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Xu D, Zhang L. Increasing Agmatine Production in Escherichia coli through Metabolic Engineering. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2019; 67:7908-7915. [PMID: 31268314 DOI: 10.1021/acs.jafc.9b03038] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
In this study, to obtain higher agmatine yields using the previously developed E. coli strain AUX4 (JM109 ΔspeC ΔspeF ΔspeB ΔargR), the genes encoding glutamate dehydrogenase (gdhA), glutamine synthetase (glnA), phosphoenolpyruvate carboxylase (ppc), aspartate aminotransferase (aspC), transhydrogenase (pntAB), and biosynthetic arginine decarboxylase (speA) were sequentially overexpressed by replacing their native promoters with the heterologous strong trp, core-trc, or 5Ptacs promoters to generate the plasmid-free E. coli strain AUX11. The fermentation results obtained using a 3-L bioreactor showed that AUX11 produced 2.93 g L-1 agmatine with the yield of 0.29 g agmatine g-1 glucose in the batch fermentation, and the fed-batch fermentation of AUX11 allowed the production of 40.43 g L-1 agmatine with the productivity of 1.26 g L-1 h-1 agmatine. The results showed that the engineered E. coli strain AUX11 can be used for the industrial fermentative production of agmatine.
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Affiliation(s)
- Daqing Xu
- College of Life Sciences , Hebei Agricultural University , Baoding 071000 , China
| | - Lirong Zhang
- College of Plant Protection , Hebei Agricultural University , Baoding 071000 , China
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52
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Deb SS, Reshamwala SMS, Lali AM. Activation of alternative metabolic pathways diverts carbon flux away from isobutanol formation in an engineered Escherichia coli strain. Biotechnol Lett 2019; 41:823-836. [PMID: 31093837 DOI: 10.1007/s10529-019-02683-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2018] [Accepted: 05/02/2019] [Indexed: 12/12/2022]
Abstract
OBJECTIVE Metabolic engineering efforts are guided by identifying gene targets for overexpression and/or deletion. Isobutanol, a biofuel candidate, is biosynthesized using the valine biosynthesis pathway and enzymes of the Ehrlich pathway. Most reported studies for isobutanol production in Escherichia coli employ multicopy plasmids, an approach that suffers from disadvantages such as plasmid instability, increased metabolic burden, and use of antibiotics to maintain selection pressure. Cofactor imbalance is another issue that may limit production of isobutanol, as two enzymes of the pathway utilize NADPH as a cofactor. RESULTS To address these issues, we constructed E. coli strains with chromosomally-integrated, codon-optimized isobutanol pathway genes (ilvGM, ilvC, kivd, adh) selected on the basis of their cofactor preferences. Genes involved in diverting pyruvate flux toward fermentation byproducts were deleted. Metabolite analyses of the constructed strains revealed extracellular accumulation of significant amounts of isobutyraldehyde, a pathway intermediate, and the overflow metabolites 2,3-butanediol and acetol. CONCLUSIONS These results demonstrate that the genetic modifications carried out led to activation of alternative pathways that diverted carbon flux toward formation of unwanted metabolites. The present study highlights how precursor metabolites can be metabolized through enzymatic routes that have not been considered important in previous studies due to the different strategies employed therein. The insights gained from the present study will allow rational genetic modification of host cells for production of metabolites of interest.
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Affiliation(s)
- Shalini S Deb
- DBT-ICT Centre for Energy Biosciences, Institute of Chemical Technology, Nathatlal Parekh Marg, Matunga (East), Mumbai, Maharashtra, 400019, India
| | - Shamlan M S Reshamwala
- DBT-ICT Centre for Energy Biosciences, Institute of Chemical Technology, Nathatlal Parekh Marg, Matunga (East), Mumbai, Maharashtra, 400019, India.
| | - Arvind M Lali
- DBT-ICT Centre for Energy Biosciences, Institute of Chemical Technology, Nathatlal Parekh Marg, Matunga (East), Mumbai, Maharashtra, 400019, India
- Department of Chemical Engineering, Institute of Chemical Technology, Nathatlal Parekh Marg, Matunga (East), Mumbai, Maharashtra, 400019, India
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Wang YY, Xu JZ, Zhang WG. Metabolic engineering of l-leucine production in Escherichia coli and Corynebacterium glutamicum: a review. Crit Rev Biotechnol 2019; 39:633-647. [PMID: 31055970 DOI: 10.1080/07388551.2019.1577214] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
l-Leucine, as an essential branched-chain amino acid for humans and animals, has recently been attracting much attention because of its potential for a fast-growing market demand. The applicability ranges from flavor enhancers, animal feed additives and ingredients in cosmetic to specialty nutrients in pharmaceutical and medical fields. Microbial fermentation is the major method for producing l-leucine by using Escherichia coli and Corynebacterium glutamicum as host bacteria. This review gives an overview of the metabolic pathway of l-leucine (i.e. production, import and export systems) and highlights the main regulatory mechanisms of operons in E. coli and C. glutamicum l-leucine biosynthesis. We summarize here the current trends in metabolic engineering techniques and strategies for manipulating l-leucine producing strains. Finally, future perspectives to construct industrially advantageous strains are considered with respect to recent advances in biology.
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Affiliation(s)
- Ying-Yu Wang
- a The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology , Jiangnan University , WuXi , People's Republic of China
| | - Jian-Zhong Xu
- a The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology , Jiangnan University , WuXi , People's Republic of China.,b The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology , Jiangnan University , WuXi , People's Republic of China
| | - Wei-Guo Zhang
- a The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology , Jiangnan University , WuXi , People's Republic of China
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54
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Savrasova EA, Stoynova NV. Application of leucine dehydrogenase Bcd from Bacillus subtilis for l-valine synthesis in Escherichia coli under microaerobic conditions. Heliyon 2019; 5:e01406. [PMID: 30993221 PMCID: PMC6449708 DOI: 10.1016/j.heliyon.2019.e01406] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Revised: 03/05/2019] [Accepted: 03/20/2019] [Indexed: 12/02/2022] Open
Abstract
Microaerobic cultivation conditions have been shown experimentally and theoretically to improve the performance of a number of bioproduction systems. However, under these conditions, the production of l-valine by Escherichia coli is decreased mainly because of a redox cofactor imbalance and a decreased l-glutamate supply. The synthesis of one mole of l-valine from one mole of glucose generates two moles of NADH via glycolysis but consumes a total of two moles of NADPH, one in the ketol-acid reductoisomerase (KARI) reaction and the other in the regeneration of l-glutamate as an amino group donor for the branched-chain amino acid aminotransferase (BCAT) reaction. The improvement of l-valine synthesis under oxygen deprivation may be due to solving these problems. Increased l-valine synthesis under oxygen deprivation conditions was previously shown in Corynebacterium glutamicum (Hasegawa et al., 2012). In this study, we have proposed the use of NADH-dependent leucine dehydrogenase (LeuDH; EC 1.4.1.9) Bcd from B. subtilis instead of the native NADPH-dependent pathway including aminotransferase encoded by ilvE to improve l-valine production in E. coli under microaerobic conditions. We have created l-valine-producing strains on the base of the aminotransferase B-deficient strain V1 (B-7 ΔilvBN ΔilvIH ΔilvGME::PL-ilvBNN17KDA) by introducing one chromosomal copy of the bcd gene or the ilvE gene. Evaluation of the l-valine production by the obtained strains under microaerobic and aerobic conditions revealed that leucine dehydrogenase Bcd had a higher potential for l-valine production under microaerobic conditions. The Bcd-possessing strain exhibited 2.2-fold higher l-valine accumulation (up to 9.1 g/L) and 2.0-fold higher yield (up to 35.3%) under microaerobic conditions than the IlvE-possessing strain. The obtained results could be interpreted as follows: an altering of redox cofactor balance in the l-valine biosynthesis pathway increased the production and yield by E. coli cells under microaerobic conditions. Thus, the effective synthesis of l-valine by means of “valine fermentation” was shown in E. coli. This methodology has the advantages of being an economical and environmentally friendly process.
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55
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Chen CY, Chang YC, Lin BL, Lin KF, Huang CH, Hsieh DL, Ko TP, Tsai MD. Use of Cryo-EM To Uncover Structural Bases of pH Effect and Cofactor Bispecificity of Ketol-Acid Reductoisomerase. J Am Chem Soc 2019; 141:6136-6140. [DOI: 10.1021/jacs.9b01354] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Chin-Yu Chen
- Department of Life Sciences, National Central University, Taoyuan 32001, Taiwan
| | | | | | - Kuan-Fu Lin
- Department of Life Sciences, National Central University, Taoyuan 32001, Taiwan
| | - Chun-Hsiang Huang
- Experimental Facility Division, National Synchrotron Radiation Research Center, Hsinchu 30076, Taiwan
| | - Dong-Lin Hsieh
- Department of Life Sciences, National Central University, Taoyuan 32001, Taiwan
| | | | - Ming-Daw Tsai
- Institute of Biochemical Sciences, National Taiwan University, Taipei 106, Taiwan
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56
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Bonk B, Weis JW, Tidor B. Machine Learning Identifies Chemical Characteristics That Promote Enzyme Catalysis. J Am Chem Soc 2019; 141:4108-4118. [PMID: 30761897 PMCID: PMC6407039 DOI: 10.1021/jacs.8b13879] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2018] [Indexed: 11/28/2022]
Abstract
Despite tremendous progress in understanding and engineering enzymes, knowledge of how enzyme structures and their dynamics induce observed catalytic properties is incomplete, and capabilities to engineer enzymes fall far short of industrial needs. Here, we investigate the structural and dynamic drivers of enzyme catalysis for the rate-limiting step of the industrially important enzyme ketol-acid reductoisomerase (KARI) and identify a region of the conformational space of the bound enzyme-substrate complex that, when populated, leads to large increases in reactivity. We apply computational statistical mechanical methods that implement transition interface sampling to simulate the kinetics of the reaction and combine this with machine learning techniques from artificial intelligence to select features relevant to reactivity and to build predictive models for reactive trajectories. We find that conformational descriptors alone, without the need for dynamic ones, are sufficient to predict reactivity with greater than 85% accuracy (90% AUC). Key descriptors distinguishing reactive from almost-reactive trajectories quantify substrate conformation, substrate bond polarization, and metal coordination geometry and suggest their role in promoting substrate reactivity. Moreover, trajectories constrained to visit a region of the reactant well, separated from the rest by a simple hyperplane defined by ten conformational parameters, show increases in computed reactivity by many orders of magnitude. This study provides evidence for the existence of reactivity promoting regions within the conformational space of the enzyme-substrate complex and develops methodology for identifying and validating these particularly reactive regions of phase space. We suggest that identification of reactivity promoting regions and re-engineering enzymes to preferentially populate them may lead to significant rate enhancements.
