 2-PE after 120 h fed-batch operation in shake flask cultures. CONCLUSIONS The CRISPR-mediated multigene integration system expands the genome-editing toolset for K. marxianus, a promising multi-stress tolerant host for the biosynthesis of 2-PE and other aromatic compounds derived from the Shikimate pathway.
Collapse
Affiliation(s)
- Mengwan Li
- Department of Chemical and Environmental Engineering, University of California Riverside, Riverside, CA, 92521, USA
| | - Xuye Lang
- Department of Chemical and Environmental Engineering, University of California Riverside, Riverside, CA, 92521, USA
| | - Marcos Moran Cabrera
- Department of Chemical and Environmental Engineering, University of California Riverside, Riverside, CA, 92521, USA
| | - Sawyer De Keyser
- Department of Chemical and Environmental Engineering, University of California Riverside, Riverside, CA, 92521, USA
| | - Xiyan Sun
- Department of Chemical and Environmental Engineering, University of California Riverside, Riverside, CA, 92521, USA
| | - Nancy Da Silva
- Department of Chemical and Biomolecular Engineering, University of California Irvine, Irvine, CA, 92697, USA
| | - Ian Wheeldon
- Department of Chemical and Environmental Engineering, University of California Riverside, Riverside, CA, 92521, USA.
- Center for Industrial Biotechnology, University of California Riverside, Riverside, CA, 92527, USA.
| |
Collapse
|
8
|
Zhu Z, Jiang J, Fa Y. Overcoming the Biological Contamination in Microalgae and Cyanobacteria Mass Cultivations for Photosynthetic Biofuel Production. Molecules 2020; 25:molecules25225220. [PMID: 33182530 PMCID: PMC7698126 DOI: 10.3390/molecules25225220] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 11/06/2020] [Accepted: 11/09/2020] [Indexed: 02/08/2023] Open
Abstract
Microalgae and cyanobacteria have shown significant potential for the development of the next biofuels innovation because of their own characteristics as photosynthetic microorganisms. However, it is confronted with a lot of severe challenges on the economic scaling-up of the microalgae- and cyanobacteria-based biofuels production. One of these major challenges is the lack of a reliable preventing and controlling culture system of biological contamination, which can attack the cell growth or product accumulation causing crashing effects. To increase the commercial viability of microalgae- and cyanobacteria-based biofuels production, overcoming the biological contaminations should be at the top of the priority list. Here, we highlight the importance of two categories of biological contaminations and their controlling strategies in the mass cultivations of microalgae and cyanobacteria, and outline the directions that should be exploited in the future.
Collapse
Affiliation(s)
- Zhi Zhu
- The Key Laboratory of Biotechnology for Medicinal Plants of Jiangsu Province and School of Life Science, Jiangsu Normal University, Xuzhou 221116, China;
| | - Jihong Jiang
- The Key Laboratory of Biotechnology for Medicinal Plants of Jiangsu Province and School of Life Science, Jiangsu Normal University, Xuzhou 221116, China;
- Correspondence: (J.J.); (Y.F.)
| | - Yun Fa
- CAS Key Laboratory of Bio-Based Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Correspondence: (J.J.); (Y.F.)
| |
Collapse
|
9
|
Wang M, Luan G, Lu X. Engineering ethanol production in a marine cyanobacterium Synechococcus sp. PCC7002 through simultaneously removing glycogen synthesis genes and introducing ethanolgenic cassettes. J Biotechnol 2020; 317:1-4. [DOI: 10.1016/j.jbiotec.2020.04.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 03/31/2020] [Accepted: 04/06/2020] [Indexed: 10/24/2022]
|
10
|
Braga A, Faria N. Bioprocess Optimization for the Production of Aromatic Compounds With Metabolically Engineered Hosts: Recent Developments and Future Challenges. Front Bioeng Biotechnol 2020; 8:96. [PMID: 32154231 PMCID: PMC7044121 DOI: 10.3389/fbioe.2020.00096] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Accepted: 02/03/2020] [Indexed: 12/18/2022] Open
Abstract
The most common route to produce aromatic chemicals - organic compounds containing at least one benzene ring in their structure - is chemical synthesis. These processes, usually starting from an extracted fossil oil molecule such as benzene, toluene, or xylene, are highly environmentally unfriendly due to the use of non-renewable raw materials, high energy consumption and the usual production of toxic by-products. An alternative way to produce aromatic compounds is extraction from plants. These extractions typically have a low yield and a high purification cost. This motivates the search for alternative platforms to produce aromatic compounds through low-cost and environmentally friendly processes. Microorganisms are able to synthesize aromatic amino acids through the shikimate pathway. The construction of microbial cell factories able to produce the desired molecule from renewable feedstock becomes a promising alternative. This review article focuses on the recent advances in microbial production of aromatic products, with a special emphasis on metabolic engineering strategies, as well as bioprocess optimization. The recent combination of these two techniques has resulted in the development of several alternative processes to produce phenylpropanoids, aromatic alcohols, phenolic aldehydes, and others. Chemical species that were unavailable for human consumption due to the high cost and/or high environmental impact of their production, have now become accessible.
Collapse
Affiliation(s)
- Adelaide Braga
- Centre of Biological Engineering, University of Minho, Braga, Portugal
| | | |
Collapse
|
11
|
Kwak S, Yun EJ, Lane S, Oh EJ, Kim KH, Jin YS. Redirection of the Glycolytic Flux Enhances Isoprenoid Production in Saccharomyces cerevisiae. Biotechnol J 2019; 15:e1900173. [PMID: 31466140 DOI: 10.1002/biot.201900173] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Revised: 08/08/2019] [Indexed: 01/07/2023]
Abstract
Sufficient supply of reduced nicotinamide adenine dinucleotide phosphate (NADPH) is a prerequisite of the overproduction of isoprenoids and related bioproducts in Saccharomyces cerevisiae. Although S. cerevisiae highly depends on the oxidative pentose phosphate (PP) pathway to produce NADPH, its metabolic flux toward the oxidative PP pathway is limited due to the rigid glycolysis flux. To maximize NADPH supply for the isoprenoid production in yeast, upper glycolytic metabolic fluxes are reduced by introducing mutations into phosphofructokinase (PFK) along with overexpression of ZWF1 encoding glucose-6-phosphate (G6P) dehydrogenase. The PFK mutations (Pfk1 S724D and Pfk2 S718D) result in less glycerol production and more accumulation of G6P, which is a gateway metabolite toward the oxidative PP pathway. When combined with the PFK mutations, overexpression of ZWF1 caused substantial increases of [NADPH]/[NADP+ ] ratios whereas the effect of ZWF1 overexpression alone in the wild-type strain is not noticeable. Also, the introduction of ZWF1 overexpression and the PFK mutations into engineered yeast overexpressing acetyl-CoA C-acetyltransferase (ERG10), truncated HMG-CoA reductase isozyme 1 (tHMG1), and amorphadiene synthase (ADS) leads to a titer of 497 mg L-1 of amorphadiene (3.7-fold over the parental strain). These results suggest that perturbation of upper glycolytic fluxes, in addition to ZWF1 overexpression, is necessary for efficient NADPH supply through the oxidative PP pathway and enhanced production of isoprenoids by engineered S. cerevisiae.
Collapse
Affiliation(s)
- Suryang Kwak
- Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Eun Ju Yun
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.,Department of Biotechnology, Korea University, Seoul, 02841, Republic of Korea
| | - Stephan Lane
- Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Eun Joong Oh
- Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Kyoung Heon Kim
- Department of Biotechnology, Korea University, Seoul, 02841, Republic of Korea
| | - Yong-Su Jin
- Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| |
Collapse
|
12
|
Kim J, Cheong YE, Jung I, Kim KH. Metabolomic and Transcriptomic Analyses of Escherichia coli for Efficient Fermentation of L-Fucose. Mar Drugs 2019; 17:E82. [PMID: 30699916 PMCID: PMC6410053 DOI: 10.3390/md17020082] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2018] [Revised: 01/22/2019] [Accepted: 01/24/2019] [Indexed: 12/22/2022] Open
Abstract
L-Fucose, one of the major monomeric sugars in brown algae, possesses high potential for use in the large-scale production of bio-based products. Although fucose catabolic pathways have been enzymatically evaluated, the effects of fucose as a carbon source on intracellular metabolism in industrial microorganisms such as Escherichia coli are still not identified. To elucidate the effects of fucose on cellular metabolism and to find clues for efficient conversion of fucose into bio-based products, comparative metabolomic and transcriptomic analyses were performed on E. coli on L-fucose and on D-glucose as a control. When fucose was the carbon source for E. coli, integration of the two omics analyses revealed that excess gluconeogenesis and quorum sensing led to severe depletion of ATP, resulting in accumulation and export of fucose extracellularly. Therefore, metabolic engineering and optimization are needed for E. coil to more efficiently ferment fucose. This is the first multi-omics study investigating the effects of fucose on cellular metabolism in E. coli. These omics data and their biological interpretation could be used to assist metabolic engineering of E. coli producing bio-based products using fucose-containing brown macroalgae.
