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Bañares AB, Nisola GM, Valdehuesa KNG, Lee WK, Chung WJ. Engineering of xylose metabolism in Escherichia coli for the production of valuable compounds. Crit Rev Biotechnol 2021; 41:649-668. [PMID: 33563072 DOI: 10.1080/07388551.2021.1873243] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The lignocellulosic sugar d-xylose has recently gained prominence as an inexpensive alternative substrate for the production of value-added compounds using genetically modified organisms. Among the prokaryotes, Escherichia coli has become the de facto host for the development of engineered microbial cell factories. The favored status of E. coli resulted from a century of scientific explorations leading to a deep understanding of its systems. However, there are limited literature reviews that discuss engineered E. coli as a platform for the conversion of d-xylose to any target compounds. Additionally, available critical review articles tend to focus on products rather than the host itself. This review aims to provide relevant and current information about significant advances in the metabolic engineering of d-xylose metabolism in E. coli. This focusses on unconventional and synthetic d-xylose metabolic pathways as several review articles have already discussed the engineering of native d-xylose metabolism. This paper, in particular, is essential to those who are working on engineering of d-xylose metabolism using E. coli as the host.
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Affiliation(s)
- Angelo B Bañares
- Environmental Waste Recycle Institute (EWRI), Department of Energy Science and Technology (DEST), Myongji University, Yongin, Gyeonggi, South Korea
| | - Grace M Nisola
- Environmental Waste Recycle Institute (EWRI), Department of Energy Science and Technology (DEST), Myongji University, Yongin, Gyeonggi, South Korea
| | - Kris N G Valdehuesa
- Environmental Waste Recycle Institute (EWRI), Department of Energy Science and Technology (DEST), Myongji University, Yongin, Gyeonggi, South Korea
| | - Won-Keun Lee
- Division of Bioscience and Bioinformatics, Myongji University, Yongin, Gyeonggi, South Korea
| | - Wook-Jin Chung
- Environmental Waste Recycle Institute (EWRI), Department of Energy Science and Technology (DEST), Myongji University, Yongin, Gyeonggi, South Korea
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52
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Metabolic engineering of E. coli for pyocyanin production. Metab Eng 2021; 64:15-25. [PMID: 33454430 DOI: 10.1016/j.ymben.2021.01.002] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Revised: 11/17/2020] [Accepted: 01/10/2021] [Indexed: 01/07/2023]
Abstract
Pyocyanin is a secondary metabolite from Pseudomonas aeruginosa that belongs to the class of phenazines, which are aromatic nitrogenous compounds with numerous biological functions. Besides its antifungal and antimicrobial activities, pyocyanin is a remarkable redox-active molecule with potential applications ranging from the pharma industry to the development of microbial fuel cells. Nevertheless, pyocyanin production has been restricted to P. aeruginosa strains, limiting its practical applicability. In this study, the pyocyanin biosynthetic pathway was engineered for the first time for high level production of this compound in a heterologous host. Escherichia coli cells harboring the nine-gene pathway divided into two plasmids were able to produce and secrete pyocyanin at higher levels than some Pseudomonas aeruginosa strains. The influence of culture and induction parameters were evaluated, and the optimized conditions led to an increase of 3.5-fold on pyocyanin accumulation. Pathway balancing was achieved by testing a set of plasmids with different copy numbers to optimize the expression levels of pyocyanin biosynthetic genes, resulting in a fourfold difference in product titer among the engineered strains. Further improvements were achieved by co-expression of Vitreoscilla hemoglobin Vhb, which relieved oxygen limitations and led to a final titer of 18.8 mg/L pyocyanin. These results show promise to use E. coli for phenazines production, and the engineered strain developed here has the potential to be used in electro-fermentation systems where pyocyanin plays a role as electron-shuttle.