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Affiliation(s)
- Brian
M. Bonk
- Department
of Biological Engineering, Massachusetts
Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
- Computer
Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - James W. Weis
- Computer
Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
- Computational
and Systems Biology, Massachusetts Institute
of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
- Department
of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Bruce Tidor
- Department
of Biological Engineering, Massachusetts
Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
- Computer
Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
- Computational
and Systems Biology, Massachusetts Institute
of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
- Department
of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
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Ghosh IN, Martien J, Hebert AS, Zhang Y, Coon JJ, Amador-Noguez D, Landick R. OptSSeq explores enzyme expression and function landscapes to maximize isobutanol production rate. Metab Eng 2019; 52:324-340. [DOI: 10.1016/j.ymben.2018.12.008] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Revised: 11/26/2018] [Accepted: 12/25/2018] [Indexed: 10/27/2022]
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58
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Microbial Production of Fatty Acid via Metabolic Engineering and Synthetic Biology. BIOTECHNOL BIOPROC E 2019. [DOI: 10.1007/s12257-018-0374-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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59
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Chen X, Li Y, Tong T, Liu L. Spatial modulation and cofactor engineering of key pathway enzymes for fumarate production in
Candida glabrata. Biotechnol Bioeng 2019; 116:622-630. [DOI: 10.1002/bit.26906] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Revised: 12/11/2018] [Accepted: 12/20/2018] [Indexed: 12/16/2022]
Affiliation(s)
- Xiulai Chen
- State Key Laboratory of Food Science and Technology, Jiangnan UniversityWuxi China
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan UniversityWuxi China
| | - Yang Li
- State Key Laboratory of Food Science and Technology, Jiangnan UniversityWuxi China
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan UniversityWuxi China
| | - Tian Tong
- State Key Laboratory of Food Science and Technology, Jiangnan UniversityWuxi China
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan UniversityWuxi China
| | - Liming Liu
- State Key Laboratory of Food Science and Technology, Jiangnan UniversityWuxi China
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan UniversityWuxi China
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan UniversityWuxi China
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60
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Bai W, Geng W, Wang S, Zhang F. Biosynthesis, regulation, and engineering of microbially produced branched biofuels. BIOTECHNOLOGY FOR BIOFUELS 2019; 12:84. [PMID: 31011367 PMCID: PMC6461809 DOI: 10.1186/s13068-019-1424-9] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Accepted: 04/03/2019] [Indexed: 05/13/2023]
Abstract
The steadily increasing demand on transportation fuels calls for renewable fuel replacements. This has attracted a growing amount of research to develop advanced biofuels that have similar physical, chemical, and combustion properties with petroleum-derived fossil fuels. Early generations of biofuels, such as ethanol, butanol, and straight-chain fatty acid-derived esters or hydrocarbons suffer from various undesirable properties and can only be blended in limited amounts. Recent research has shifted to the production of branched-chain biofuels that, compared to straight-chain fuels, have higher octane values, better cold flow, and lower cloud points, making them more suitable for existing engines, particularly for diesel and jet engines. This review focuses on several types of branched-chain biofuels and their immediate precursors, including branched short-chain (C4-C8) and long-chain (C15-C19)-alcohols, alkanes, and esters. We discuss their biosynthesis, regulation, and recent efforts in their overproduction by engineered microbes.
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Affiliation(s)
- Wenqin Bai
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, Saint Louis, MO 63130 USA
| | - Weitao Geng
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, Saint Louis, MO 63130 USA
| | - Shaojie Wang
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, Saint Louis, MO 63130 USA
| | - Fuzhong Zhang
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, Saint Louis, MO 63130 USA
- Division of Biological & Biomedical Sciences, Washington University in St. Louis, Saint Louis, MO 63130 USA
- Institute of Materials Science & Engineering, Washington University in St. Louis, Saint Louis, MO 63130 USA
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61
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You ZN, Chen Q, Shi SC, Zheng MM, Pan J, Qian XL, Li CX, Xu JH. Switching Cofactor Dependence of 7β-Hydroxysteroid Dehydrogenase for Cost-Effective Production of Ursodeoxycholic Acid. ACS Catal 2018. [DOI: 10.1021/acscatal.8b03561] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Zhi-Neng You
- Laboratory of Biocatalysis and Synthetic Biotechnology, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Qi Chen
- Laboratory of Biocatalysis and Synthetic Biotechnology, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
- Shanghai Collaborative Innovation Center for Biomanufacturing, School of Biotechnology, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Shou-Cheng Shi
- Laboratory of Biocatalysis and Synthetic Biotechnology, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Ming-Min Zheng
- Laboratory of Biocatalysis and Synthetic Biotechnology, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Jiang Pan
- Laboratory of Biocatalysis and Synthetic Biotechnology, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
- Shanghai Collaborative Innovation Center for Biomanufacturing, School of Biotechnology, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Xiao-Long Qian
- Suzhou Bioforany EnzyTech Co. Ltd., No. 8 Yanjiuyuan Road, Economic Development Zone, Changshu, Jiangsu 215512, China
| | - Chun-Xiu Li
- Laboratory of Biocatalysis and Synthetic Biotechnology, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
- Shanghai Collaborative Innovation Center for Biomanufacturing, School of Biotechnology, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Jian-He Xu
- Laboratory of Biocatalysis and Synthetic Biotechnology, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
- Shanghai Collaborative Innovation Center for Biomanufacturing, School of Biotechnology, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
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62
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Welter K. (R)Evolution aus dem Labor. CHEM UNSERER ZEIT 2018. [DOI: 10.1002/ciuz.201880030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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63
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Abstract
Photorespiration limits plant carbon fixation by releasing CO2 and using cellular resources to recycle the product of ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) oxygenation, 2-phosphoglycolate. We systematically designed synthetic photorespiration bypasses that combine existing and new-to-nature enzymatic activities and that do not release CO2. Our computational model shows that these bypasses could enhance carbon fixation rate under a range of physiological conditions. To realize the designed bypasses, a glycolate reduction module, which does not exist in nature, is needed to be engineered. By reshaping the substrate and cofactor specificity of two natural enzymes, we established glycolate reduction to glycolaldehyde. With the addition of three natural enzymes, we observed recycling of glycolate to the key Calvin Cycle intermediate ribulose 1,5-bisphosphate with no carbon loss. Photorespiration recycles ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) oxygenation product, 2-phosphoglycolate, back into the Calvin Cycle. Natural photorespiration, however, limits agricultural productivity by dissipating energy and releasing CO2. Several photorespiration bypasses have been previously suggested but were limited to existing enzymes and pathways that release CO2. Here, we harness the power of enzyme and metabolic engineering to establish synthetic routes that bypass photorespiration without CO2 release. By defining specific reaction rules, we systematically identified promising routes that assimilate 2-phosphoglycolate into the Calvin Cycle without carbon loss. We further developed a kinetic–stoichiometric model that indicates that the identified synthetic shunts could potentially enhance carbon fixation rate across the physiological range of irradiation and CO2, even if most of their enzymes operate at a tenth of Rubisco’s maximal carboxylation activity. Glycolate reduction to glycolaldehyde is essential for several of the synthetic shunts but is not known to occur naturally. We, therefore, used computational design and directed evolution to establish this activity in two sequential reactions. An acetyl-CoA synthetase was engineered for higher stability and glycolyl-CoA synthesis. A propionyl-CoA reductase was engineered for higher selectivity for glycolyl-CoA and for use of NADPH over NAD+, thereby favoring reduction over oxidation. The engineered glycolate reduction module was then combined with downstream condensation and assimilation of glycolaldehyde to ribulose 1,5-bisphosphate, thus providing proof of principle for a carbon-conserving photorespiration pathway.