Collapse
Affiliation(s)
- Jungyeon Kim
- Department of Biotechnology, Graduate School, Korea University, Seoul 02841, Korea.
| | - Yu Eun Cheong
- Department of Biotechnology, Graduate School, Korea University, Seoul 02841, Korea.
| | - Inho Jung
- Department of Biotechnology, Graduate School, Korea University, Seoul 02841, Korea.
- Forest Product Analysis and Certification Division, Korea Forestry Promotion Institute, Seoul 07570, Korea.
| | - Kyoung Heon Kim
- Department of Biotechnology, Graduate School, Korea University, Seoul 02841, Korea.
| |
Collapse
|
13
|
Kumari P, Yusuf F, Gaur NA. Novel Microbial Modification Tools to Convert Lipids into Other Value-Added Products. Methods Mol Biol 2019; 1995:161-171. [PMID: 31148128 DOI: 10.1007/978-1-4939-9484-7_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
CRISPR-Cas9 Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) and CRISPR associated (Cas) is a microbial adaptive immune system that has revolutionized the field of molecular biology and genome engineering. The Type II CRISPR system consists of Cas9 nuclease of Streptococcus pyogenes and the RNA complex that guides Cas9 nuclease to a specific sequence of DNA in the genome. The CRISPR-Cas9 technology has reformed our ability to edit DNA and to regulate expression levels of genes of interest to high precision and accuracy. It is a powerful technology, which is used for genome engineering of a wide range of organisms for various applications. Here, we describe a method involving CRISPR-Cas9-mediated genome editing via nonhomologous end joining (NHEJ) or homology-directed repair (HDR) mechanisms for biotechnological applications in yeast. The complete procedure of genome editing including target sequence selection, cloning gRNA with a target sequence, transformation, and verification of the desired mutation/deletion or insertion can be achieved within 2-3 weeks in yeast.
Collapse
Affiliation(s)
- Priya Kumari
- Yeast Biofuel Group, DBT-ICGEB Centre for Advanced Bioenergy Research, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Farnaz Yusuf
- Yeast Biofuel Group, DBT-ICGEB Centre for Advanced Bioenergy Research, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Naseem A Gaur
- Yeast Biofuel Group, DBT-ICGEB Centre for Advanced Bioenergy Research, International Centre for Genetic Engineering and Biotechnology, New Delhi, India.
| |
Collapse
|
14
|
Erian AM, Gibisch M, Pflügl S. Engineered E. coli W enables efficient 2,3-butanediol production from glucose and sugar beet molasses using defined minimal medium as economic basis. Microb Cell Fact 2018; 17:190. [PMID: 30501633 PMCID: PMC6267845 DOI: 10.1186/s12934-018-1038-0] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Accepted: 11/23/2018] [Indexed: 12/03/2022] Open
Abstract
Background Efficient microbial production of chemicals is often hindered by the cytotoxicity of the products or by the pathogenicity of the host strains. Hence 2,3-butanediol, an important drop-in chemical, is an interesting alternative target molecule for microbial synthesis since it is non-cytotoxic. Metabolic engineering of non-pathogenic and industrially relevant microorganisms, such as Escherichia coli, have already yielded in promising 2,3-butanediol titers showing the potential of microbial synthesis of 2,3-butanediol. However, current microbial 2,3-butanediol production processes often rely on yeast extract as expensive additive, rendering these processes infeasible for industrial production. Results The aim of this study was to develop an efficient 2,3-butanediol production process with E. coli operating on the premise of using cost-effective medium without complex supplements, considering second generation feedstocks. Different gene donors and promoter fine-tuning allowed for construction of a potent E. coli strain for the production of 2,3-butanediol as important drop-in chemical. Pulsed fed-batch cultivations of E. coli W using microaerobic conditions showed high diol productivity of 4.5 g l−1 h−1. Optimizing oxygen supply and elimination of acetoin and by-product formation improved the 2,3-butanediol titer to 68 g l−1, 76% of the theoretical maximum yield, however, at the expense of productivity. Sugar beet molasses was tested as a potential substrate for industrial production of chemicals. Pulsed fed-batch cultivations produced 56 g l−1 2,3-butanediol, underlining the great potential of E. coli W as production organism for high value-added chemicals. Conclusion A potent 2,3-butanediol producing E. coli strain was generated by considering promoter fine-tuning to balance cell fitness and production capacity. For the first time, 2,3-butanediol production was achieved with promising titer, rate and yield and no acetoin formation from glucose in pulsed fed-batch cultivations using chemically defined medium without complex hydrolysates. Furthermore, versatility of E. coli W as production host was demonstrated by efficiently converting sucrose from sugar beet molasses into 2,3-butanediol. Electronic supplementary material The online version of this article (10.1186/s12934-018-1038-0) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Anna Maria Erian
- Institute for Chemical, Environmental and Bioscience Engineering, Research Area Biochemical Engineering, Technische Universität Wien, Gumpendorfer Straße 1a, 1060, Vienna, Austria
| | - Martin Gibisch
- Institute for Chemical, Environmental and Bioscience Engineering, Research Area Biochemical Engineering, Technische Universität Wien, Gumpendorfer Straße 1a, 1060, Vienna, Austria
| | - Stefan Pflügl
- Institute for Chemical, Environmental and Bioscience Engineering, Research Area Biochemical Engineering, Technische Universität Wien, Gumpendorfer Straße 1a, 1060, Vienna, Austria.
| |
Collapse
|
15
|
Horinouchi T, Maeda T, Furusawa C. Understanding and engineering alcohol-tolerant bacteria using OMICS technology. World J Microbiol Biotechnol 2018; 34:157. [PMID: 30341456 PMCID: PMC6208762 DOI: 10.1007/s11274-018-2542-4] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Accepted: 10/13/2018] [Indexed: 12/16/2022]
Abstract
Microbes are capable of producing alcohols, making them an important source of alternative energy that can replace fossil fuels. However, these alcohols can be toxic to the microbes themselves, retaring or inhibiting cell growth and decreasing the production yield. One solution is improving the alcohol tolerance of such alcohol-producing organisms. Advances in omics technologies, including transcriptomic, proteomic, metabolomic, and genomic technologies, have helped us understand the complex mechanisms underlying alcohol toxicity, and such advances could assist in devising strategies for engineering alcohol-tolerant strains. This review highlights these advances and discusses strategies for improving alcohol tolerance using omics analyses.
Collapse
Affiliation(s)
- Takaaki Horinouchi
- Center for Biosystems Dynamics Research (BDR), RIKEN, 6-2-3 Furuedai, Suita, Osaka, 565-0874, Japan.
| | - Tomoya Maeda
- Center for Biosystems Dynamics Research (BDR), RIKEN, 6-2-3 Furuedai, Suita, Osaka, 565-0874, Japan
| | - Chikara Furusawa
- Center for Biosystems Dynamics Research (BDR), RIKEN, 6-2-3 Furuedai, Suita, Osaka, 565-0874, Japan.
- Universal Biology Institute, The University of Tokyo, 7-3-1 Hongo, Tokyo, 113-0033, Japan.
| |
Collapse
|
16
|
Otten A, Wooten M, Medrano A, Fathi Y, Meloni G. Investigation of Oxidation Reaction Products of 2-Phenylethanol Using Synchrotron Photoionization. J Phys Chem A 2018; 122:6789-6798. [PMID: 30044638 DOI: 10.1021/acs.jpca.8b03985] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A photolytically Cl-initiated oxidation reaction of 2-phenylethanol (2PE) was carried out at the Advanced Light Source (ALS) in the Lawrence Berkeley National Laboratory. Using the multiplex photoionization mass spectrometer, coupled with the tunable vacuum ultraviolet radiation of the ALS, data were collected at low pressure (4-6 Torr) and temperature (298-550 K) regimes. Data analysis was performed via characterization of the reaction species photoionization spectra and kinetic traces. Products and reaction pathways are also computed using the CBS-QB3 composite method. The present results suggest primary products m/ z = 30 (formaldehyde), 106 (benzaldehyde), and 120 (phenylacetaldehyde) at 298 K, and m/ z = 120 (phenylacetaldehyde) at 550 K. Branching fractions at room temperature are 27 ± 6.5% for formaldehyde, 24 ± 4.5% for benzaldehyde, and 25 ± 5.8% for phenylacetaldehyde and 60 ± 14% for phenylacetaldehyde at 550 K.