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Li Q, Wu M, Wen Z, Jiang Y, Wang X, Zhao Y, Liu J, Yang J, Jiang Y, Yang S. Optimization of n-butanol synthesis in Lactobacillus brevis via the functional expression of thl, hbd, crt and ter. ACTA ACUST UNITED AC 2020; 47:1099-1108. [DOI: 10.1007/s10295-020-02331-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Accepted: 11/02/2020] [Indexed: 12/15/2022]
Abstract
Abstract
N-butanol is an important chemical and can be naturally synthesized by Clostridium species; however, the poor n-butanol tolerance of Clostridium impedes the further improvement in titer. In this study, Lactobacillus brevis, which possesses a higher butanol tolerance, was selected as host for heterologous butanol production. The Clostridium acetobutylicum genes thl, hbd, and crt which encode thiolase, β-hydroxybutyryl-CoA dehydrogenase, and crotonase, and the Treponema denticola gene ter, which encodes trans-enoyl-CoA reductase were cloned into a single plasmid to express the butanol synthesis pathway in L. brevis. A titer of 40 mg/L n-butanol was initially achieved with plasmid pLY15-opt, in which all pathway genes are codon-optimized. A titer of 450 mg/L of n-butanol was then synthesized when ter was further overexpressed in this pathway. The role of metabolic flux was reinforced with pLY15, in which only the ter gene was codon-optimized, which greatly increased the n-butanol titer to 817 mg/L. Our strategy significantly improved n-butanol synthesis in L. brevis and the final titer is the highest achieved amongst butanol-tolerant lactic acid bacteria.
Graphic abstract
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Affiliation(s)
- Qi Li
- grid.412600.1 0000 0000 9479 9538 College of Life Sciences Sichuan Normal University 610101 Chengdu China
- grid.9227.e 0000000119573309 Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences Chinese Academy of Sciences 200032 Shanghai China
| | - Meixian Wu
- grid.9227.e 0000000119573309 Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences Chinese Academy of Sciences 200032 Shanghai China
| | - Zhiqiang Wen
- grid.9227.e 0000000119573309 Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences Chinese Academy of Sciences 200032 Shanghai China
| | - Yuan Jiang
- grid.9227.e 0000000119573309 Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences Chinese Academy of Sciences 200032 Shanghai China
| | - Xin Wang
- grid.9227.e 0000000119573309 Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences Chinese Academy of Sciences 200032 Shanghai China
| | - Yawei Zhao
- grid.9227.e 0000000119573309 Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences Chinese Academy of Sciences 200032 Shanghai China
| | - Jinle Liu
- grid.9227.e 0000000119573309 Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences Chinese Academy of Sciences 200032 Shanghai China
| | - Junjie Yang
- grid.9227.e 0000000119573309 Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences Chinese Academy of Sciences 200032 Shanghai China
| | - Yu Jiang
- grid.419092.7 0000 0004 0467 2285 Huzhou Center of Industrial Biotechnology Shanghai Institutes for Biological Sciences 313000 Huzhou China
| | - Sheng Yang
- grid.9227.e 0000000119573309 Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences Chinese Academy of Sciences 200032 Shanghai China
- grid.419092.7 0000 0004 0467 2285 Huzhou Center of Industrial Biotechnology Shanghai Institutes for Biological Sciences 313000 Huzhou China
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54
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How to outwit nature: Omics insight into butanol tolerance. Biotechnol Adv 2020; 46:107658. [PMID: 33220435 DOI: 10.1016/j.biotechadv.2020.107658] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 11/10/2020] [Accepted: 11/13/2020] [Indexed: 12/16/2022]
Abstract
The energy crisis, depletion of oil reserves, and global climate changes are pressing problems of developed societies. One possibility to counteract that is microbial production of butanol, a promising new fuel and alternative to many petrochemical reagents. However, the high butanol toxicity to all known microbial species is the main obstacle to its industrial implementation. The present state of the art review aims to expound the recent advances in modern omics approaches to resolving this insurmountable to date problem of low butanol tolerance. Genomics, transcriptomics, and proteomics show that butanol tolerance is a complex phenomenon affecting multiple genes and their expression. Efflux pumps, stress and multidrug response, membrane transport, and redox-related genes are indicated as being most important during butanol challenge, in addition to fine-tuning of global regulators of transcription (Spo0A, GntR), which may further improve tolerance. Lipidomics shows that the alterations in membrane composition (saturated lipids and plasmalogen increase) are very much species-specific and butanol-related. Glycomics discloses the pleiotropic effect of CcpA, the role of alternative sugar transport, and the production of exopolysaccharides as alternative routes to overcoming butanol stress. Unfortunately, the strain that simultaneously syntheses and tolerates butanol in concentrations that allow its commercialization has not yet been discovered or produced. Omics insight will allow the purposeful increase of butanol tolerance in natural and engineered producers and the effective heterologous expression of synthetic butanol pathways in strains hereditary butanol-resistant up to 3.2 - 4.9% (w/v). Future breakthrough can be achieved by a detailed study of the membrane proteome, of which 21% are proteins with unknown functions.