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64
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Wu W, Zhang Y, Liu D, Chen Z. Efficient mining of natural NADH-utilizing dehydrogenases enables systematic cofactor engineering of lysine synthesis pathway of Corynebacterium glutamicum. Metab Eng 2018; 52:77-86. [PMID: 30458240 DOI: 10.1016/j.ymben.2018.11.006] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Revised: 10/22/2018] [Accepted: 11/16/2018] [Indexed: 12/01/2022]
Abstract
Increasing the availability of NADPH is commonly used to improve lysine production by Corynebacterium glutamicum since 4 mol of NADPH are required for the synthesis of 1 mol of lysine. Alternatively, engineering of enzymes in lysine synthesis pathway to utilize NADH directly can also be explored for cofactor balance during lysine overproduction. To achieve such a goal, enzyme mining was used in this study to quickly identify a full set of NADH-utilizing dehydrogenases, namely aspartate dehydrogenase from Pseudomonas aeruginosa (PaASPDH), aspartate-semialdehyde dehydrogenase from Tistrella mobilis (TmASADH), dihydrodipicolinate reductase from Escherichia coli (EcDHDPR), and diaminopimelate dehydrogenase from Pseudothermotoga thermarum (PtDAPDH). This allowed us to systematically perturb cofactor utilization of lysine synthesis pathway of C. glutamicum for the first time. Individual overexpression of PaASPDH, TmASADH, EcDHDPR, and PtDAPDH in C. glutamicum LC298, a basic lysine producer, increased the production of lysine by 30.7%, 32.4%, 17.4%, and 36.8%, respectively. Combinatorial replacement of NADPH-dependent dehydrogenases in C. glutamicum ATCC 21543, a lysine hyperproducer, also resulted in significantly improved lysine production. The highest increase of lysine production (30.7%) was observed for a triple-mutant strain (27.7 g/L, 0.35 g/g glucose) expressing PaASPDH, TmASADH, and EcDHDPR. A quadruple-mutant strain expressing all of the four NADH-utilizing enzymes allowed high lysine production (24.1 g/L, 0.30 g/g glucose) almost independent of the oxidative pentose phosphate pathway. Collectively, our results demonstrated that a combination of enzyme mining and cofactor engineering was a highly efficient approach to improve lysine production. Similar strategies can be applied for the production of other amino acids or their derivatives.
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Affiliation(s)
- Wenjun Wu
- Key Laboratory of Industrial Biocatalysis (Ministry of Education), Department of Chemical Engineering, Tsinghua University, Beijing 100084, China
| | - Ye Zhang
- Key Laboratory of Industrial Biocatalysis (Ministry of Education), Department of Chemical Engineering, Tsinghua University, Beijing 100084, China
| | - Dehua Liu
- Key Laboratory of Industrial Biocatalysis (Ministry of Education), Department of Chemical Engineering, Tsinghua University, Beijing 100084, China; Tsinghua Innovation Center in Dongguan, Dongguan 523808, China; Center for Synthetic and Systems Biology, Tsinghua University, Beijing 100084, China
| | - Zhen Chen
- Key Laboratory of Industrial Biocatalysis (Ministry of Education), Department of Chemical Engineering, Tsinghua University, Beijing 100084, China; Tsinghua Innovation Center in Dongguan, Dongguan 523808, China; Center for Synthetic and Systems Biology, Tsinghua University, Beijing 100084, China.
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65
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Acedos MG, Santos VE, Garcia-Ochoa F. Resting cells isobutanol production by Shimwellia blattae (p424IbPSO): Influence of growth culture conditions. Biotechnol Prog 2018; 34:1073-1080. [PMID: 30281946 DOI: 10.1002/btpr.2705] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Revised: 05/31/2018] [Accepted: 08/08/2018] [Indexed: 01/19/2023]
Abstract
Isobutanol is a promising gasoline additive and could even be a potential substitute used directly as combustible. In this work, the production of isobutanol from glucose by Shimwellia blattae (p424IbPSO) in resting cell cultures is studied. This production has two stages, involving a resting cell phase that has not been studied before. The cell growth was carried out under different operating conditions: temperature and medium composition (YE, ammonium, and IPTG concentrations), looking for the highest isobutanol production. Moreover, the cells were collected at three different growth times checking their isobutanol production capacity. The best operating conditions have been determined as: 30°C of temperature, a medium containing 1.5 g L-1 YE and 1.4 g L-1 of ammonium as nitrogen sources, adding 0.5 mM IPTG as inducer. The cells collected at early growth times are significantly more active. The use of S. blattae (p424IbPSO) in resting cells is a good strategy for the production of isobutanol from glucose yielding better results than in batch growth cultures, a yield of 60% attainment of theoretical maximum yield is obtained under optimal conditions. In addition, it has been demonstrated that if the cells are cultured at higher temperatures and with high IPTG concentrations, inclusion bodies are formed in the cytoplasm inhibiting the isobutanol production in the resting cell stage.
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Affiliation(s)
- Miguel G Acedos
- Dept. of Chemical and Materials Engineering, Universidad Complutense, Madrid, 28040, Spain
| | - Victoria E Santos
- Dept. of Chemical and Materials Engineering, Universidad Complutense, Madrid, 28040, Spain
| | - Felix Garcia-Ochoa
- Dept. of Chemical and Materials Engineering, Universidad Complutense, Madrid, 28040, Spain
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66
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NADH/NADPH bi-cofactor-utilizing and thermoactive ketol-acid reductoisomerase from Sulfolobus acidocaldarius. Sci Rep 2018; 8:7176. [PMID: 29739976 PMCID: PMC5940873 DOI: 10.1038/s41598-018-25361-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Accepted: 04/19/2018] [Indexed: 11/13/2022] Open
Abstract
Ketol-acid reductoisomerase (KARI) is a bifunctional enzyme in the second step of branched-chain amino acids biosynthetic pathway. Most KARIs prefer NADPH as a cofactor. However, KARI with a preference for NADH is desirable in industrial applications including anaerobic fermentation for the production of branched-chain amino acids or biofuels. Here, we characterize a thermoacidophilic archaeal Sac-KARI from Sulfolobus acidocaldarius and present its crystal structure at a 1.75-Å resolution. By comparison with other holo-KARI structures, one sulphate ion is observed in each binding site for the 2′-phosphate of NADPH, implicating its NADPH preference. Sac-KARI has very high affinity for NADPH and NADH, with KM values of 0.4 μM for NADPH and 6.0 μM for NADH, suggesting that both are good cofactors at low concentrations although NADPH is favoured over NADH. Furthermore, Sac-KARI can catalyze 2(S)-acetolactate (2S-AL) with either cofactor from 25 to 60 °C, but the enzyme has higher activity by using NADPH. In addition, the catalytic activity of Sac-KARI increases significantly with elevated temperatures and reaches an optimum at 60 °C. Bi-cofactor utilization and the thermoactivity of Sac-KARI make it a potential candidate for use in metabolic engineering or industrial applications under anaerobic or harsh conditions.
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67
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Liu J, Li H, Zhao G, Caiyin Q, Qiao J. Redox cofactor engineering in industrial microorganisms: strategies, recent applications and future directions. J Ind Microbiol Biotechnol 2018; 45:313-327. [PMID: 29582241 DOI: 10.1007/s10295-018-2031-7] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Accepted: 03/22/2018] [Indexed: 02/07/2023]
Abstract
NAD and NADP, a pivotal class of cofactors, which function as essential electron donors or acceptors in all biological organisms, drive considerable catabolic and anabolic reactions. Furthermore, they play critical roles in maintaining intracellular redox homeostasis. However, many metabolic engineering efforts in industrial microorganisms towards modification or introduction of metabolic pathways, especially those involving consumption, generation or transformation of NAD/NADP, often induce fluctuations in redox state, which dramatically impede cellular metabolism, resulting in decreased growth performance and biosynthetic capacity. Here, we comprehensively review the cofactor engineering strategies for solving the problematic redox imbalance in metabolism modification, as well as their features, suitabilities and recent applications. Some representative examples of in vitro biocatalysis are also described. In addition, we briefly discuss how tools and methods from the field of synthetic biology can be applied for cofactor engineering. Finally, future directions and challenges for development of cofactor redox engineering are presented.
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Affiliation(s)
- Jiaheng Liu
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, 300072, People's Republic of China
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, People's Republic of China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin, 300072, People's Republic of China
| | - Huiling Li
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, 300072, People's Republic of China
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, People's Republic of China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin, 300072, People's Republic of China
| | - Guangrong Zhao
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, 300072, People's Republic of China
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, People's Republic of China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin, 300072, People's Republic of China
| | - Qinggele Caiyin
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, 300072, People's Republic of China
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, People's Republic of China
| | - Jianjun Qiao
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, 300072, People's Republic of China.
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, People's Republic of China.
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin, 300072, People's Republic of China.
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68
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Xu JZ, Yang HK, Zhang WG. NADPH metabolism: a survey of its theoretical characteristics and manipulation strategies in amino acid biosynthesis. Crit Rev Biotechnol 2018; 38:1061-1076. [PMID: 29480038 DOI: 10.1080/07388551.2018.1437387] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
Reduced nicotinamide adenine nucleotide phosphate (NADPH), which is one of the key cofactors in the metabolic network, plays an important role in the biochemical reactions, and physiological function of amino acid-producing strains. The manipulation of NADPH availability and form is an efficient and easy method of redirecting the carbon flux to the amino acid biosynthesis in industrial strains. In this review, we survey the metabolic mode of NADPH. Furthermore, we summarize the research developments in the understanding of the relationship between NADPH metabolism and amino acid biosynthesis. Detailed strategies to manipulate NADPH availability are addressed based on this knowledge. Finally, the uses of NADPH manipulation strategies to enhance the metabolic function of amino acid-producing strains are discussed.