Collapse
Affiliation(s)
- Adam Otten
- Department of Chemistry , University of San Francisco , San Francisco , California 94117 , United States
| | - Magaly Wooten
- Department of Chemistry , University of San Francisco , San Francisco , California 94117 , United States
| | - Anthony Medrano
- Department of Chemistry , University of San Francisco , San Francisco , California 94117 , United States
| | - Yasmin Fathi
- Department of Chemistry , University of San Francisco , San Francisco , California 94117 , United States
| | - Giovanni Meloni
- Department of Physical and Chemical Sciences , University of L'Aquila , L'Aquila 67100 , Italy
| |
Collapse
|
17
|
Liu C, Zhang K, Cao W, Zhang G, Chen G, Yang H, Wang Q, Liu H, Xian M, Zhang H. Genome mining of 2-phenylethanol biosynthetic genes from Enterobacter sp. CGMCC 5087 and heterologous overproduction in Escherichia coli. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:305. [PMID: 30455734 PMCID: PMC6223000 DOI: 10.1186/s13068-018-1297-3] [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: 08/09/2018] [Accepted: 10/22/2018] [Indexed: 05/22/2023]
Abstract
BACKGROUND 2-Phenylethanol (2-PE) is a higher aromatic alcohol that is widely used in the perfumery, cosmetics, and food industries and is also a potentially valuable next-generation biofuel. In our previous study, a new strain Enterobacter sp. CGMCC 5087 was isolated to produce 2-PE from glucose through the phenylpyruvate pathway. RESULTS In this study, candidate genes for 2-PE biosynthesis were identified from Enterobacter sp. CGMCC 5087 by draft whole-genome sequence, metabolic engineering, and shake flask fermentation. Subsequently, the identified genes encoding the 2-keto acid decarboxylase (Kdc) and alcohol dehydrogenase (Adh) enzymes from Enterobacter sp. CGMCC 5087 were introduced into E. coli BL21(DE3) to construct a high-efficiency microbial cell factory for 2-PE production using the prokaryotic phenylpyruvate pathway. The enzymes Kdc4427 and Adh4428 from Enterobacter sp. CGMCC 5087 showed higher performances than did the corresponding enzymes ARO10 and ADH2 from Saccharomyces cerevisiae, respectively. The E. coli cell factory was further improved by overexpressing two upstream shikimate pathway genes, aroF/aroG/aroH and pheA, to enhance the metabolic flux of the phenylpyruvate pathway, which resulted in 2-PE production of 260 mg/L. The combined overexpression of tktA and ppsA increased the precursor supply of erythrose-4-phosphate and phosphoenolpyruvate, which resulted in 2-PE production of 320 mg/L, with a productivity of 13.3 mg/L/h. CONCLUSIONS The present study achieved the highest titer of de novo 2-PE production of in a recombinant E. coli system. This study describes a new, efficient 2-PE producer that lays foundation for the industrial-scale production of 2-PE and its derivatives in the future.
Collapse
Affiliation(s)
- Changqing Liu
- CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No.189 Songling Road, Laoshan District, Qingdao, 266101 China
- University of Chinese Academy of Sciences, Beijing, China
| | - Kai Zhang
- CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No.189 Songling Road, Laoshan District, Qingdao, 266101 China
- University of Chinese Academy of Sciences, Beijing, China
| | - Wenyan Cao
- CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No.189 Songling Road, Laoshan District, Qingdao, 266101 China
- University of Chinese Academy of Sciences, Beijing, China
| | - Ge Zhang
- CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No.189 Songling Road, Laoshan District, Qingdao, 266101 China
- University of Chinese Academy of Sciences, Beijing, China
- Key Laboratory for Tobacco Gene Resources’ Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, 266101 People’s Republic of China
| | - Guoqiang Chen
- CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No.189 Songling Road, Laoshan District, Qingdao, 266101 China
- University of Chinese Academy of Sciences, Beijing, China
- Key Laboratory for Tobacco Gene Resources’ Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, 266101 People’s Republic of China
| | - Haiyan Yang
- CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No.189 Songling Road, Laoshan District, Qingdao, 266101 China
- University of Chinese Academy of Sciences, Beijing, China
| | - Qian Wang
- Key Laboratory for Tobacco Gene Resources’ Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, 266101 People’s Republic of China
| | - Haobao Liu
- Key Laboratory for Tobacco Gene Resources’ Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, 266101 People’s Republic of China
| | - Mo Xian
- CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No.189 Songling Road, Laoshan District, Qingdao, 266101 China
- University of Chinese Academy of Sciences, Beijing, China
| | - Haibo Zhang
- CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No.189 Songling Road, Laoshan District, Qingdao, 266101 China
- University of Chinese Academy of Sciences, Beijing, China
| |
Collapse
|
18
|
Zhu L, Zheng H, Hu X, Xu Y. A computational method using differential gene expression to predict altered metabolism of multicellular organisms. MOLECULAR BIOSYSTEMS 2017; 13:2418-2427. [PMID: 28972214 DOI: 10.1039/c7mb00462a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Altered metabolism is often identified as a cause or an effect of physiology and pathogenesis. But it is difficult to predict the metabolic flux distributions of multicellular organisms due to the lack of an explicit metabolic objective function. Here we present a computational method which can successfully describe the differences in metabolism between two different conditions on a large scale. By integrating gene expression data with an existing comprehensive reconstruction of the global human metabolic network, we qualitatively predicted significantly differential fluxes without prior knowledge or the rate of metabolite uptake and secretion. Therefore, this method can be applied for both microorganisms and multicellular organisms. Different from traditional enrichment analysis methods and constraint-based models, we consider conditions and interactions within the metabolic network simultaneously. To apply the proposed method, we predicted altered fluxes for E. coli strains and clear cell renal cell carcinoma, while the E. coli strains are growing aerobically in a chemostat with different dilution rates and clear cell renal cell carcinoma is compared with normal kidney cells. Then we map the significantly differential reactions to metabolic subsystems defined in the original metabolic network for ccRCC to observe the altered metabolism. In contrast with existing studies, our results show a high accuracy of the E. coli experiment and a more reasonable prediction of the ccRCC experiment. The method presented here provides a computational approach for the genome-wide study of altered metabolism under pairs of conditions for both microorganisms and multicellular organisms.
Collapse
Affiliation(s)
- Lvxing Zhu
- School of Computer Science and Technology, University of Science and Technology of China, Hefei, People's Republic of China
| | | | | | | |
Collapse
|
19
|
Ye W, Li J, Han R, Xu G, Dong J, Ni Y. Engineering coenzyme A-dependent pathway from Clostridium saccharobutylicum in Escherichia coli for butanol production. BIORESOURCE TECHNOLOGY 2017; 235:140-148. [PMID: 28365341 DOI: 10.1016/j.biortech.2017.03.085] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Revised: 03/13/2017] [Accepted: 03/14/2017] [Indexed: 06/07/2023]
Abstract
Clostridium saccharobutylicum has been proved to be efficient in butanol fermentation from various feedstocks. Whereas, lack of genetic manipulation system has severely hindered the engineering of C. saccharobutylicum for more extensive applications. In this study, recombinant Escherichia coli harboring heterologous coenzyme A-dependent pathway from C. saccharobutylicum DSM 13864 was constructed, which consisted of solventogenic pathway genes: acetoacetyl-CoA thiolase (thlA), aldehyde/alcohol dehydrogenase (adhE2) and bcs-operon (crt-bcd1-etfB2-fixB2-hbd). Then, a butanol titer of 67mg/L was attained. After replacing thlA with acetyl-CoA acetyltransferase (atoB) from E. coli and deleting the competitive branch genes lactate dehydrogenase (ldhA), aldehyde/alcohol dehydrogenase (adhE1) and fumarate reductase (frdBC), the butanol titer was successfully improved for 3.8-fold (254mg/L). Under the optimum fermentation conditions, the final butanol titer reached 584mg/L after 120h. This result demonstrates the feasibility of adapting CoA-dependent solventogenic pathway from C. saccharobutylicum in E. coli for butanol synthesis.
Collapse
Affiliation(s)
- Weihua Ye
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China; Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Jin Li
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China; Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Ruizhi Han
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China; Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Guochao Xu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China; Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Jinjun Dong
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China; Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Ye Ni
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China; Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China.
| |
Collapse
|
20
|
Horinouchi T, Sakai A, Kotani H, Tanabe K, Furusawa C. Improvement of isopropanol tolerance of Escherichia coli using adaptive laboratory evolution and omics technologies. J Biotechnol 2017. [PMID: 28645581 DOI: 10.1016/j.jbiotec.2017.06.408] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Isopropanol (IPA) is the secondary alcohol that can be dehydrated to yield propylene. To produce IPA using microorganisms, a significant issue is that the toxicity of IPA causes retardation or inhibition of cell growth, decreasing the yield. One possible strategy to overcome this problem is to improve IPA tolerance of production organisms. For the understanding of tolerance to IPA, we performed parallel adaptive laboratory evolution (ALE) of Escherichia coli under IPA stress. To identify the genotypic change during ALE, we performed genome re-sequencing analyses of obtained tolerant strains. To verify which mutations were contributed to IPA tolerance, we constructed the mutant strains and quantify the IPA tolerance of the constructed mutants. From these analyses, we found that five mutations (relA, marC, proQ, yfgO, and rraA) provided the increase of IPA tolerance. To understand the phenotypic change during ALE, we performed transcriptome analysis of tolerant strains. From transcriptome analysis, we found that expression levels of genes related to biosynthetic pathways of amino acids, iron ion homeostasis, and energy metabolisms were changed in the tolerant strains. Results from these experiments provide fundamental bases for designing IPA tolerant strains for industrial purposes.