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55
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Abstract
Diamines are important monomers for polyamide plastics; they include 1,3-diaminopropane, 1,4-diaminobutane, 1,5-diaminopentane, and 1,6-diaminohexane, among others. With increasing attention on environmental problems and green sustainable development, utilizing renewable raw materials for the synthesis of diamines is crucial for the establishment of a sustainable plastics industry. Recently, high-performance microbial factories, such as Escherichia coli and Corynebacterium glutamicum, have been widely used in the production of diamines. In particular, several synthetic pathways of 1,6-diaminohexane have been proposed based on glutamate or adipic acid. Here, we reviewed approaches for the biosynthesis of diamines, including metabolic engineering and biocatalysis, and the application of bio-based diamines in nylon materials. The related challenges and opportunities in the development of renewable bio-based diamines and nylon materials are also discussed.
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56
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Microbial production of limonene and its derivatives: Achievements and perspectives. Biotechnol Adv 2020; 44:107628. [DOI: 10.1016/j.biotechadv.2020.107628] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2020] [Revised: 08/24/2020] [Accepted: 08/25/2020] [Indexed: 12/14/2022]
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57
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Banerjee D, Eng T, Lau AK, Sasaki Y, Wang B, Chen Y, Prahl JP, Singan VR, Herbert RA, Liu Y, Tanjore D, Petzold CJ, Keasling JD, Mukhopadhyay A. Genome-scale metabolic rewiring improves titers rates and yields of the non-native product indigoidine at scale. Nat Commun 2020; 11:5385. [PMID: 33097726 PMCID: PMC7584609 DOI: 10.1038/s41467-020-19171-4] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 09/30/2020] [Indexed: 01/06/2023] Open
Abstract
High titer, rate, yield (TRY), and scalability are challenging metrics to achieve due to trade-offs between carbon use for growth and production. To achieve these metrics, we take the minimal cut set (MCS) approach that predicts metabolic reactions for elimination to couple metabolite production strongly with growth. We compute MCS solution-sets for a non-native product indigoidine, a sustainable pigment, in Pseudomonas putida KT2440, an emerging industrial microbe. From the 63 solution-sets, our omics guided process identifies one experimentally feasible solution requiring 14 simultaneous reaction interventions. We implement a total of 14 genes knockdowns using multiplex-CRISPRi. MCS-based solution shifts production from stationary to exponential phase. We achieve 25.6 g/L, 0.22 g/l/h, and ~50% maximum theoretical yield (0.33 g indigoidine/g glucose). These phenotypes are maintained from batch to fed-batch mode, and across scales (100-ml shake flasks, 250-ml ambr®, and 2-L bioreactors).
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Affiliation(s)
- Deepanwita Banerjee
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, 94608, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Thomas Eng
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, 94608, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Andrew K Lau
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, 94608, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Yusuke Sasaki
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, 94608, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Brenda Wang
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, 94608, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Yan Chen
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, 94608, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Jan-Philip Prahl
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Advanced Biofuel and Bioproduct Process Development Unit, Lawrence Berkeley National Laboratory, Emeryville, CA, 94608, USA
| | - Vasanth R Singan
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Robin A Herbert
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, 94608, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Yuzhong Liu
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, 94608, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Deepti Tanjore
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Advanced Biofuel and Bioproduct Process Development Unit, Lawrence Berkeley National Laboratory, Emeryville, CA, 94608, USA
| | - Christopher J Petzold
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, 94608, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Jay D Keasling
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, 94608, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- QB3 Institute, University of California-Berkeley, 5885 Hollis Street, 4th Floor, Emeryville, CA, 94608, USA
- Department of Chemical & Biomolecular Engineering, University of California, Berkeley, CA, 94720, USA
- Department of Bioengineering, University of California, Berkeley, CA, 94720, USA
- Novo Nordisk Foundation Center for Biosustainability, Technical University Denmark, 2970, Horsholm, Denmark
- Synthetic Biochemistry Center, Institute for Synthetic Biology, Shenzhen Institutes for Advanced Technologies, Shenzhen, China
| | - Aindrila Mukhopadhyay
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, 94608, USA.