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Affiliation(s)
- Jian-Zhong Xu
- a The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology , Jiangnan University , WuXi , PR China.,b The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology , Jiangnan University , WuXi , PR China
| | - Han-Kun Yang
- a The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology , Jiangnan University , WuXi , PR China
| | - Wei-Guo Zhang
- a The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology , Jiangnan University , WuXi , PR China
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69
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Chánique AM, Parra LP. Protein Engineering for Nicotinamide Coenzyme Specificity in Oxidoreductases: Attempts and Challenges. Front Microbiol 2018; 9:194. [PMID: 29491854 PMCID: PMC5817062 DOI: 10.3389/fmicb.2018.00194] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Accepted: 01/29/2018] [Indexed: 01/10/2023] Open
Abstract
Oxidoreductases are ubiquitous enzymes that catalyze an extensive range of chemical reactions with great specificity, efficiency, and selectivity. Most oxidoreductases are nicotinamide cofactor-dependent enzymes with a strong preference for NADP or NAD. Because these coenzymes differ in stability, bioavailability and costs, the enzyme preference for a specific coenzyme is an important issue for practical applications. Different approaches for the manipulation of coenzyme specificity have been reported, with different degrees of success. Here we present various attempts for the switching of nicotinamide coenzyme preference in oxidoreductases by protein engineering. This review covers 103 enzyme engineering studies from 82 articles and evaluates the accomplishments in terms of coenzyme specificity and catalytic efficiency compared to wild type enzymes of different classes. We analyzed different protein engineering strategies and related them with the degree of success in inverting the cofactor specificity. In general, catalytic activity is compromised when coenzyme specificity is reversed, however when switching from NAD to NADP, better results are obtained. In most of the cases, rational strategies were used, predominantly with loop exchange generating the best results. In general, the tendency of removing acidic residues and incorporating basic residues is the strategy of choice when trying to change specificity from NAD to NADP, and vice versa. Computational strategies and algorithms are also covered as helpful tools to guide protein engineering strategies. This mini review aims to give a general introduction to the topic, giving an overview of tools and information to work in protein engineering for the reversal of coenzyme specificity.
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Affiliation(s)
- Andrea M Chánique
- Department of Chemical and Bioprocesses Engineering, School of Engineering, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Loreto P Parra
- Department of Chemical and Bioprocesses Engineering, School of Engineering, Pontificia Universidad Católica de Chile, Santiago, Chile.,Schools of Engineering, Medicine and Biological Sciences, Institute for Biological and Medical Engineering, Pontificia Universidad Católica de Chile, Santiago, Chile
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70
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Rational design of a synthetic Entner-Doudoroff pathway for enhancing glucose transformation to isobutanol in Escherichia coli. J Ind Microbiol Biotechnol 2018; 45:187-199. [PMID: 29380153 DOI: 10.1007/s10295-018-2017-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Accepted: 01/23/2018] [Indexed: 01/18/2023]
Abstract
Isobutanol as a more desirable biofuel has attracted much attention. In our previous work, an isobutanol-producing strain Escherichia coli LA09 had been obtained by rational redox status improvement under guidance of the genome-scale metabolic model. However, the low transformation from sugar to isobutanol is a limiting factor for isobutanol production by E. coli LA09. In this study, the intracellular metabolic profiles of the isobutanol-producing E. coli LA09 with different initial glucose concentrations were investigated and the metabolic reaction of fructose 6-phosphate to 1, 6-diphosphate fructose in glycolytic pathway was identified as the rate-limiting step of glucose transformation. Thus, redesigned carbon catabolism was implemented by altering flux of sugar metabolism. Here, the heterologous Entner-Doudoroff (ED) pathway from Zymomonas mobilis was constructed, and the adaptation of upper and lower parts of ED pathway was further improved with artificial promoters to alleviate the accumulation of toxic intermediate metabolite 2-keto-3-deoxy-6-phospho-gluconate (KDPG). Finally, the best isobutanol-producing E. coli ED02 with higher glucose transformation and isobutanol production was obtained. In the fermentation of strain E. coli ED02 with 45 g/L initial glucose, the isobutanol titer, yield and average producing rate were, respectively, increased by 56.8, 47.4 and 88.1% to 13.67 g/L, 0.50 C-mol/C-mol and 0.456 g/(L × h) in a shorter time of 30 h, compared with that of the starting strain E. coli LA09.
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71
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Balke K, Beier A, Bornscheuer UT. Hot spots for the protein engineering of Baeyer-Villiger monooxygenases. Biotechnol Adv 2018; 36:247-263. [DOI: 10.1016/j.biotechadv.2017.11.007] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Revised: 11/15/2017] [Accepted: 11/17/2017] [Indexed: 10/18/2022]
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72
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Siripong W, Wolf P, Kusumoputri TP, Downes JJ, Kocharin K, Tanapongpipat S, Runguphan W. Metabolic engineering of Pichia pastoris for production of isobutanol and isobutyl acetate. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:1. [PMID: 29321810 PMCID: PMC5757298 DOI: 10.1186/s13068-017-1003-x] [Citation(s) in RCA: 129] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Accepted: 12/21/2017] [Indexed: 05/18/2023]
Abstract
BACKGROUND Interests in renewable fuels have exploded in recent years as the serious effects of global climate change become apparent. Microbial production of high-energy fuels by economically efficient bioprocesses has emerged as an attractive alternative to the traditional production of transportation fuels. Here, we engineered Pichia pastoris, an industrial workhorse in heterologous enzyme production, to produce the biofuel isobutanol from two renewable carbon sources, glucose and glycerol. Our strategy exploited the yeast's amino acid biosynthetic pathway and diverted the amino acid intermediates to the 2-keto acid degradation pathway for higher alcohol production. To further demonstrate the versatility of our yeast platform, we incorporated a broad-substrate-range alcohol-O-acyltransferase to generate a variety of volatile esters, including isobutyl acetate ester and isopentyl acetate ester. RESULTS The engineered strain overexpressing the keto-acid degradation pathway was able to produce 284 mg/L of isobutanol when supplemented with 2-ketoisovalerate. To improve the production of isobutanol and eliminate the need to supplement the production media with the expensive 2-ketoisovalerate intermediate, we overexpressed a portion of the amino acid l-valine biosynthetic pathway in the engineered strain. While heterologous expression of the pathway genes from the yeast Saccharomyces cerevisiae did not lead to improvement in isobutanol production in the engineered P. pastoris, overexpression of the endogenous l-valine biosynthetic pathway genes led to a strain that is able to produce 0.89 g/L of isobutanol. Fine-tuning the expression of bottleneck enzymes by employing an episomal plasmid-based expression system further improved the production titer of isobutanol to 2.22 g/L, a 43-fold improvement from the levels observed in the original strain. Finally, heterologous expression of a broad-substrate-range alcohol-O-acyltransferase led to the production of isobutyl acetate ester and isopentyl acetate ester at 51 and 24 mg/L, respectively. CONCLUSIONS In this study, we engineered high-level production of the biofuel isobutanol and the corresponding acetate ester by P. pastoris from readily available carbon sources. We envision that our work will provide an economic route to this important class of compounds and establish P. pastoris as a versatile production platform for fuels and chemicals.
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Affiliation(s)
- Wiparat Siripong
- National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Paholyothin Road, Klong 1, Klong Luang, Pathumthani 12120 Thailand
| | - Philipp Wolf
- Leipzig University, Brüderstraße 34, 04103 Leipzig, Germany
| | - Theodora Puspowangi Kusumoputri
- Atma Jaya University, Jl. Jend. Sudirman No.51, RT.5/RW.4, Karet Semanggi, Setia Budi, Kota Jakarta Selatan, Daerah Khusus Ibukota Jakarta, 12930 Indonesia
| | | | - Kanokarn Kocharin
- National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Paholyothin Road, Klong 1, Klong Luang, Pathumthani 12120 Thailand
| | - Sutipa Tanapongpipat
- National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Paholyothin Road, Klong 1, Klong Luang, Pathumthani 12120 Thailand
| | - Weerawat Runguphan
- National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Paholyothin Road, Klong 1, Klong Luang, Pathumthani 12120 Thailand
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73
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Li KH, Yu YH, Dong HJ, Zhang WB, Ma JC, Wang HH. Biological Functions of ilvC in Branched-Chain Fatty Acid Synthesis and Diffusible Signal Factor Family Production in Xanthomonas campestris. Front Microbiol 2017; 8:2486. [PMID: 29312195 PMCID: PMC5733099 DOI: 10.3389/fmicb.2017.02486] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Accepted: 11/29/2017] [Indexed: 12/16/2022] Open
Abstract
In bacteria, the metabolism of branched-chain amino acids (BCAAs) is tightly associated with branched-chain fatty acids (BCFAs) synthetic pathways. Although previous studies have reported on BCFAs biosynthesis, more detailed associations between BCAAs metabolism and BCFAs biosynthesis remain to be addressed. In this study, we deleted the ilvC gene, which encodes ketol-acid reductoisomerase in the BCAAs synthetic pathway, from the Xanthomonas campestris pv. campestris (Xcc) genome. We characterized gene functions in BCFAs biosynthesis and production of the diffusible signal factor (DSF) family signals. Disruption of ilvC caused Xcc to become auxotrophic for valine and isoleucine, and lose the ability to synthesize BCFAs via carbohydrate metabolism. Furthermore, ilvC mutant reduced the ability to produce DSF-family signals, especially branched-chain DSF-family signals, which might be the main reason for Xcc reduction of pathogenesis toward host plants. In this report, we confirmed that BCFAs do not have major functions in acclimatizing Xcc cells to low temperatures.