Collapse
Affiliation(s)
- Takaaki Horinouchi
- Quantitative Biology Center, RIKEN, 6-2-3 Furuedai, Suita, Osaka 565-0874, Japan.
| | - Aki Sakai
- Quantitative Biology Center, RIKEN, 6-2-3 Furuedai, Suita, Osaka 565-0874, Japan
| | - Hazuki Kotani
- Quantitative Biology Center, RIKEN, 6-2-3 Furuedai, Suita, Osaka 565-0874, Japan
| | - Kumi Tanabe
- Quantitative Biology Center, RIKEN, 6-2-3 Furuedai, Suita, Osaka 565-0874, Japan
| | - Chikara Furusawa
- Quantitative Biology Center, RIKEN, 6-2-3 Furuedai, Suita, Osaka 565-0874, Japan; Universal Biology Institute, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
| |
Collapse
|
21
|
Wang C, Pfleger BF, Kim SW. Reassessing Escherichia coli as a cell factory for biofuel production. Curr Opin Biotechnol 2017; 45:92-103. [DOI: 10.1016/j.copbio.2017.02.010] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Revised: 02/05/2017] [Accepted: 02/09/2017] [Indexed: 11/29/2022]
|
22
|
Zhu Z, Luan G, Tan X, Zhang H, Lu X. Rescuing ethanol photosynthetic production of cyanobacteria in non-sterilized outdoor cultivations with a bicarbonate-based pH-rising strategy. BIOTECHNOLOGY FOR BIOFUELS 2017; 10:93. [PMID: 28416967 PMCID: PMC5391583 DOI: 10.1186/s13068-017-0765-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Accepted: 03/18/2017] [Indexed: 06/07/2023]
Abstract
BACKGROUND Ethanol photosynthetic production based on cyanobacteria cell factories utilizing CO2 and solar energy provides an attractive solution for sustainable production of green fuels. However, the scaling up processes of cyanobacteria cell factories were usually threatened or even devastated by biocontaminations, which restricted biomass or products accumulations of cyanobacteria cells. Thus it is of great significance to develop reliable biocontamination-controlling strategies for promoting ethanol photosynthetic production in large scales. RESULTS The scaling up process of a previously developed Synechocystis strain Syn-HZ24 for ethanol synthesis was severely inhibited and devastated by a specific contaminant, Pannonibacter phragmitetus, which overcame the growths of cyanobacteria cells and completely consumed the ethanol accumulation in the cultivation systems. Physiological analysis revealed that growths and ethanol-consuming activities of the contaminant were sensitive to alkaline conditions, while ethanol-synthesizing cyanobacteria strain Syn-HZ24 could tolerate alkaline pH conditions as high as 11.0, indicating that pH-increasing strategy might be a feasible approach for rescuing ethanol photosynthetic production in outdoor cultivation systems. Thus, we designed and evaluated a Bicarbonate-based Integrated Carbon Capture System (BICCS) derived pH-rising strategy to rescue the ethanol photosynthetic production in non-sterilized conditions. In lab scale artificially simulated systems, pH values of BG11 culture medium were maintained around 11.0 by 180 mM NaHCO3 and air steam, under which the infection of Pannonibacter phragmitetus was significantly restricted, recovering ethanol production of Syn-HZ24 by about 80%. As for outdoor cultivations, ethanol photosynthetic production of Syn-HZ24 was also successfully rescued by the BICCS-derived pH-rising strategy, obtaining a final ethanol concentration of 0.9 g/L after 10 days cultivation. CONCLUSIONS In this work, a novel product-consuming biocontamination pattern in cyanobacteria cultivations, causing devastated ethanol photosynthetic production, was identified and characterized. Physiological analysis of the essential ethanol-consuming contaminant directed the design and application of a pH-rising strategy, which effectively and selectively controlled the contamination and rescued ethanol photosynthetic production. Our work demonstrated the importance of reliable contamination control systems and strategies for large scale outdoor cultivations of cyanobacteria, and provided an inspiring paradigm for targeting effective solutions.
Collapse
Affiliation(s)
- Zhi Zhu
- Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Qingdao, 266101 China
- Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Qingdao, 266101 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Guodong Luan
- Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Qingdao, 266101 China
- Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Qingdao, 266101 China
| | - Xiaoming Tan
- Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Qingdao, 266101 China
- Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Qingdao, 266101 China
| | - Haocui Zhang
- Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Qingdao, 266101 China
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072 China
| | - Xuefeng Lu
- Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Qingdao, 266101 China
- Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Qingdao, 266101 China
| |
Collapse
|
23
|
Xiong D, Lu S, Wu J, Liang C, Wang W, Wang W, Jin JM, Tang SY. Improving key enzyme activity in phenylpropanoid pathway with a designed biosensor. Metab Eng 2017; 40:115-123. [DOI: 10.1016/j.ymben.2017.01.006] [Citation(s) in RCA: 76] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Revised: 12/09/2016] [Accepted: 01/18/2017] [Indexed: 01/02/2023]
|
24
|
Ghosh A, Ando D, Gin J, Runguphan W, Denby C, Wang G, Baidoo EEK, Shymansky C, Keasling JD, García Martín H. 13C Metabolic Flux Analysis for Systematic Metabolic Engineering of S. cerevisiae for Overproduction of Fatty Acids. Front Bioeng Biotechnol 2016; 4:76. [PMID: 27761435 PMCID: PMC5050205 DOI: 10.3389/fbioe.2016.00076] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Accepted: 09/20/2016] [Indexed: 11/24/2022] Open
Abstract
Efficient redirection of microbial metabolism into the abundant production of desired bioproducts remains non-trivial. Here, we used flux-based modeling approaches to improve yields of fatty acids in Saccharomyces cerevisiae. We combined 13C labeling data with comprehensive genome-scale models to shed light onto microbial metabolism and improve metabolic engineering efforts. We concentrated on studying the balance of acetyl-CoA, a precursor metabolite for the biosynthesis of fatty acids. A genome-wide acetyl-CoA balance study showed ATP citrate lyase from Yarrowia lipolytica as a robust source of cytoplasmic acetyl-CoA and malate synthase as a desirable target for downregulation in terms of acetyl-CoA consumption. These genetic modifications were applied to S. cerevisiae WRY2, a strain that is capable of producing 460 mg/L of free fatty acids. With the addition of ATP citrate lyase and downregulation of malate synthase, the engineered strain produced 26% more free fatty acids. Further increases in free fatty acid production of 33% were obtained by knocking out the cytoplasmic glycerol-3-phosphate dehydrogenase, which flux analysis had shown was competing for carbon flux upstream with the carbon flux through the acetyl-CoA production pathway in the cytoplasm. In total, the genetic interventions applied in this work increased fatty acid production by ~70%.