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
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58
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Wang Z, Xue T, Hu D, Ma Y. A Novel Butanol Tolerance-Promoting Function of the Transcription Factor Rob in Escherichia coli. Front Bioeng Biotechnol 2020; 8:524198. [PMID: 33072717 PMCID: PMC7537768 DOI: 10.3389/fbioe.2020.524198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Accepted: 08/24/2020] [Indexed: 11/13/2022] Open
Abstract
Producing high concentrations of biobutanol is challenging, primarily because of the toxicity of butanol toward cells. In our previous study, several butanol tolerance-promoting genes were identified from butanol-tolerant Escherichia coli mutants and inactivation of the transcriptional regulator factor Rob was shown to improve butanol tolerance. Here, the butanol tolerance characteristics and mechanism regulated by inactivated Rob are investigated. Comparative transcriptome analysis of strain DTrob, with a truncated rob in the genome, and the control BW25113 revealed 285 differentially expressed genes (DEGs) to be associated with butanol tolerance and categorized as having transport, localization, and oxidoreductase activities. Expression of 25 DEGs representing different functional categories was analyzed by quantitative reverse transcription PCR (qRT-PCR) to assess the reliability of the RNA-Seq data, and 92% of the genes showed the same expression trend. Based on functional complementation experiments of key DEGs, deletions of glgS and yibT increased the butanol tolerance of E. coli, whereas overexpression of fadB resulted in increased cell density and a slight increase in butanol tolerance. A metabolic network analysis of these DEGs revealed that six genes (fadA, fadB, fadD, fadL, poxB, and acs) associated with acetyl-CoA production were significantly upregulated in DTrob, suggesting that Rob inactivation might enhance butanol tolerance by increasing acetyl-CoA. Interestingly, DTrob produced more acetate in response to butanol stress than the wild-type strain, resulting in the upregulation expression of some genes involved in acetate metabolism. Altogether, the results of this study reveal the mechanism underlying increased butanol tolerance in E. coli regulated by Rob inactivation.
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Affiliation(s)
- Zhiquan Wang
- Biomass Conversion Laboratory, R&D Center for Petrochemical Technology, Tianjin University, Tianjin, China.,Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
| | - Tingli Xue
- Biomass Conversion Laboratory, R&D Center for Petrochemical Technology, Tianjin University, Tianjin, China.,Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
| | - Dongsheng Hu
- Biomass Conversion Laboratory, R&D Center for Petrochemical Technology, Tianjin University, Tianjin, China.,Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
| | - Yuanyuan Ma
- Biomass Conversion Laboratory, R&D Center for Petrochemical Technology, Tianjin University, Tianjin, China.,Collaborative Innovation Centre of Chemical Science and Engineering, and Key Laboratory for Green Chemical Technology, Tianjin University, Tianjin, China.,State Key Laboratory of Biobased Material and Green Papermaking, Qilu University of Technology, Shandong Academy of Sciences, Jinan, China.,Frontier Technology Institute, Tianjin University, Tianjin, China
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59
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Novak K, Baar J, Freitag P, Pflügl S. Metabolic engineering of Escherichia coli W for isobutanol production on chemically defined medium and cheese whey as alternative raw material. J Ind Microbiol Biotechnol 2020; 47:1117-1132. [PMID: 33068182 PMCID: PMC7728641 DOI: 10.1007/s10295-020-02319-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 10/03/2020] [Indexed: 11/28/2022]
Abstract
The aim of this study was to establish isobutanol production on chemically defined medium in Escherichia coli. By individually expressing each gene of the pathway, we constructed a plasmid library for isobutanol production. Strain screening on chemically defined medium showed successful production in the robust E. coli W strain, and expression vector IB 4 was selected as the most promising construct due to its high isobutanol yields and efficient substrate uptake. The investigation of different aeration strategies in combination with strain improvement and the implementation of a pulsed fed-batch were key for the development of an efficient production process. E. coli W ΔldhA ΔadhE Δpta ΔfrdA enabled aerobic isobutanol production at 38% of the theoretical maximum. Use of cheese whey as raw material resulted in longer process stability, which allowed production of 20 g l−1 isobutanol. Demonstrating isobutanol production on both chemically defined medium and a residual waste stream, this study provides valuable information for further development of industrially relevant isobutanol production processes.