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Affiliation(s)
- Kai-Huai Li
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, China
| | - Yong-Hong Yu
- Guangdong Food and Drug Vocational College, Guangzhou, China
| | - Hui-Juan Dong
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, China
| | - Wen-Bin Zhang
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, China
| | - Jin-Cheng Ma
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, China
| | - Hai-Hong Wang
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, China
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74
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Wang M, Chen B, Fang Y, Tan T. Cofactor engineering for more efficient production of chemicals and biofuels. Biotechnol Adv 2017; 35:1032-1039. [DOI: 10.1016/j.biotechadv.2017.09.008] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Revised: 09/14/2017] [Accepted: 09/15/2017] [Indexed: 01/04/2023]
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75
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Uncovering the role of branched-chain amino acid transaminases in Saccharomyces cerevisiae isobutanol biosynthesis. Metab Eng 2017; 44:302-312. [DOI: 10.1016/j.ymben.2017.10.001] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Revised: 09/29/2017] [Accepted: 10/02/2017] [Indexed: 12/20/2022]
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76
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You C, Huang R, Wei X, Zhu Z, Zhang YHP. Protein engineering of oxidoreductases utilizing nicotinamide-based coenzymes, with applications in synthetic biology. Synth Syst Biotechnol 2017; 2:208-218. [PMID: 29318201 PMCID: PMC5655348 DOI: 10.1016/j.synbio.2017.09.002] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2017] [Revised: 09/08/2017] [Accepted: 09/22/2017] [Indexed: 01/01/2023] Open
Abstract
Two natural nicotinamide-based coenzymes (NAD and NADP) are indispensably required by the vast majority of oxidoreductases for catabolism and anabolism, respectively. Most NAD(P)-dependent oxidoreductases prefer one coenzyme as an electron acceptor or donor to the other depending on their different metabolic roles. This coenzyme preference associated with coenzyme imbalance presents some challenges for the construction of high-efficiency in vivo and in vitro synthetic biology pathways. Changing the coenzyme preference of NAD(P)-dependent oxidoreductases is an important area of protein engineering, which is closely related to product-oriented synthetic biology projects. This review focuses on the methodology of nicotinamide-based coenzyme engineering, with its application in improving product yields and decreasing production costs. Biomimetic nicotinamide-containing coenzymes have been proposed to replace natural coenzymes because they are more stable and less costly than natural coenzymes. Recent advances in the switching of coenzyme preference from natural to biomimetic coenzymes are also covered in this review. Engineering coenzyme preferences from natural to biomimetic coenzymes has become an important direction for coenzyme engineering, especially for in vitro synthetic pathways and in vivo bioorthogonal redox pathways.
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Affiliation(s)
- Chun You
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, People's Republic of China
| | - Rui Huang
- Biological Systems Engineering Department, Virginia Tech, 304 Seitz Hall, Blacksburg, VA 24061, USA
| | - Xinlei Wei
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, People's Republic of China
| | - Zhiguang Zhu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, People's Republic of China
| | - Yi-Heng Percival Zhang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, People's Republic of China.,Biological Systems Engineering Department, Virginia Tech, 304 Seitz Hall, Blacksburg, VA 24061, USA
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77
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Meadows CW, Kang A, Lee TS. Metabolic Engineering for Advanced Biofuels Production and Recent Advances Toward Commercialization. Biotechnol J 2017; 13. [DOI: 10.1002/biot.201600433] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2017] [Revised: 06/13/2017] [Indexed: 12/27/2022]
Affiliation(s)
- Corey W. Meadows
- Joint BioEnergy Institute5885 Hollis StreetEmeryvilleCA94608USA
- Biological Systems & Engineering DivisionLawrence Berkeley National LaboratoryBerkeleyCA94720USA
| | - Aram Kang
- Joint BioEnergy Institute5885 Hollis StreetEmeryvilleCA94608USA
- Biological Systems & Engineering DivisionLawrence Berkeley National LaboratoryBerkeleyCA94720USA
| | - Taek S. Lee
- Joint BioEnergy Institute5885 Hollis StreetEmeryvilleCA94608USA
- Biological Systems & Engineering DivisionLawrence Berkeley National LaboratoryBerkeleyCA94720USA
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78
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Jung HM, Kim YH, Oh MK. Formate and Nitrate Utilization in Enterobacter aerogenes for Semi-Anaerobic Production of Isobutanol. Biotechnol J 2017; 12. [PMID: 28731532 DOI: 10.1002/biot.201700121] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Revised: 07/07/2017] [Indexed: 11/07/2022]
Abstract
Anaerobic bioprocessing is preferred because of its economic advantages. However, low productivity and decreased growth of the host strain have limited the use of the anaerobic process. Anaerobic respiration can be applied to anoxic processing using formate and nitrate metabolism to improve the productivity of value-added metabolites. A isobutanol-producing strains is constructed using Enterobacter aerogenes as a host strain by metabolic engineering approaches. The byproduct pathway (ldhA, budA, and pflB) is knocked out, and heterologous keto-acid decarboxylase (kivD) and alcohol dehydrogenase (adhA) are expressed along with the L-valine synthesis pathway (ilvCD and budB). The pyruvate formate-lyase mutant shows decreased growth rates when cultivated in semi-anaerobic conditions, which results in a decline in productivity. When formate and nitrate are supplied in the culture medium, the growth rates and amount of isobutanol production is restored (4.4 g L-1 , 0.23 g g-1 glucose, 0.18 g L-1 h-1 ). To determine the function of the formate and nitrate coupling reaction system, the mutant strains that could not utilize formate or nitrate is contructed. Decreased growth and productivity are observed in the nitrate reductase (narG) mutant strain. This is the first report of engineering isobutanol-producing E. aerogenes to increase strain fitness via augmentation of formate and nitrate metabolism during anaerobic cultivation.
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Affiliation(s)
- Hwi-Min Jung
- Department of Chemical and Biological Engineering, Korea University, Seoul, Korea
| | - Yong Hwan Kim
- School of Energy and Chemical Engineering, UNIST, Ulsan, Korea
| | - Min-Kyu Oh
- Department of Chemical and Biological Engineering, Korea University, Seoul, Korea
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79
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Abstract
Bulk gold (Au) is known to be chemically inactive. However, when the size of Au nanoparticles (Au NPs) decreases to close to 1 nm or sub-nanometer dimensions, these ultrasmall Au nanoclusters (Au NCs) begin to possess interesting physical and chemical properties and likewise spawn different applications when working with bulk Au or even Au NPs. In this study, we found that it is possible to confer antimicrobial activity to Au NPs through precise control of their size down to NC dimension (typically less than 2 nm). Au NCs could kill both Gram-positive and Gram-negative bacteria. This wide-spectrum antimicrobial activity is attributed to the ultrasmall size of Au NCs, which would allow them to better interact with bacteria. The interaction between ultrasmall Au NCs and bacteria could induce a metabolic imbalance in bacterial cells after the internalization of Au NCs, leading to an increase of intracellular reactive oxygen species production that kills bacteria consequently.
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Affiliation(s)
- Kaiyuan Zheng
- Department of Chemical and Biomolecular Engineering, National University of Singapore , 4 Engineering Drive 4, Singapore 117585
| | - Magdiel I Setyawati
- Department of Chemical and Biomolecular Engineering, National University of Singapore , 4 Engineering Drive 4, Singapore 117585
| | - David Tai Leong
- Department of Chemical and Biomolecular Engineering, National University of Singapore , 4 Engineering Drive 4, Singapore 117585
| | - Jianping Xie
- Department of Chemical and Biomolecular Engineering, National University of Singapore , 4 Engineering Drive 4, Singapore 117585
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80
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Solanki K, Abdallah W, Banta S. Engineering the cofactor specificity of an alcohol dehydrogenase via single mutations or insertions distal to the 2'-phosphate group of NADP(H). Protein Eng Des Sel 2017; 30:373-380. [PMID: 28201792 DOI: 10.1093/protein/gzx009] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Accepted: 01/25/2017] [Indexed: 01/04/2023] Open
Abstract
There have been many reports exploring the engineering of the cofactor specificity of aldo-keto reductases (AKRs), as this class of proteins is ubiquitous and exhibits many useful activities. A common approach is the mutagenesis of amino acids involved in interactions with the 2'-phosphate group of NADP(H) in the cofactor binding pocket. We recently performed a 'loop-grafting' approach to engineer the substrate specificity of the thermostable alcohol dehydrogenase D (AdhD) from Pyrococcus furiosus and we found that a loop insertion after residue 211, which is on the back side of the cofactor binding pocket, could also alter cofactor specificity. Here, we further explore this approach by introducing single point mutations and single amino acid insertions at the loop insertion site. Six different mutants of AdhD were created by either converting glycine 211 to cysteine or serine or by inserting alanine, serine, glycine or cysteine between the 211 and 212 residues. Several mutants gained activity with NADP+ above the wild-type enzyme. And remarkably, it was found that all of the mutants investigated resulted in some degree of reversal of cofactor specificity in the oxidative direction. These changes were generally a result of changes in conformations of the ternary enzyme/cofactor/substrate complexes as opposed to changes in affinities or binding energies of the cofactors. This study highlights the role that amino acids which are distal to the cofactor binding pocket but are involved in substrate interactions can influence cofactor specificity in AdhD, and this strategy should translate to other AKR family members.
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Affiliation(s)
- Kusum Solanki
- Department of Chemical Engineering, Columbia University in the City of New York, New York, NY 10027, USA
| | - Walaa Abdallah
- Department of Chemical Engineering, Columbia University in the City of New York, New York, NY 10027, USA
| | - Scott Banta
- Department of Chemical Engineering, Columbia University in the City of New York, New York, NY 10027, USA
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81
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Nguyen DMN, Schut GJ, Zadvornyy OA, Tokmina-Lukaszewska M, Poudel S, Lipscomb GL, Adams LA, Dinsmore JT, Nixon WJ, Boyd ES, Bothner B, Peters JW, Adams MWW. Two functionally distinct NADP +-dependent ferredoxin oxidoreductases maintain the primary redox balance of Pyrococcus furiosus. J Biol Chem 2017; 292:14603-14616. [PMID: 28705933 DOI: 10.1074/jbc.m117.794172] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Revised: 07/10/2017] [Indexed: 01/08/2023] Open
Abstract
Electron bifurcation has recently gained acceptance as the third mechanism of energy conservation in which energy is conserved through the coupling of exergonic and endergonic reactions. A structure-based mechanism of bifurcation has been elucidated recently for the flavin-based enzyme NADH-dependent ferredoxin NADP+ oxidoreductase I (NfnI) from the hyperthermophillic archaeon Pyrococcus furiosus. NfnI is thought to be involved in maintaining the cellular redox balance, producing NADPH for biosynthesis by recycling the two other primary redox carriers, NADH and ferredoxin. The P. furiosus genome encodes an NfnI paralog termed NfnII, and the two are differentially expressed, depending on the growth conditions. In this study, we show that deletion of the genes encoding either NfnI or NfnII affects the cellular concentrations of NAD(P)H and particularly NADPH. This results in a moderate to severe growth phenotype in deletion mutants, demonstrating a key role for each enzyme in maintaining redox homeostasis. Despite their similarity in primary sequence and cofactor content, crystallographic, kinetic, and mass spectrometry analyses reveal that there are fundamental structural differences between the two enzymes, and NfnII does not catalyze the NfnI bifurcating reaction. Instead, it exhibits non-bifurcating ferredoxin NADP oxidoreductase-type activity. NfnII is therefore proposed to be a bifunctional enzyme and also to catalyze a bifurcating reaction, although its third substrate, in addition to ferredoxin and NADP(H), is as yet unknown.