Collapse
Affiliation(s)
- Amit Ghosh
- Lawrence Berkeley National Laboratory, Biological Systems and Engineering Division, Berkeley, CA, USA; Joint BioEnergy Institute, Emeryville, CA, USA; Indian Institute of Technology (IIT), School of Energy Science and Engineering, Kharagpur, India
| | - David Ando
- Lawrence Berkeley National Laboratory, Biological Systems and Engineering Division, Berkeley, CA, USA; Joint BioEnergy Institute, Emeryville, CA, USA
| | - Jennifer Gin
- Lawrence Berkeley National Laboratory, Biological Systems and Engineering Division, Berkeley, CA, USA; Joint BioEnergy Institute, Emeryville, CA, USA
| | - Weerawat Runguphan
- Lawrence Berkeley National Laboratory, Biological Systems and Engineering Division, Berkeley, CA, USA; Joint BioEnergy Institute, Emeryville, CA, USA; National Center for Genetic Engineering and Biotechnology (BIOTEC), Pathum Thani, Thailand
| | - Charles Denby
- Lawrence Berkeley National Laboratory, Biological Systems and Engineering Division, Berkeley, CA, USA; Joint BioEnergy Institute, Emeryville, CA, USA
| | - George Wang
- Lawrence Berkeley National Laboratory, Biological Systems and Engineering Division, Berkeley, CA, USA; Joint BioEnergy Institute, Emeryville, CA, USA
| | - Edward E K Baidoo
- Lawrence Berkeley National Laboratory, Biological Systems and Engineering Division, Berkeley, CA, USA; Joint BioEnergy Institute, Emeryville, CA, USA
| | - Chris Shymansky
- Lawrence Berkeley National Laboratory, Biological Systems and Engineering Division, Berkeley, CA, USA; Joint BioEnergy Institute, Emeryville, CA, USA; Department of Chemical and Biomolecular Engineering, University of California Berkeley, Berkeley, CA, USA
| | - Jay D Keasling
- Lawrence Berkeley National Laboratory, Biological Systems and Engineering Division, Berkeley, CA, USA; Joint BioEnergy Institute, Emeryville, CA, USA; Department of Chemical and Biomolecular Engineering, University of California Berkeley, Berkeley, CA, USA; Department of Bioengineering, University of California Berkeley, Berkeley, CA, USA; Novo Nordisk Foundation Center for Biosustainability, Technical University Denmark, Horsholm, Denmark
| | - Héctor García Martín
- Lawrence Berkeley National Laboratory, Biological Systems and Engineering Division, Berkeley, CA, USA; Joint BioEnergy Institute, Emeryville, CA, USA
| |
Collapse
|
25
|
Koppolu V, Vasigala VK. Role of Escherichia coli in Biofuel Production. Microbiol Insights 2016; 9:29-35. [PMID: 27441002 PMCID: PMC4946582 DOI: 10.4137/mbi.s10878] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Revised: 06/26/2016] [Accepted: 06/28/2016] [Indexed: 12/19/2022] Open
Abstract
Increased energy consumption coupled with depleting petroleum reserves and increased greenhouse gas emissions have renewed our interest in generating fuels from renewable energy sources via microbial fermentation. Central to this problem is the choice of microorganism that catalyzes the production of fuels at high volumetric productivity and yield from cheap and abundantly available renewable energy sources. Microorganisms that are metabolically engineered to redirect renewable carbon sources into desired fuel products are contemplated as best choices to obtain high volumetric productivity and yield. Considering the availability of vast knowledge in genomic and metabolic fronts, Escherichia coli is regarded as a primary choice for the production of biofuels. Here, we reviewed the microbial production of liquid biofuels that have the potential to be used either alone or in combination with the present-day fuels. We specifically highlighted the metabolic engineering and synthetic biology approaches used to improve the production of biofuels from E. coli over the past few years. We also discussed the challenges that still exist for the biofuel production from E. coli and their possible solutions.
Collapse
Affiliation(s)
- Veerendra Koppolu
- Scientist, Department of Analytical Biotechnology, MedImmune/AstraZeneca, Gaithersburg, MD, USA.; Former affiliation: Department of Molecular Biosciences, University of Kansas, Lawrence, KS, USA
| | - Veneela Kr Vasigala
- Rangaraya Medical College, NTR University of Health Sciences, Kakinada, AP, India
| |
Collapse
|
26
|
Staggs KW, Nielsen DR. Improving n-butanol production in batch and semi-continuous processes through integrated product recovery. Process Biochem 2015. [DOI: 10.1016/j.procbio.2015.06.009] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
|
27
|
Activity of Lactobacillus brevis Alcohol Dehydrogenase on Primary and Secondary Alcohol Biofuel Precursors. FERMENTATION-BASEL 2015. [DOI: 10.3390/fermentation1010024] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
|
28
|
Luan G, Qi Y, Wang M, Li Z, Duan Y, Tan X, Lu X. Combinatory strategy for characterizing and understanding the ethanol synthesis pathway in cyanobacteria cell factories. BIOTECHNOLOGY FOR BIOFUELS 2015; 8:184. [PMID: 26594240 PMCID: PMC4654843 DOI: 10.1186/s13068-015-0367-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2015] [Accepted: 10/28/2015] [Indexed: 05/09/2023]
Abstract
BACKGROUND Photosynthetic production of chemicals and fuels by recycling CO2 in cyanobacteria is a promising solution facing energy shortage and resource declination. Ethanol is an attractive and demonstrative biofuel product, and ethanol synthesis in cyanobacteria has been achieved by assembling of a pathway consisting of pyruvate decarboxylase (PDCzm) and alcohol dehydrogenase II (slr1192). For enabling more powerful ethanol photosynthetic production, an optimized and balanced catalyzing route was required. In this work, we provided a paradigm for systematically characterizing and optimizing the PDCzm-slr1192 pathway from engineered cyanobacteria strains, combining in vitro reconstitution, genetic engineering and feeding-cultivation. RESULTS We reconstituted the PDCzm-slr1192 pathway in vitro and performed specific titration assays for enzymes, substrates, cofactors, and metal ions. In the in vitro system, K 50 of PDCzm was 0.326 μM, with a V max of 2.074 μM/s; while for slr1192, the values were 0.109 μM and 1.722 μM/s, respectively. Titration response discrepancy indicated that PDCzm rather than slr1192 was the rate-limiting factor for ethanol synthesis. In addition, a 4:6 concentration ratio of PDCzm-slr1192 would endow the reaction with a maximal specific catalytic activity. Titration assays for other components were also performed. K m values for NADPH, pyruvate, TPP, Mg(2+) and acetaldehyde were 0.136, 6.496, 0.011, 0.104, and 0.393 mM, respectively. We further constructed Synechocystis mutant strains with diverse PDCzm-slr1192 concentrations and ratios, and compared the growth and ethanol synthesis performances. The results revealed that activities of PDCzm indeed held control over the ethanol generation capacities. We performed pyruvate-feeding treatment with the newly developed Syn-YQ4 strain, and confirmed that improvement of pyruvate supply would direct more carbon flow to ethanol formation. CONCLUSIONS We systematically characterized and optimized the PDCzm-slr1192 pathway in engineered cyanobacteria for ethanol production. Information gained from in vitro monitoring and genetic engineering revealed that for further enhancing ethanol synthesis capacities, PDCzm activities needed enhancement, and the PDCzm-slr1192 ratio should be improved and held to about 1:1.5. Considering actual metabolites concentrations of cyanobacteria cells, enhancing pyruvate supply was also a promising strategy for further updating the current ethanol photosynthetic cell factories.
Collapse
Affiliation(s)
- Guodong Luan
- />Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Qingdao, 266101 China
- />Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Qingdao, 266101 China
| | - Yunjing Qi
- />Qingdao University of Science and Technology, Qingdao, 266061 China
| | - Min Wang
- />Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Qingdao, 266101 China
- />Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Qingdao, 266101 China
| | - Zhimin Li
- />Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Qingdao, 266101 China
- />Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Qingdao, 266101 China
- />College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang, 330045 Jiangxi China
| | - Yangkai Duan
- />Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Qingdao, 266101 China
- />Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Qingdao, 266101 China
- />University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Xiaoming Tan
- />Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Qingdao, 266101 China
- />Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Qingdao, 266101 China
| | - Xuefeng Lu
- />Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Qingdao, 266101 China
- />Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Qingdao, 266101 China
| |
Collapse
|
29
|
Yan J, Liu Y, Wang C, Han B, Li S. Assembly of lipase and P450 fatty acid decarboxylase to constitute a novel biosynthetic pathway for production of 1-alkenes from renewable triacylglycerols and oils. BIOTECHNOLOGY FOR BIOFUELS 2015; 8:34. [PMID: 25763106 PMCID: PMC4355466 DOI: 10.1186/s13068-015-0219-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2014] [Accepted: 02/04/2015] [Indexed: 05/21/2023]
Abstract
BACKGROUND Biogenic hydrocarbons (biohydrocarbons) are broadly accepted to be the ideal 'drop-in' biofuel alternative to petroleum-based fuels due to their highly similar chemical composition and physical characteristics. The biological production of aliphatic hydrocarbons is largely dependent on engineering of the complicated enzymatic network surrounding fatty acid biosynthesis. RESULT In this work, we developed a novel system for bioproduction of terminal fatty alkenes (1-alkenes) from renewable and low-cost triacylglycerols (TAGs) based on the lipase hydrolysis coupled to the P450 catalyzed decarboxylation. This artificial biosynthetic pathway was constituted using both cell-free systems including purified enzymes or cell-free extracts, and cell-based systems including mixed resting cells or growing cells. The issues of high cost of fatty acid feedstock and complicated biosynthesis network were addressed by replacement of the de novo biosynthesized fatty acids with the fed cheap TAGs. This recombinant tandem enzymatic pathway consisting of the Thermomyces lanuginosus lipase (Tll) and the P450 fatty acid decarboxylase OleTJE resulted in the production of 1-alkenes from purified TAGs or natural oils with 6.7 to 46.0% yields. CONCLUSION Since this novel hydrocarbon-producing pathway only requires two catalytically efficient enzymatic steps, it may hold great potential for industrial application by fulfilling the large-scale and cost-effective conversion of renewable TAGs into biohydrocarbons. This work highlights the power of designing and implementing an artificial pathway for production of advanced biofuels.