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Affiliation(s)
- Katharina Novak
- Institute for Chemical, Environmental and Bioscience Engineering, Research Area Biochemical Engineering, Technische Universität Wien, Gumpendorfer Straße 1a, 1060, Vienna, Austria
| | - Juliane Baar
- Institute for Chemical, Environmental and Bioscience Engineering, Research Area Biochemical Engineering, Technische Universität Wien, Gumpendorfer Straße 1a, 1060, Vienna, Austria
| | - Philipp Freitag
- Institute for Chemical, Environmental and Bioscience Engineering, Research Area Biochemical Engineering, Technische Universität Wien, Gumpendorfer Straße 1a, 1060, Vienna, Austria
| | - Stefan Pflügl
- Institute for Chemical, Environmental and Bioscience Engineering, Research Area Biochemical Engineering, Technische Universität Wien, Gumpendorfer Straße 1a, 1060, Vienna, Austria.
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60
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Jawed K, Abdelaal AS, Koffas MAG, Yazdani SS. Improved Butanol Production Using FASII Pathway in E. coli. ACS Synth Biol 2020; 9:2390-2398. [PMID: 32813973 DOI: 10.1021/acssynbio.0c00154] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
n-Butanol is often considered a potential substitute for gasoline due to its physicochemical properties being closely related to those of gasoline. In this study, we extend our earlier work to convert endogenously producing butyrate via the FASII pathway using thioesterase TesBT to its corresponding alcohol, i.e., butanol. We first assembled pathway genes, i.e., car encoding carboxylic acid reductase from Mycobacterium marinum, sfp encoding phosphopantetheinyl transferase from Bacillus subtilis, and adh2 encoding alcohol dehydrogenase from S. cerevisiae, responsible for bioconversion of butyrate to butanol in three different configurations (Operon, Pseudo-Operon, and Monocistronic) to achieve optimum expression of each gene and compared with the clostridial solventogenic pathway for in vivo conversion of butyrate to butanol under aerobic conditions. An E. coli strain harboring car, sfp, and adh2 in pseudo-operon configuration was able to convert butyrate to butanol with 100% bioconversion efficiency when supplemented with 1 g/L of butyrate. Further, co-cultivation of an upstream strain (butyrate-producing) with a downstream strain (butyrate to butanol converting) at different inoculation ratios was investigated, and an optimized ratio of 1:4 (upstream strain: downstream strain) was found to produce ∼2 g/L butanol under fed-batch fermentation. Further, a mono-cultivation approach was applied by transforming a plasmid harboring tesBT gene into the downstream strain. This approach produced 0.42 g/L in a test tube and ∼2.9 g/L butanol under fed-batch fermentation. This is the first report where both mono- and co-cultivation approaches were tested and compared for butanol production, and butanol titers achieved using both strategies are the highest reported values in recombinant E. coli utilizing FASII pathway.