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Affiliation(s)
- Diep M N Nguyen
- From the Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602
| | - Gerrit J Schut
- From the Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602
| | - Oleg A Zadvornyy
- the Institute of Biological Chemistry, Washington State University, Pullman, Washington 99164, and
| | | | - Saroj Poudel
- Microbiology and Immunology, Montana State University, Bozeman, Montana 59717
| | - Gina L Lipscomb
- From the Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602
| | - Leslie A Adams
- From the Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602
| | - Jessica T Dinsmore
- From the Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602
| | - William J Nixon
- From the Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602
| | - Eric S Boyd
- Microbiology and Immunology, Montana State University, Bozeman, Montana 59717
| | | | - John W Peters
- the Institute of Biological Chemistry, Washington State University, Pullman, Washington 99164, and
| | - Michael W W Adams
- From the Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602,
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82
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Zhao C, Zhao Q, Li Y, Zhang Y. Engineering redox homeostasis to develop efficient alcohol-producing microbial cell factories. Microb Cell Fact 2017; 16:115. [PMID: 28646866 PMCID: PMC5483285 DOI: 10.1186/s12934-017-0728-3] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2017] [Accepted: 06/16/2017] [Indexed: 12/11/2022] Open
Abstract
The biosynthetic pathways of most alcohols are linked to intracellular redox homeostasis, which is crucial for life. This crucial balance is primarily controlled by the generation of reducing equivalents, as well as the (reduction)-oxidation metabolic cycle and the thiol redox homeostasis system. As a main oxidation pathway of reducing equivalents, the biosynthesis of most alcohols includes redox reactions, which are dependent on cofactors such as NADH or NADPH. Thus, when engineering alcohol-producing strains, the availability of cofactors and redox homeostasis must be considered. In this review, recent advances on the engineering of cellular redox homeostasis systems to accelerate alcohol biosynthesis are summarized. Recent approaches include improving cofactor availability, manipulating the affinity of redox enzymes to specific cofactors, as well as globally controlling redox reactions, indicating the power of these approaches, and opening a path towards improving the production of a number of different industrially-relevant alcohols in the near future.
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Affiliation(s)
- Chunhua Zhao
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, No. 1 West Beichen Road Chaoyang District, Beijing, 100101 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Qiuwei Zhao
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, No. 1 West Beichen Road Chaoyang District, Beijing, 100101 China
| | - Yin Li
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, No. 1 West Beichen Road Chaoyang District, Beijing, 100101 China
| | - Yanping Zhang
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, No. 1 West Beichen Road Chaoyang District, Beijing, 100101 China
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83
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Liu Y, Zhuang Y, Ding D, Xu Y, Sun J, Zhang D. Biosensor-Based Evolution and Elucidation of a Biosynthetic Pathway in Escherichia coli. ACS Synth Biol 2017; 6:837-848. [PMID: 28121425 DOI: 10.1021/acssynbio.6b00328] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The successful evolution of metabolite-producing microbes requires a high-throughput screening method to obtain the desired properties within a short time. In this study, we developed a transcription-factor-driven device that combines a metabolite-responsive element and a selection module. This device was able to specifically sense intracellular l-phenylalanine (l-Phe) and convert this signal into an observable phenotype. Applying this device, we successfully improved l-Phe production by screening hyperproducing phenotypes from a ribonucleotide binding site library and a random mutagenesis library. In addition, several site mutations introduced by random mutagenesis were identified and elucidated to facilitate the improvement of l-Phe production. Our results present a paradigm for screening of compounds that are not easily observable to raise the yield of targeted compounds from a large candidate library. This approach may guide further applications in rewiring metabolic circuits and facilitate the directed evolution of recombinant strains.
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Affiliation(s)
- Yongfei Liu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- Key
Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Yinyin Zhuang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Dongqin Ding
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- Key
Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Yiran Xu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Jibin Sun
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- Key
Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Dawei Zhang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- Key
Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
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84
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Generoso WC, Brinek M, Dietz H, Oreb M, Boles E. Secretion of 2,3-dihydroxyisovalerate as a limiting factor for isobutanol production in Saccharomyces cerevisiae. FEMS Yeast Res 2017; 17:3821180. [DOI: 10.1093/femsyr/fox029] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2017] [Accepted: 05/11/2017] [Indexed: 01/23/2023] Open
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85
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Chen X, Gao C, Guo L, Hu G, Luo Q, Liu J, Nielsen J, Chen J, Liu L. DCEO Biotechnology: Tools To Design, Construct, Evaluate, and Optimize the Metabolic Pathway for Biosynthesis of Chemicals. Chem Rev 2017; 118:4-72. [DOI: 10.1021/acs.chemrev.6b00804] [Citation(s) in RCA: 109] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Xiulai Chen
- State
Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- Key
Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Cong Gao
- State
Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- Key
Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Liang Guo
- State
Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- Key
Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Guipeng Hu
- State
Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- Key
Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Qiuling Luo
- State
Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- Key
Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Jia Liu
- State
Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- Key
Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Jens Nielsen
- Department
of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg SE-412 96, Sweden
- Novo
Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK2800 Lyngby, Denmark
| | - Jian Chen
- State
Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- Key
Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Liming Liu
- State
Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- Department
of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg SE-412 96, Sweden
- Key
Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
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86
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Liu Z, Zhang Y, Jia X, Hu M, Deng Z, Xu Y, Liu T. In Vitro Reconstitution and Optimization of the Entire Pathway to Convert Glucose into Fatty Acid. ACS Synth Biol 2017; 6:701-709. [PMID: 28080041 DOI: 10.1021/acssynbio.6b00348] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Glucose and fatty acids play essential physiological roles in nearly all living organisms, and the pathway that converts glucose into fatty acid is pivotal to the central metabolic network. We have successfully reconstituted a pathway that converts glucose to fatty acid in vitro using 30 purified proteins. Through systematic titration and optimization of the glycolytic pathway and pyruvate dehydrogenase, we increased the yield of free fatty acid from nondetectable to a level that exceeded 9% of the theoretical yield. We also reconstituted the entire pentose-phosphate pathway of Escherichia coli and established a pentose phosphate-glycolysis hybrid pathway, replacing GAPDH to enhance NADPH availability. Our efforts provide a useful platform for research involving these core biochemical transformations.
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Affiliation(s)
- Zheng Liu
- Department
of Endocrinology, Zhongnan Hospital of Wuhan University, Wuhan 430071, China
| | - Yuchen Zhang
- Key
Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education and Wuhan University School of Pharmaceutical Sciences, Wuhan 430071, China
| | - Xiaoge Jia
- Key
Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education and Wuhan University School of Pharmaceutical Sciences, Wuhan 430071, China
| | - Mengzhu Hu
- Key
Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education and Wuhan University School of Pharmaceutical Sciences, Wuhan 430071, China
| | - Zixin Deng
- Key
Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education and Wuhan University School of Pharmaceutical Sciences, Wuhan 430071, China
| | - Yancheng Xu
- Department
of Endocrinology, Zhongnan Hospital of Wuhan University, Wuhan 430071, China
| | - Tiangang Liu
- Key
Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education and Wuhan University School of Pharmaceutical Sciences, Wuhan 430071, China
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87
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Cahn JKB, Werlang CA, Baumschlager A, Brinkmann-Chen S, Mayo SL, Arnold FH. A General Tool for Engineering the NAD/NADP Cofactor Preference of Oxidoreductases. ACS Synth Biol 2017; 6:326-333. [PMID: 27648601 DOI: 10.1021/acssynbio.6b00188] [Citation(s) in RCA: 93] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The ability to control enzymatic nicotinamide cofactor utilization is critical for engineering efficient metabolic pathways. However, the complex interactions that determine cofactor-binding preference render this engineering particularly challenging. Physics-based models have been insufficiently accurate and blind directed evolution methods too inefficient to be widely adopted. Building on a comprehensive survey of previous studies and our own prior engineering successes, we present a structure-guided, semirational strategy for reversing enzymatic nicotinamide cofactor specificity. This heuristic-based approach leverages the diversity and sensitivity of catalytically productive cofactor binding geometries to limit the problem to an experimentally tractable scale. We demonstrate the efficacy of this strategy by inverting the cofactor specificity of four structurally diverse NADP-dependent enzymes: glyoxylate reductase, cinnamyl alcohol dehydrogenase, xylose reductase, and iron-containing alcohol dehydrogenase. The analytical components of this approach have been fully automated and are available in the form of an easy-to-use web tool: Cofactor Specificity Reversal-Structural Analysis and Library Design (CSR-SALAD).