Collapse
Affiliation(s)
- Jinyong Yan
- />Key Laboratory of Biofuels, and Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, 266101 Qingdao, Shandong China
| | - Yi Liu
- />Key Laboratory of Biofuels, and Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, 266101 Qingdao, Shandong China
- />University of Chinese Academy of Sciences, No. 19A Yuquan Road, 100049 Beijing, China
| | - Cong Wang
- />Key Laboratory of Biofuels, and Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, 266101 Qingdao, Shandong China
| | - Bingnan Han
- />Key Laboratory for Marine Drugs, Department of Pharmacy, Renji Hospital, Shanghai Jiao Tong University School of Medicine, No. 145 Shandongzhong Road, 200127 Shanghai, China
| | - Shengying Li
- />Key Laboratory of Biofuels, and Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, 266101 Qingdao, Shandong China
| |
Collapse
|
30
|
Yu AQ, Pratomo Juwono NK, Leong SSJ, Chang MW. Production of Fatty Acid-derived valuable chemicals in synthetic microbes. Front Bioeng Biotechnol 2014; 2:78. [PMID: 25566540 PMCID: PMC4275033 DOI: 10.3389/fbioe.2014.00078] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2014] [Accepted: 12/10/2014] [Indexed: 12/18/2022] Open
Abstract
Fatty acid derivatives, such as hydroxy fatty acids, fatty alcohols, fatty acid methyl/ethyl esters, and fatty alka(e)nes, have a wide range of industrial applications including plastics, lubricants, and fuels. Currently, these chemicals are obtained mainly through chemical synthesis, which is complex and costly, and their availability from natural biological sources is extremely limited. Metabolic engineering of microorganisms has provided a platform for effective production of these valuable biochemicals. Notably, synthetic biology-based metabolic engineering strategies have been extensively applied to refactor microorganisms for improved biochemical production. Here, we reviewed: (i) the current status of metabolic engineering of microbes that produce fatty acid-derived valuable chemicals, and (ii) the recent progress of synthetic biology approaches that assist metabolic engineering, such as mRNA secondary structure engineering, sensor-regulator system, regulatable expression system, ultrasensitive input/output control system, and computer science-based design of complex gene circuits. Furthermore, key challenges and strategies were discussed. Finally, we concluded that synthetic biology provides useful metabolic engineering strategies for economically viable production of fatty acid-derived valuable chemicals in engineered microbes.
Collapse
Affiliation(s)
- Ai-Qun Yu
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore , Singapore , Singapore ; Synthetic Biology Research Program, National University of Singapore , Singapore , Singapore
| | - Nina Kurniasih Pratomo Juwono
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore , Singapore , Singapore ; Synthetic Biology Research Program, National University of Singapore , Singapore , Singapore
| | - Susanna Su Jan Leong
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore , Singapore , Singapore ; Synthetic Biology Research Program, National University of Singapore , Singapore , Singapore ; Singapore Institute of Technology , Singapore , Singapore
| | - Matthew Wook Chang
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore , Singapore , Singapore ; Synthetic Biology Research Program, National University of Singapore , Singapore , Singapore
| |
Collapse
|
31
|
Wang M, Fan L, Tan T. 1-Butanol production from glycerol by engineered Klebsiella pneumoniae. RSC Adv 2014. [DOI: 10.1039/c4ra09016k] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
|
32
|
Zhou J, Wang C, Yang L, Choi ES, Kim SW. Geranyl diphosphate synthase: an important regulation point in balancing a recombinant monoterpene pathway in Escherichia coli. Enzyme Microb Technol 2014; 68:50-5. [PMID: 25435505 DOI: 10.1016/j.enzmictec.2014.10.005] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2014] [Revised: 10/16/2014] [Accepted: 10/17/2014] [Indexed: 11/15/2022]
Abstract
The expression level of geranyl diphosphate synthase (GPPS) was suspected to play a key role for geraniol production in recombinant Escherichia coli harboring an entire mevalonate pathway operon and a geraniol synthesis operon. The expression of GPPS was optimized by using ribosomal binding sites (RBSs) designed to have different translation initiation rates (TIRs). The RBS strength in TIR window of 500 arbitrary unit (au)-1400 au for GPPS appears to be suitable for balancing the geraniol biosynthesis pathway in this study. With the TIR of 500 au, the highest production titer of geraniol was obtained at a level of 1119mg/L, which represented a 6-fold increase in comparison with the previous titer of 183mg/L. The TIRs of GPPS locating out of range of the optimal window (500-1400 au) caused significant decreases of cell growth and geraniol production. It was suspected to result from metabolic imbalance and plasmid instability in geraniol production by inappropriate expression level of GPP synthase. Our results collectively indicated GPPS as an important regulation point in balancing a recombinant geraniol synthesis pathway. The GPPS-based regulation approach could be applicable for optimizing microbial production of other monoterpenes.
Collapse
Affiliation(s)
- Jia Zhou
- Division of Applied Life Science (BK21 Plus), PMBBRC, Gyeongsang National University, Jinju 660-701, Republic of Korea
| | - Chonglong Wang
- Division of Applied Life Science (BK21 Plus), PMBBRC, Gyeongsang National University, Jinju 660-701, Republic of Korea
| | - Liyang Yang
- Division of Applied Life Science (BK21 Plus), PMBBRC, Gyeongsang National University, Jinju 660-701, Republic of Korea
| | - Eui-Sung Choi
- Industrial Biotechnology Research Center, KRIBB, Daejeon 305-806, Republic of Korea.
| | - Seon-Won Kim
- Division of Applied Life Science (BK21 Plus), PMBBRC, Gyeongsang National University, Jinju 660-701, Republic of Korea.
| |
Collapse
|
33
|
Zhang H, Cao M, Jiang X, Zou H, Wang C, Xu X, Xian M. De-novo synthesis of 2-phenylethanol by Enterobacter sp. CGMCC 5087. BMC Biotechnol 2014; 14:30. [PMID: 24766677 PMCID: PMC4005845 DOI: 10.1186/1472-6750-14-30] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2013] [Accepted: 11/11/2013] [Indexed: 11/30/2022] Open
Abstract
Background 2-phenylethanl (2-PE) and its derivatives are important chemicals, which are widely used in food materials and fine chemical industries and polymers and it’s also a potentially valuable alcohol for next-generation biofuel. However, the biosynthesis of 2-PE are mainly biotransformed from phenylalanine, the price of which barred the production. Therefore, it is necessary to seek more sustainable technologies for 2-PE production. Results A new strain which produces 2-PE through the phenylpyruvate pathway was isolated and identified as Enterobacter sp. CGMCC 5087. The strain is able to use renewable monosaccharide as the carbon source and NH4Cl as the nitrogen source to produce 2-PE. Two genes of rate-limiting enzymes, chorismate mutase p-prephenate dehydratase (PheA) and 3-deoxy-d-arabino-heptulosonic acid 7-phosphate synthase (DAHP), were cloned from Escherichia coli and overexpressed in E. sp. CGMCC 5087. The engineered E. sp. CGMCC 5087 produces 334.9 mg L-1 2-PE in 12 h, which is 3.26 times as high as the wild strain. Conclusions The phenylpyruvate pathway and the substrate specificity of 2-keto-acid decarboxylase towards phenylpyruvate were found in E. sp. CGMCC 5087. Combined with the low-cost monosaccharide as the substrate, the finding provides a novel and potential way for 2-PE production.
Collapse
Affiliation(s)
| | | | | | | | | | | | - Mo Xian
- CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No,189 Songling Road, Laoshan District, Qingdao, PR 266101, China.
| |
Collapse
|
34
|
Breunig JS, Hackett SR, Rabinowitz JD, Kruglyak L. Genetic basis of metabolome variation in yeast. PLoS Genet 2014; 10:e1004142. [PMID: 24603560 PMCID: PMC3945093 DOI: 10.1371/journal.pgen.1004142] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2013] [Accepted: 12/06/2013] [Indexed: 12/17/2022] Open
Abstract
Metabolism, the conversion of nutrients into usable energy and biochemical building blocks, is an essential feature of all cells. The genetic factors responsible for inter-individual metabolic variability remain poorly understood. To investigate genetic causes of metabolome variation, we measured the concentrations of 74 metabolites across ~ 100 segregants from a Saccharomyces cerevisiae cross by liquid chromatography-tandem mass spectrometry. We found 52 quantitative trait loci for 34 metabolites. These included linkages due to overt changes in metabolic genes, e.g., linking pyrimidine intermediates to the deletion of ura3. They also included linkages not directly related to metabolic enzymes, such as those for five central carbon metabolites to ira2, a Ras/PKA pathway regulator, and for the metabolites, S-adenosyl-methionine and S-adenosyl-homocysteine to slt2, a MAP kinase involved in cell wall integrity. The variant of ira2 that elevates metabolite levels also increases glucose uptake and ethanol secretion. These results highlight specific examples of genetic variability, including in genes without prior known metabolic regulatory function, that impact yeast metabolism.