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Affiliation(s)
- Kamran Jawed
- Microbial Engineering Group, International Centre for Genetic Engineering and Biotechnology, 110067 New Delhi, India
- Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, New York 12180, United States
| | - Ali Samy Abdelaal
- Microbial Engineering Group, International Centre for Genetic Engineering and Biotechnology, 110067 New Delhi, India
- Department of Genetics, Faculty of Agriculture, Damietta University, 34511 Damietta, Egypt
| | - Mattheos A. G. Koffas
- Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, New York 12180, United States
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, New York 12180, United States
| | - Syed Shams Yazdani
- Microbial Engineering Group, International Centre for Genetic Engineering and Biotechnology, 110067 New Delhi, India
- DBT-ICGEB Centre for Advanced Bioenergy Research, International Centre for Genetic Engineering and Biotechnology, 110067 New Delhi, India
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61
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Guo H, Wang H, Huo YX. Engineering Critical Enzymes and Pathways for Improved Triterpenoid Biosynthesis in Yeast. ACS Synth Biol 2020; 9:2214-2227. [PMID: 32786348 DOI: 10.1021/acssynbio.0c00124] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Triterpenoids represent a diverse group of phytochemicals that are widely distributed in the plant kingdom and have many biological activities. The heterologous production of triterpenoids in Saccharomyces cerevisiae has been successfully implemented by introducing various triterpenoid biosynthetic pathways. By engineering related enzymes as well as through yeast metabolism, the yield of various triterpenoids is significantly improved from the milligram per liter scale to the gram per liter scale. This achievement demonstrates that engineering critical enzymes is considered a potential strategy to overcome the main hurdles of the industrial application of these potent natural products. Here, we review strategies for designing enzymes to improve the yield of triterpenoids in S. cerevisiae in terms of three main aspects: 1, elevating the supply of the precursor 2,3-oxidosqualene; 2, optimizing triterpenoid-involved reactions; and 3, lowering the competition of the native sterol pathway. Then, we provide challenges and prospects for further enhancing triterpenoid production in S. cerevisiae.
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Affiliation(s)
- Hao Guo
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, Beijing, 100081, P. R. China
| | - Huiyan Wang
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, Beijing, 100081, P. R. China
| | - Yi-Xin Huo
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, Beijing, 100081, P. R. China
- SIP-UCLA Institute for Technology Advancement, Suzhou, 215123, P. R. China
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, 266101, P. R. China
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62
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Liu L, Zhou S, Deng Y. The 3-ketoacyl-CoA thiolase: an engineered enzyme for carbon chain elongation of chemical compounds. Appl Microbiol Biotechnol 2020; 104:8117-8129. [PMID: 32830293 DOI: 10.1007/s00253-020-10848-w] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 08/09/2020] [Accepted: 08/17/2020] [Indexed: 01/03/2023]
Abstract
Because of their function of catalyzing the rearrangement of the carbon chains, thiolases have attracted increasing attentions over the past decades. The 3-ketoacyl-CoA thiolase (KAT) is a member of the thiolase, which is capable of catalyzing the Claisen condensation reaction between the two acyl-CoAs, thereby achieving carbon chain elongation. In this way, diverse value-added compounds might be synthesized starting from simple small CoA thioesters. However, most KATs are hampered by low stability and poor substrate specificity, which has hindered the development of large-scale biosynthesis. In this review, the common characteristics in the three-dimensional structure of KATs from different sources are summarized. Moreover, structure-guided rational engineering is discussed as a strategy for enhancing the performance of KATs. Finally, we reviewed the metabolic engineering applications of KATs for producing various energy-storage molecules, such as n-butanol, fatty acids, dicarboxylic acids, and polyhydroxyalkanoates. KEY POINTS: • Summarize the structural characteristics and catalyzation mechanisms of KATs. • Review on the rational engineering to enhance the performance of KATs. • Discuss the applications of KATs for producing energy-storage molecules.
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Affiliation(s)
- Lixia Liu
- National Engineering Laboratory for Cereal Fermentation Technology (NELCF), Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, People's Republic of China.,Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, People's Republic of China
| | - Shenghu Zhou
- National Engineering Laboratory for Cereal Fermentation Technology (NELCF), Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, People's Republic of China.,Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, People's Republic of China
| | - Yu Deng
- National Engineering Laboratory for Cereal Fermentation Technology (NELCF), Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, People's Republic of China. .,Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, People's Republic of China.