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Affiliation(s)
- Jackson K. B. Cahn
- Division of Chemistry and Chemical Engineering, and ‡Division of Biology and Biological
Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Caroline A. Werlang
- Division of Chemistry and Chemical Engineering, and ‡Division of Biology and Biological
Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Armin Baumschlager
- Division of Chemistry and Chemical Engineering, and ‡Division of Biology and Biological
Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Sabine Brinkmann-Chen
- Division of Chemistry and Chemical Engineering, and ‡Division of Biology and Biological
Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Stephen L. Mayo
- Division of Chemistry and Chemical Engineering, and ‡Division of Biology and Biological
Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Frances H. Arnold
- Division of Chemistry and Chemical Engineering, and ‡Division of Biology and Biological
Engineering, California Institute of Technology, Pasadena, California 91125, United States
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88
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Engineering the leucine biosynthetic pathway for isoamyl alcohol overproduction in Saccharomyces cerevisiae. ACTA ACUST UNITED AC 2017; 44:107-117. [DOI: 10.1007/s10295-016-1855-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Accepted: 10/30/2016] [Indexed: 10/20/2022]
Abstract
Abstract
Isoamyl alcohol can be used not only as a biofuel, but also as a precursor for various chemicals. Saccharomyces cerevisiae inherently produces a small amount of isoamyl alcohol via the leucine degradation pathway, but the yield is very low. In the current study, several strategies were devised to overproduce isoamyl alcohol in budding yeast. The engineered yeast cells with the cytosolic isoamyl alcohol biosynthetic pathway produced significantly higher amounts of isobutanol over isoamyl alcohol, suggesting that the majority of the metabolic flux was diverted to the isobutanol biosynthesis due to the broad substrate specificity of Ehrlich pathway enzymes. To channel the key intermediate 2-ketosiovalerate (KIV) towards α-IPM biosynthesis, we introduced an artificial protein scaffold to pull dihydroxyacid dehydratase and α-IPM synthase into the close proximity, and the resulting strain yielded more than twofold improvement of isoamyl alcohol. The best isoamyl alcohol producer yielded 522.76 ± 38.88 mg/L isoamyl alcohol, together with 540.30 ± 48.26 mg/L isobutanol and 82.56 ± 8.22 mg/L 2-methyl-1-butanol. To our best knowledge, our work represents the first study to bypass the native compartmentalized α-IPM biosynthesis pathway for the isoamyl alcohol overproduction in budding yeast. More importantly, artificial protein scaffold based on the feature of quaternary structure of enzymes would be useful in improving the catalytic efficiency and the product specificity of other enzymatic reactions.
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89
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Abstract
Alcohols (CnHn+2OH) are classified into primary, secondary, and tertiary alcohols, which can be branched or unbranched. They can also feature more than one OH-group (two OH-groups = diol; three OH-groups = triol). Presently, except for ethanol and sugar alcohols, they are mainly produced from fossil-based resources, such as petroleum, gas, and coal. Methanol and ethanol have the highest annual production volume accounting for 53 and 91 million tons/year, respectively. Most alcohols are used as fuels (e.g., ethanol), solvents (e.g., butanol), and chemical intermediates.This chapter gives an overview of recent research on the production of short-chain unbranched alcohols (C1-C5), focusing in particular on propanediols (1,2- and 1,3-propanediol), butanols, and butanediols (1,4- and 2,3-butanediol). It also provides a short summary on biobased higher alcohols (>C5) including branched alcohols.
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90
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91
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Chen H, Zhu Z, Huang R, Zhang YHP. Coenzyme Engineering of a Hyperthermophilic 6-Phosphogluconate Dehydrogenase from NADP + to NAD + with Its Application to Biobatteries. Sci Rep 2016; 6:36311. [PMID: 27805055 PMCID: PMC5090862 DOI: 10.1038/srep36311] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Accepted: 10/13/2016] [Indexed: 01/30/2023] Open
Abstract
Engineering the coenzyme specificity of redox enzymes plays an important role in metabolic engineering, synthetic biology, and biocatalysis, but it has rarely been applied to bioelectrochemistry. Here we develop a rational design strategy to change the coenzyme specificity of 6-phosphogluconate dehydrogenase (6PGDH) from a hyperthermophilic bacterium Thermotoga maritima from its natural coenzyme NADP+ to NAD+. Through amino acid-sequence alignment of NADP+- and NAD+-preferred 6PGDH enzymes and computer-aided substrate-coenzyme docking, the key amino acid residues responsible for binding the phosphate group of NADP+ were identified. Four mutants were obtained via site-directed mutagenesis. The best mutant N32E/R33I/T34I exhibited a ~6.4 × 104-fold reversal of the coenzyme selectivity from NADP+ to NAD+. The maximum power density and current density of the biobattery catalyzed by the mutant were 0.135 mW cm−2 and 0.255 mA cm−2, ~25% higher than those obtained from the wide-type 6PGDH-based biobattery at the room temperature. By using this 6PGDH mutant, the optimal temperature of running the biobattery was as high as 65 °C, leading to a high power density of 1.75 mW cm−2. This study demonstrates coenzyme engineering of a hyperthermophilic 6PGDH and its application to high-temperature biobatteries.
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Affiliation(s)
- Hui Chen
- Biological Systems Engineering Department, Virginia Tech, 304 Seitz Hall, Blacksburg, Virginia 24061, USA
| | - Zhiguang Zhu
- Cell Free Bioinnovations Inc. 1800 Kraft Drive, Suite 222, Blacksburg, VA 24060, USA.,Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin 300308, China
| | - Rui Huang
- Biological Systems Engineering Department, Virginia Tech, 304 Seitz Hall, Blacksburg, Virginia 24061, USA
| | - Yi-Heng Percival Zhang
- Biological Systems Engineering Department, Virginia Tech, 304 Seitz Hall, Blacksburg, Virginia 24061, USA.,Cell Free Bioinnovations Inc. 1800 Kraft Drive, Suite 222, Blacksburg, VA 24060, USA.,Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin 300308, China
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92
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Wu W, Tran-Gyamfi MB, Jaryenneh JD, Davis RW. Cofactor engineering of ketol-acid reductoisomerase (IlvC) and alcohol dehydrogenase (YqhD) improves the fusel alcohol yield in algal protein anaerobic fermentation. ALGAL RES 2016. [DOI: 10.1016/j.algal.2016.08.013] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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93
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Dong X, Chen X, Qian Y, Wang Y, Wang L, Qiao W, Liu L. Metabolic engineering of Escherichia coli W3110 to produce L-malate. Biotechnol Bioeng 2016; 114:656-664. [PMID: 27668703 DOI: 10.1002/bit.26190] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Revised: 09/05/2016] [Accepted: 09/19/2016] [Indexed: 11/07/2022]
Abstract
A four-carbon dicarboxylic acid L-malate has recently attracted attention due to its potential applications in the fields of medicine and agriculture. In this study, Escherichia coli W3110 was engineered and optimized for L-malate production via one-step L-malate synthesis pathway. First, deletion of the genes encoding lactate dehydrogenase (ldhA), pyruvate oxidase (poxB), pyruvate formate lyase (pflB), phosphotransacetylase (pta), and acetate kinase A (ackA) in pta-ackA pathway led to accumulate 20.9 g/L pyruvate. Then, overexpression of NADP+ -dependent malic enzyme C490S mutant in this multi-deletion mutant resulted in the direct conversion of pyruvate into L-malate (3.62 g/L). Next, deletion of the genes responsible for succinate biosynthesis further enhanced L-malate production up to 7.78 g/L. Finally, L-malate production was elevated to 21.65 g/L with the L-malate yield to 0.36 g/g in a 5 L bioreactor by overexpressing the pos5 gene encoding NADH kinase in the engineered E. coli F0931 strain. This study demonstrates the potential utility of one-step pathway for efficient L-malate production. Biotechnol. Bioeng. 2017;114: 656-664. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Xiaoxiang Dong
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China.,Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China.,Laboratory of Food Microbial-Manufacturing Engineering, Jiangnan University, Wuxi, China
| | - Xiulai Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China.,Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China.,Laboratory of Food Microbial-Manufacturing Engineering, Jiangnan University, Wuxi, China
| | - Yuanyuan Qian
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China.,Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China.,Laboratory of Food Microbial-Manufacturing Engineering, Jiangnan University, Wuxi, China
| | - Yuancai Wang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China.,Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China.,Laboratory of Food Microbial-Manufacturing Engineering, Jiangnan University, Wuxi, China
| | - Li Wang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China.,Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China.,Laboratory of Food Microbial-Manufacturing Engineering, Jiangnan University, Wuxi, China
| | - Weihua Qiao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China.,Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China.,Laboratory of Food Microbial-Manufacturing Engineering, Jiangnan University, Wuxi, China
| | - Liming Liu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China.,Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China.,Laboratory of Food Microbial-Manufacturing Engineering, Jiangnan University, Wuxi, China
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94
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Maneffa A, Priecel P, Lopez-Sanchez JA. Biomass-Derived Renewable Aromatics: Selective Routes and Outlook for p-Xylene Commercialisation. CHEMSUSCHEM 2016; 9:2736-2748. [PMID: 27624185 DOI: 10.1002/cssc.201600605] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Revised: 06/20/2016] [Indexed: 06/06/2023]
Abstract
Methylbenzenes are among the most important organic chemicals today and, among them, p-xylene deserves particular attention because of its production volume and its application in the manufacture of polyethylene terephthalate (PET). There is great interest in producing this commodity chemical more sustainably from biomass sources, particularly driven by manufacturers willing to produce more sustainable synthetic fibres and PET bottles for beverages. A renewable source for p-xylene would allow achieving this goal with minimal disruption to existing processes for PET production. Despite the fact that recently some routes to renewable p-xylene have been identified, there is no clear consensus on their feasibility or implications. We have critically reviewed the current state-of-the-art with focus on catalytic routes and possible outlook for commercialisation. Pathways to obtain p-xylene from a biomass-derived route include methanol-to-aromatics (MTA), ethanol dehydration, ethylene dimerization, furan cycloaddition or catalytic fast pyrolysis and hydrotreating of lignin. Some of the processes identified suggest near-future possibilities, but also more speculative or longer-term sources for synthesis of p-xylene are highlighted.