Collapse
Affiliation(s)
- Jeffrey S. Breunig
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, United States of America
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, United States of America
| | - Sean R. Hackett
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, United States of America
- Graduate Program in Quantitative and Computational Biology, Princeton University, Princeton, New Jersey, United States of America
| | - Joshua D. Rabinowitz
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, United States of America
- Department of Chemistry, Princeton University, Princeton, New Jersey, United States of America
| | - Leonid Kruglyak
- Departments of Human Genetics and Biological Chemistry, David Geffen School of Medicine, UCLA, Los Angeles, California, United States of America
- Howard Hughes Medical Institute, UCLA, Los Angeles, California, United States of America
| |
Collapse
|
35
|
Roehner N, Myers CJ. A methodology to annotate systems biology markup language models with the synthetic biology open language. ACS Synth Biol 2014; 3:57-66. [PMID: 23977879 DOI: 10.1021/sb400066m] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Recently, we have begun to witness the potential of synthetic biology, noted here in the form of bacteria and yeast that have been genetically engineered to produce biofuels, manufacture drug precursors, and even invade tumor cells. The success of these projects, however, has often failed in translation and application to new projects, a problem exacerbated by a lack of engineering standards that combine descriptions of the structure and function of DNA. To address this need, this paper describes a methodology to connect the systems biology markup language (SBML) to the synthetic biology open language (SBOL), existing standards that describe biochemical models and DNA components, respectively. Our methodology involves first annotating SBML model elements such as species and reactions with SBOL DNA components. A graph is then constructed from the model, with vertices corresponding to elements within the model and edges corresponding to the cause-and-effect relationships between these elements. Lastly, the graph is traversed to assemble the annotating DNA components into a composite DNA component, which is used to annotate the model itself and can be referenced by other composite models and DNA components. In this way, our methodology can be used to build up a hierarchical library of models annotated with DNA components. Such a library is a useful input to any future genetic technology mapping algorithm that would automate the process of composing DNA components to satisfy a behavioral specification. Our methodology for SBML-to-SBOL annotation is implemented in the latest version of our genetic design automation (GDA) software tool, iBioSim.
Collapse
Affiliation(s)
- Nicholas Roehner
- Department of Bioengineering, University of Utah, Salt Lake
City, Utah 84112, United States
| | - Chris J. Myers
- Department of Electrical
and Computer Engineering, University of Utah, Salt Lake City, Utah 84112, United States
| |
Collapse
|
36
|
Hallenbeck PC. Bioenergy from Microorganisms: An Overview. MICROBIAL BIOENERGY: HYDROGEN PRODUCTION 2014. [DOI: 10.1007/978-94-017-8554-9_1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
|
37
|
Wang Q, Song Y, Jin Y, Liu H, Zhang H, Sun Y, Liu G. Biosynthesis of 2-phenylethanol using tobacco waste as feedstock. BIOCATAL BIOTRANSFOR 2013. [DOI: 10.3109/10242422.2013.857315] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
|
38
|
Chou HH, Keasling JD. Programming adaptive control to evolve increased metabolite production. Nat Commun 2013; 4:2595. [DOI: 10.1038/ncomms3595] [Citation(s) in RCA: 134] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2013] [Accepted: 09/11/2013] [Indexed: 11/09/2022] Open
|
39
|
Abstract
Alka(e)nes are the predominant constituents of gasoline, diesel, and jet fuels. They can be produced naturally by a wide range of microorganisms. Bio-alka(e)nes can be used as drop-in biofuels. To date, five microbial pathways that convert free fatty acids or fatty acid derivatives into alka(e)nes have been identified or reconstituted. The discoveries open a door to achieve microbial production of alka(e)nes with high efficiency. The modules derived from these alka(e)ne biosynthetic pathways can be assembled as biological parts and synthetic biology strategies can be employed to optimize the metabolic pathways and improve alka(e)ne production.
Collapse
Affiliation(s)
- Weihua Wang
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences , Qingdao , China
| | - Xuefeng Lu
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences , Qingdao , China
| |
Collapse
|
40
|
Kelle A. Beyond patchwork precaution in the dual-use governance of synthetic biology. SCIENCE AND ENGINEERING ETHICS 2013; 19:1121-39. [PMID: 22535577 PMCID: PMC3735959 DOI: 10.1007/s11948-012-9365-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2011] [Accepted: 04/12/2012] [Indexed: 05/31/2023]
Abstract
The emergence of synthetic biology holds the potential of a major breakthrough in the life sciences by transforming biology into a predictive science. The dual-use characteristics of similar breakthroughs during the twentieth century have led to the application of benignly intended research in e.g. virology, bacteriology and aerobiology in offensive biological weapons programmes. Against this background the article raises the question whether the precautionary governance of synthetic biology can aid in preventing this techno-science witnessing the same fate? In order to address this question, this paper proceeds in four steps: it firstly introduces the emerging techno-science of synthetic biology and presents some of its potential beneficial applications. It secondly analyses contributions to the bioethical discourse on synthetic biology as well as precautionary reasoning and its application to life science research in general and synthetic biology more specifically. The paper then identifies manifestations of a moderate precautionary principle in the emerging synthetic biology dual-use governance discourse. Using a dual-use governance matrix as heuristic device to analyse some of the proposed measures, it concludes that the identified measures can best be described as "patchwork precaution" and that a more systematic approach to construct a web of dual-use precaution for synthetic biology is needed in order to guard more effectively against the field's future misuse for harmful applications.
Collapse
Affiliation(s)
- Alexander Kelle
- Department of Politics, Languages and International Studies, University of Bath, Bath, BA2 7AY, UK.
| |
Collapse
|
41
|
Zhang J, Lu X, Li JJ. Conversion of fatty aldehydes into alk (a/e)nes by in vitro reconstituted cyanobacterial aldehyde-deformylating oxygenase with the cognate electron transfer system. BIOTECHNOLOGY FOR BIOFUELS 2013; 6:86. [PMID: 23759169 PMCID: PMC3691600 DOI: 10.1186/1754-6834-6-86] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2013] [Accepted: 06/03/2013] [Indexed: 05/04/2023]
Abstract
BACKGROUND Biosynthesis of fatty alk(a/e)ne in cyanobacteria has been considered as a potential basis for the sunlight-driven and carbon-neutral bioprocess producing advanced solar biofuels. Aldehyde-deformylating oxygenase (ADO) is a key enzyme involved in that pathway. The heterologous or chemical reducing systems were generally used in in vitro ADO activity assay. The cognate electron transfer system from cyanobacteria to support ADO activity is still unknown. RESULTS We identified the potential endogenous reducing system including ferredoxin (Fd) and ferredoxin-NADP+ reductase (FNR) to support ADO activity in Synechococcus elongatus PCC7942. ADO (Synpcc7942_1593), FNR (SynPcc7942_0978), and Fd (SynPcc7942_1499) from PCC7942 were cloned, overexpressed, purified, and characterized. ADO activity was successfully supported with the endogenous electron transfer system, which worked more effectively than the heterologous and chemical ones. The results of the hybrid Fd/FNR reducing systems demonstrated that ADO was selective against Fd. And it was observed that the cognate reducing system produced less H2O2 than the heterologous one by 33% during ADO-catalyzed reactions. Importantly, kcat value of ADO 1593 using the homologous Fd/FNR electron transfer system is 3.7-fold higher than the chemical one. CONCLUSIONS The cognate electron transfer system from cyanobacteria to support ADO activity was identified and characterized. For the first time, ADO was functionally in vitro reconstituted with the endogenous reducing system from cyanobacteria, which supported greater activity than the surrogate and chemical ones, and produced less H2O2 than the heterologous one. The identified Fd/FNR electron transfer system will be potentially useful for improving ADO activity and further enhancing the biosynthetic efficiency of hydrocarbon biofuels in cyanobacteria.
Collapse
Affiliation(s)
- Jingjing Zhang
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Qingdao, 266101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xuefeng Lu
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Qingdao, 266101, China
| | - Jian-Jun Li
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Qingdao, 266101, China
| |
Collapse
|
42
|
Metabolic engineering of Synechocystis sp. strain PCC 6803 for isobutanol production. Appl Environ Microbiol 2012. [PMID: 23183979 DOI: 10.1128/aem.02827-12] [Citation(s) in RCA: 104] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Global warming and decreasing fossil fuel reserves have prompted great interest in the synthesis of advanced biofuels from renewable resources. In an effort to address these concerns, we performed metabolic engineering of the cyanobacterium Synechocystis sp. strain PCC 6803 to develop a strain that can synthesize isobutanol under both autotrophic and mixotrophic conditions. With the expression of two heterologous genes from the Ehrlich pathway, the engineered strain can accumulate 90 mg/liter of isobutanol from 50 mM bicarbonate in a gas-tight shaking flask. The strain does not require any inducer (i.e., isopropyl β-d-1-thiogalactopyranoside [IPTG]) or antibiotics to maintain its isobutanol production. In the presence of glucose, isobutanol synthesis is only moderately promoted (titer = 114 mg/liter). Based on isotopomer analysis, we found that, compared to the wild-type strain, the mutant significantly reduced its glucose utilization and mainly employed autotrophic metabolism for biomass growth and isobutanol production. Since isobutanol is toxic to the cells and may also be degraded photochemically by hydroxyl radicals during the cultivation process, we employed in situ removal of the isobutanol using oleyl alcohol as a solvent trap. This resulted in a final net concentration of 298 mg/liter of isobutanol under mixotrophic culture conditions.