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63
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Naseri G, Mueller-Roeber B. A Step-by-Step Protocol for COMPASS, a Synthetic Biology Tool for Combinatorial Gene Assembly. Methods Mol Biol 2020; 2205:277-303. [PMID: 32809205 DOI: 10.1007/978-1-0716-0908-8_16] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2023]
Abstract
For industry-scale production of high-value chemicals in microbial cell factories, the elimination of metabolic flux imbalances is a critical aspect. However, a priori knowledge about the genetic design of optimal production pathways is typically not available. COMPASS, COMbinatorial Pathway ASSembly, is a rapid cloning method for the balanced expression of multiple genes in biochemical pathways. The method generates thousands of individual DNA constructs in modular, parallel, and high-throughput manner. COMPASS employs inducible artificial transcription factors derived from plant (Arabidopsis thaliana) regulators to control the expression of pathway genes in yeast (Saccharomyces cerevisiae). It utilizes homologous recombination for parts assembly and employs a positive selection scheme to identify correctly assembled pathway variants after both in vivo and in vitro recombination. Finally, COMPASS is equipped with a CRISPR/Cas9 genome modification system allowing for the one-step multilocus integration of genes. Although COMPASS was initially developed for pathway engineering, it can equally be employed for balancing gene expression in other synthetic biology projects.
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Affiliation(s)
- Gita Naseri
- Department of Molecular Biology, University of Potsdam, Potsdam, Germany
| | - Bernd Mueller-Roeber
- Department of Molecular Biology, University of Potsdam, Potsdam, Germany. .,Plant Signalling Group, Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany. .,Department of Plant Development, Center of Plant Systems Biology and Biotechnology (CPSBB), Plovdiv, Bulgaria.
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64
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Recent advances in n-butanol and butyrate production using engineered Clostridium tyrobutyricum. World J Microbiol Biotechnol 2020; 36:138. [PMID: 32794091 DOI: 10.1007/s11274-020-02914-2] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Accepted: 08/08/2020] [Indexed: 12/12/2022]
Abstract
Acidogenic clostridia naturally producing acetic and butyric acids has attracted high interest as a novel host for butyrate and n-butanol production. Among them, Clostridium tyrobutyricum is a hyper butyrate-producing bacterium, which re-assimilates acetate for butyrate biosynthesis by butyryl-CoA/acetate CoA transferase (CoAT), rather than the phosphotransbutyrylase-butyrate kinase (PTB-BK) pathway widely found in clostridia and other microbial species. To date, C. tyrobutyricum has been engineered to overexpress a heterologous alcohol/aldehyde dehydrogenase, which converts butyryl-CoA to n-butanol. Compared to conventional solventogenic clostridia, which produce acetone, ethanol, and butanol in a biphasic fermentation process, the engineered C. tyrobutyricum with a high metabolic flux toward butyryl-CoA produced n-butanol at a high yield of > 0.30 g/g and titer of > 20 g/L in glucose fermentation. With no acetone production and a high C4/C2 ratio, butanol was the only major fermentation product by the recombinant C. tyrobutyricum, allowing simplified downstream processing for product purification. In this review, novel metabolic engineering strategies to improve n-butanol and butyrate production by C. tyrobutyricum from various substrates, including glucose, xylose, galactose, sucrose, and cellulosic hydrolysates containing the mixture of glucose and xylose, are discussed. Compared to other recombinant hosts such as Clostridium acetobutylicum and Escherichia coli, the engineered C. tyrobutyricum strains with higher butyrate and butanol titers, yields and productivities are the most promising hosts for potential industrial applications.
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65
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Software and Methods for Computational Flux Balance Analysis. Methods Mol Biol 2020. [PMID: 32720154 DOI: 10.1007/978-1-0716-0195-2_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
As genetic engineering of organisms has grown easier and more precise, computational modeling of metabolic systems has played an increasingly important role in both guiding experimental interventions and in understanding the results of metabolic perturbations.