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Affiliation(s)
- Andy Maneffa
- Department of Chemistry, University of Liverpool, Crown Street, L69 7ZD, Liverpool, United Kingdom
- Department of Chemistry, University of York, Heslington, YO10 5DD, York, United Kingdom
| | - Peter Priecel
- Department of Chemistry, University of Liverpool, Crown Street, L69 7ZD, Liverpool, United Kingdom
| | - Jose A Lopez-Sanchez
- Department of Chemistry, University of Liverpool, Crown Street, L69 7ZD, Liverpool, United Kingdom.
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95
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High-Throughput Screening of Coenzyme Preference Change of Thermophilic 6-Phosphogluconate Dehydrogenase from NADP(+) to NAD(.). Sci Rep 2016; 6:32644. [PMID: 27587230 PMCID: PMC5009329 DOI: 10.1038/srep32644] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2016] [Accepted: 08/10/2016] [Indexed: 11/09/2022] Open
Abstract
Coenzyme engineering that changes NAD(P) selectivity of redox enzymes is an important tool in metabolic engineering, synthetic biology, and biocatalysis. Here we developed a high throughput screening method to identify mutants of 6-phosphogluconate dehydrogenase (6PGDH) from a thermophilic bacterium Moorella thermoacetica with reversed coenzyme selectivity from NADP+ to NAD+. Colonies of a 6PGDH mutant library growing on the agar plates were treated by heat to minimize the background noise, that is, the deactivation of intracellular dehydrogenases, degradation of inherent NAD(P)H, and disruption of cell membrane. The melted agarose solution containing a redox dye tetranitroblue tetrazolium (TNBT), phenazine methosulfate (PMS), NAD+, and 6-phosphogluconate was carefully poured on colonies, forming a second semi-solid layer. More active 6PGDH mutants were examined via an enzyme-linked TNBT-PMS colorimetric assay. Positive mutants were recovered by direct extraction of plasmid from dead cell colonies followed by plasmid transformation into E. coli TOP10. By utilizing this double-layer screening method, six positive mutants were obtained from two-round saturation mutagenesis. The best mutant 6PGDH A30D/R31I/T32I exhibited a 4,278-fold reversal of coenzyme selectivity from NADP+ to NAD+. This screening method could be widely used to detect numerous redox enzymes, particularly for thermophilic ones, which can generate NAD(P)H reacted with the redox dye TNBT.
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96
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Bassalo MC, Garst AD, Halweg-Edwards AL, Grau WC, Domaille DW, Mutalik VK, Arkin AP, Gill RT. Rapid and Efficient One-Step Metabolic Pathway Integration in E. coli. ACS Synth Biol 2016; 5:561-8. [PMID: 27072506 DOI: 10.1021/acssynbio.5b00187] [Citation(s) in RCA: 112] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Methods for importing heterologous genes into genetically tractable hosts are among the most desired tools of synthetic biology. Easy plug-and-play construction methods to rapidly test genes and pathways stably in the host genome would expedite synthetic biology and metabolic engineering applications. Here, we describe a CRISPR-based strategy that allows highly efficient, single step integration of large pathways in Escherichia coli. This strategy allows high efficiency integration in a broad range of homology arm sizes and genomic positions, with efficiencies ranging from 70 to 100% in 7 distinct loci. To demonstrate the large size capability, we integrated a 10 kb construct to implement isobutanol production in a single day. The ability to efficiently integrate entire metabolic pathways in a rapid and markerless manner will facilitate testing and engineering of novel pathways using the E. coli genome as a stable testing platform.
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Affiliation(s)
- Marcelo C Bassalo
- Department of Molecular, Cellular and Developmental Biology, ‡Department of Chemical and Biological Engineering, §Department of Chemistry and Biochemistry, University of Colorado Boulder , Boulder, Colorado 80303, United States
- Lawrence Berkeley National Laboratory, Physical Bioscience Division, ¶Department of Bioengineering, Berkeley , California 94720, United States
| | - Andrew D Garst
- Department of Molecular, Cellular and Developmental Biology, ‡Department of Chemical and Biological Engineering, §Department of Chemistry and Biochemistry, University of Colorado Boulder , Boulder, Colorado 80303, United States
- Lawrence Berkeley National Laboratory, Physical Bioscience Division, ¶Department of Bioengineering, Berkeley , California 94720, United States
| | - Andrea L Halweg-Edwards
- Department of Molecular, Cellular and Developmental Biology, ‡Department of Chemical and Biological Engineering, §Department of Chemistry and Biochemistry, University of Colorado Boulder , Boulder, Colorado 80303, United States
- Lawrence Berkeley National Laboratory, Physical Bioscience Division, ¶Department of Bioengineering, Berkeley , California 94720, United States
| | - William C Grau
- Department of Molecular, Cellular and Developmental Biology, ‡Department of Chemical and Biological Engineering, §Department of Chemistry and Biochemistry, University of Colorado Boulder , Boulder, Colorado 80303, United States
- Lawrence Berkeley National Laboratory, Physical Bioscience Division, ¶Department of Bioengineering, Berkeley , California 94720, United States
| | - Dylan W Domaille
- Department of Molecular, Cellular and Developmental Biology, ‡Department of Chemical and Biological Engineering, §Department of Chemistry and Biochemistry, University of Colorado Boulder , Boulder, Colorado 80303, United States
- Lawrence Berkeley National Laboratory, Physical Bioscience Division, ¶Department of Bioengineering, Berkeley , California 94720, United States
| | - Vivek K Mutalik
- Department of Molecular, Cellular and Developmental Biology, ‡Department of Chemical and Biological Engineering, §Department of Chemistry and Biochemistry, University of Colorado Boulder , Boulder, Colorado 80303, United States
- Lawrence Berkeley National Laboratory, Physical Bioscience Division, ¶Department of Bioengineering, Berkeley , California 94720, United States
| | - Adam P Arkin
- Department of Molecular, Cellular and Developmental Biology, ‡Department of Chemical and Biological Engineering, §Department of Chemistry and Biochemistry, University of Colorado Boulder , Boulder, Colorado 80303, United States
- Lawrence Berkeley National Laboratory, Physical Bioscience Division, ¶Department of Bioengineering, Berkeley , California 94720, United States
| | - Ryan T Gill
- Department of Molecular, Cellular and Developmental Biology, ‡Department of Chemical and Biological Engineering, §Department of Chemistry and Biochemistry, University of Colorado Boulder , Boulder, Colorado 80303, United States
- Lawrence Berkeley National Laboratory, Physical Bioscience Division, ¶Department of Bioengineering, Berkeley , California 94720, United States
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97
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Bassalo MC, Liu R, Gill RT. Directed evolution and synthetic biology applications to microbial systems. Curr Opin Biotechnol 2016; 39:126-133. [DOI: 10.1016/j.copbio.2016.03.016] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Revised: 03/12/2016] [Accepted: 03/20/2016] [Indexed: 10/22/2022]
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98
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Liao JC, Mi L, Pontrelli S, Luo S. Fuelling the future: microbial engineering for the production of sustainable biofuels. Nat Rev Microbiol 2016; 14:288-304. [DOI: 10.1038/nrmicro.2016.32] [Citation(s) in RCA: 386] [Impact Index Per Article: 48.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
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99
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Liu Z, Liu P, Xiao D, Zhang X. Improving isobutanol production in metabolically engineered Escherichia coli by co-producing ethanol and modulation of pentose phosphate pathway. J Ind Microbiol Biotechnol 2016; 43:851-60. [PMID: 26946319 DOI: 10.1007/s10295-016-1751-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Accepted: 02/16/2016] [Indexed: 11/29/2022]
Abstract
Redox imbalance has been regarded as the key limitation for anaerobic isobutanol production in metabolically engineered Escherichia coli strains. In this work, the ethanol synthetic pathway was recruited to solve the NADH redundant problem while the pentose phosphate pathway was modulated to solve the NADPH deficient problem for anaerobic isobutanol production. Recruiting the ethanol synthetic pathway in strain AS108 decreased isobutanol yield from 0.66 to 0.29 mol/mol glucose. It was found that there was a negative correlation between aldehyde/alcohol dehydrogenase (AdhE) activity and isobutanol production. Decreasing AdhE activity increased isobutanol yield from 0.29 to 0.6 mol/mol. On the other hand, modulation of the glucose 6-phosphate dehydrogenase gene of the pentose phosphate pathway increased isobutanol yield from 0.29 to 0.41 mol/mol. Combination of these two strategies had a synergistic effect on improving isobutanol production. Isobutanol titer and yield of the best strain ZL021 were 53 mM and 0.74 mol/mol, which were 51 % and 12 % higher than the starting strain AS108, respectively. The total alcohol yield of strain ZL021 was 0.81 mol/mol, which was 23 % higher than strain AS108.
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Affiliation(s)
- Zichun Liu
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China.,Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China.,Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Pingping Liu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China.,Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Dongguang Xiao
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
| | - Xueli Zhang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China. .,Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, China.
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100
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Abstract
A central challenge in the field of metabolic engineering is the efficient identification of a metabolic pathway genotype that maximizes specific productivity over a robust range of process conditions. Here we review current methods for optimizing specific productivity of metabolic pathways in living cells. New tools for library generation, computational analysis of pathway sequence-flux space, and high-throughput screening and selection techniques are discussed.
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Affiliation(s)
- Justin R Klesmith
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Timothy A Whitehead
- Department of Chemical Engineering and Materials Science, Michigan State University, East Lansing, MI 48824, USA; Department of Biosystems and Agricultural Engineering, Michigan State University, East Lansing, MI 48824, USA
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