Collapse
|
43
|
Liu CG, Xue C, Lin YH, Bai FW. Redox potential control and applications in microaerobic and anaerobic fermentations. Biotechnol Adv 2012. [PMID: 23178703 DOI: 10.1016/j.biotechadv.2012.11.005] [Citation(s) in RCA: 144] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Many fermentation products are produced under microaerobic or anaerobic conditions, in which oxygen is undetectable by dissolved oxygen probe, presenting a challenge for process monitoring and control. Extracellular redox potentials that can be detected conveniently affect intracellular redox homeostasis and metabolism, and consequently control profiles of fermentation products, which provide an alternative for monitoring and control of these fermentation processes. This article reviews updated progress in the impact of redox potentials on gene expression, protein biosynthesis and metabolism as well as redox potential control strategies for more efficient production of fermentation products, taking ethanol fermentation by the yeast Saccharomyces under microaerobic conditions and butanol production by the bacterium Clostridium under anaerobic conditions as examples.
Collapse
Affiliation(s)
- Chen-Guang Liu
- School of Life Sciences and Biotechnology, Dalian University of Technology, Dalian 116023, China
| | | | | | | |
Collapse
|
44
|
Beal J, Weiss R, Densmore D, Adler A, Appleton E, Babb J, Bhatia S, Davidsohn N, Haddock T, Loyall J, Schantz R, Vasilev V, Yaman F. An end-to-end workflow for engineering of biological networks from high-level specifications. ACS Synth Biol 2012; 1:317-31. [PMID: 23651286 DOI: 10.1021/sb300030d] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
We present a workflow for the design and production of biological networks from high-level program specifications. The workflow is based on a sequence of intermediate models that incrementally translate high-level specifications into DNA samples that implement them. We identify algorithms for translating between adjacent models and implement them as a set of software tools, organized into a four-stage toolchain: Specification, Compilation, Part Assignment, and Assembly. The specification stage begins with a Boolean logic computation specified in the Proto programming language. The compilation stage uses a library of network motifs and cellular platforms, also specified in Proto, to transform the program into an optimized Abstract Genetic Regulatory Network (AGRN) that implements the programmed behavior. The part assignment stage assigns DNA parts to the AGRN, drawing the parts from a database for the target cellular platform, to create a DNA sequence implementing the AGRN. Finally, the assembly stage computes an optimized assembly plan to create the DNA sequence from available part samples, yielding a protocol for producing a sample of engineered plasmids with robotics assistance. Our workflow is the first to automate the production of biological networks from a high-level program specification. Furthermore, the workflow's modular design allows the same program to be realized on different cellular platforms simply by swapping workflow configurations. We validated our workflow by specifying a small-molecule sensor-reporter program and verifying the resulting plasmids in both HEK 293 mammalian cells and in E. coli bacterial cells.
Collapse
Affiliation(s)
- Jacob Beal
- Raytheon BBN Technologies, 10 Moulton
St., Cambridge, Massachusetts, United States
| | - Ron Weiss
- Department of Biological Engineering, MIT, Cambridge, Massachusetts, United States
| | | | - Aaron Adler
- Raytheon BBN Technologies, 10 Moulton
St., Cambridge, Massachusetts, United States
| | | | - Jonathan Babb
- Department of Biological Engineering, MIT, Cambridge, Massachusetts, United States
| | | | - Noah Davidsohn
- Department of Biological Engineering, MIT, Cambridge, Massachusetts, United States
| | | | - Joseph Loyall
- Raytheon BBN Technologies, 10 Moulton
St., Cambridge, Massachusetts, United States
| | - Richard Schantz
- Raytheon BBN Technologies, 10 Moulton
St., Cambridge, Massachusetts, United States
| | | | - Fusun Yaman
- Raytheon BBN Technologies, 10 Moulton
St., Cambridge, Massachusetts, United States
| |
Collapse
|
45
|
Krishnanathan K, Anderson SR, Billings SA, Kadirkamanathan V. A data-driven framework for identifying nonlinear dynamic models of genetic parts. ACS Synth Biol 2012; 1:375-84. [PMID: 23651291 DOI: 10.1021/sb300009t] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
A key challenge in synthetic biology is the development of effective methodologies for characterization of component genetic parts in a form suitable for dynamic analysis and design. In this investigation we propose the use of a nonlinear dynamic modeling framework that is popular in the field of control engineering but is novel to the field of synthetic biology: Nonlinear AutoRegressive Moving Average model with eXogenous inputs (NARMAX). The framework is applied to the identification of a genetic part BBa_T9002 as a case study. A concise model is developed that exhibits accurate representation of the system dynamics and a structure that is compact and consistent across cell populations. A comparison is made with a biochemical model, derived from a simple enzymatic reaction scheme. The NARMAX model is shown to be comparably simple but exhibits much greater prediction accuracy on the experimental data. These results indicate that the data-driven NARMAX framework is an attractive technique for dynamic modeling of genetic parts.
Collapse
Affiliation(s)
| | - Sean R. Anderson
- Department of Automatic Control and Systems Engineering, University of Sheffield, Sheffield S1 3JD, U.K
| | - Stephen A. Billings
- Department of Automatic Control and Systems Engineering, University of Sheffield, Sheffield S1 3JD, U.K
| | - Visakan Kadirkamanathan
- Department of Automatic Control and Systems Engineering, University of Sheffield, Sheffield S1 3JD, U.K
| |
Collapse
|
46
|
Georgianna DR, Mayfield SP. Exploiting diversity and synthetic biology for the production of algal biofuels. Nature 2012; 488:329-35. [PMID: 22895338 DOI: 10.1038/nature11479] [Citation(s) in RCA: 361] [Impact Index Per Article: 30.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Modern life is intimately linked to the availability of fossil fuels, which continue to meet the world's growing energy needs even though their use drives climate change, exhausts finite reserves and contributes to global political strife. Biofuels made from renewable resources could be a more sustainable alternative, particularly if sourced from organisms, such as algae, that can be farmed without using valuable arable land. Strain development and process engineering are needed to make algal biofuels practical and economically viable.
Collapse
Affiliation(s)
- D Ryan Georgianna
- San Diego Center for Algae Biotechnology, Division of Biological Sciences, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92093, USA
| | | |
Collapse
|
47
|
|
48
|
Ganesh I, Ravikumar S, Hong SH. Metabolically engineered Escherichia coli as a tool for the production of bioenergy and biochemicals from glycerol. BIOTECHNOL BIOPROC E 2012. [DOI: 10.1007/s12257-011-0446-3] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
|
49
|
Zhang WL, Liu ZY, Liu Z, Li FL. Butanol production from corncob residue using Clostridium beijerinckii NCIMB 8052. Lett Appl Microbiol 2012; 55:240-6. [PMID: 22738279 DOI: 10.1111/j.1472-765x.2012.03283.x] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
AIMS To determine whether corncob residue (CCR) could be a good substrate for butanol production. METHODS AND RESULTS In this study, Ca(OH)₂ detoxification technique was used to remove inhibitors of lignocellulose enzymatic hydrolysis. During fermentation of untreated corncob residue hydrolysate (CCRH) by Clostridium beijerinckii NCIMB 8052, cell growth was inhibited and only 3·8 g l⁻¹ acetone, butanol and ethanol (ABE) was produced. After pretreatment with Ca(OH)₂, enzymatic hydrolysis of CCR resulted in 49·3 g l⁻¹ total sugars, about twofold of that of untreated one. In the fermentation of the Ca(OH)₂-detoxified CCRH, sugar utilization ratio was increased by 27·3%. When using the Ca(OH)₂-detoxified CCRH supplemented with 10 g l⁻¹ glucose, 16·0 g l⁻¹ ABE was produced, resulting in an ABE yield of 0·32 and a productivity of 0·33 g l⁻¹ h⁻¹. CONCLUSION The results in this study suggest that CCR was a good carbon source for ABE fermentation. SIGNIFICANCE AND IMPACT OF THE STUDY It is the first time to use CCR as substrate for butanol production. Ca(OH)₂ detoxification pretreatment was proved to be an effective method to improve enzymatic digestibility of lignocellulose.
Collapse
Affiliation(s)
- W L Zhang
- Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China Graduate University of Chinese Academy of Sciences, Beijing, China
| | | | | | | |
Collapse
|
50
|
Lee WH, Seo SO, Bae YH, Nan H, Jin YS, Seo JH. Isobutanol production in engineered Saccharomyces cerevisiae by overexpression of 2-ketoisovalerate decarboxylase and valine biosynthetic enzymes. Bioprocess Biosyst Eng 2012; 35:1467-75. [DOI: 10.1007/s00449-012-0736-y] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2012] [Accepted: 04/08/2012] [Indexed: 11/30/2022]
|