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66
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Liu J, Jiang Y, Chen J, Yang J, Jiang W, Zhuang W, Ying H, Yang S. Metabolic Engineering and Adaptive Evolution of Clostridium beijerinckii To Increase Solvent Production from Corn Stover Hydrolysate. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:7916-7925. [PMID: 32614183 DOI: 10.1021/acs.jafc.0c03048] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The production of acetone-butanol-ethanol by solventogenic Clostridium using lignocellulosic biomass can be a potential alternative to petroleum-based butanol. However, previous studies on nondetoxified lignocellulose hydrolysate could not provide better results when compared to those in synthetic medium. In this study, we engineered the pentose pathway of Clostridium beijerinckii NCIMB 8052, which was then subjected to adaptive laboratory evolution in the gradient mixture of synthetic medium and pretreated corn stover enzymatic hydrolysate (CSH) prepared according to the National Renewable Energy Laboratory (NREL) standard. The final resultant strain CIBTS1274A produced 20.7 g/L of total solvents in NREL CSH diluted to 6% initial total sugars, supplemented with ammonium acetate. This performance was comparable with that of corn-based butanol. In addition, this strain was successfully used in the scale-up operation using nondetoxified corn stover and corncob hydrolysate at Lignicell Refining Biotechnologies Ltd., which once was the only commercial biobutanol industry in the world.
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Affiliation(s)
- Jinle Liu
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Yu Jiang
- Huzhou Center of Industrial Biotechnology, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences, Huzhou 313000, China
| | - Jun Chen
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Junjie Yang
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Weihong Jiang
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Wei Zhuang
- School of Chemical Engineering and Energy, Zhengzhou University, Zhengzhou 450001, China
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, China
| | - Hanjie Ying
- School of Chemical Engineering and Energy, Zhengzhou University, Zhengzhou 450001, China
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, China
| | - Sheng Yang
- Huzhou Center of Industrial Biotechnology, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences, Huzhou 313000, China
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
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67
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Kramer L, Le X, Rodriguez M, Wilson MA, Guo J, Niu W. Engineering Carboxylic Acid Reductase (CAR) through a Whole-Cell Growth-Coupled NADPH Recycling Strategy. ACS Synth Biol 2020; 9:1632-1637. [PMID: 32589835 DOI: 10.1021/acssynbio.0c00290] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Rapid evolution of enzyme activities is often hindered by the lack of efficient and affordable methods to identify beneficial mutants. We report the development of a new growth-coupled selection method for evolving NADPH-consuming enzymes based on the recycling of this redox cofactor. The method relies on a genetically modified Escherichia coli strain, which overaccumulates NADPH. This method was applied to the engineering of a carboxylic acid reductase (CAR) for improved catalytic activities on 2-methoxybenzoate and adipate. Mutant enzymes with up to 17-fold improvement in catalytic efficiency were identified from single-site saturated mutagenesis libraries. Obtained mutants were successfully applied to whole-cell conversions of adipate into 1,6-hexanediol, a C6 monomer commonly used in polymer industry.
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Affiliation(s)
- Levi Kramer
- Department of Chemical & Biomolecular Engineering, University of Nebraska—Lincoln, Lincoln, Nebraska 68588, United States
| | - Xuan Le
- Department of Chemical & Biomolecular Engineering, University of Nebraska—Lincoln, Lincoln, Nebraska 68588, United States
| | - Marisa Rodriguez
- Department of Chemical & Biomolecular Engineering, University of Nebraska—Lincoln, Lincoln, Nebraska 68588, United States
| | - Mark A. Wilson
- Department of Biochemistry, University of Nebraska—Lincoln, Lincoln, Nebraska 68588, United States
| | - Jiantao Guo
- Department of Chemistry, University of Nebraska—Lincoln, Lincoln, Nebraska 68588, United States
| | - Wei Niu
- Department of Chemical & Biomolecular Engineering, University of Nebraska—Lincoln, Lincoln, Nebraska 68588, United States
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68
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Garcia S, Trinh CT. Harnessing Natural Modularity of Metabolism with Goal Attainment Optimization to Design a Modular Chassis Cell for Production of Diverse Chemicals. ACS Synth Biol 2020; 9:1665-1681. [PMID: 32470305 DOI: 10.1021/acssynbio.9b00518] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Modular design is key to achieve efficient and robust systems across engineering disciplines. Modular design potentially offers advantages to engineer microbial systems for biocatalysis, bioremediation, and biosensing, overcoming the slow and costly design-build-test-learn cycles in the conventional cell engineering approach. These systems consist of a modular (chassis) cell compatible with exchangeable modules that enable programmed functions such as overproduction of a desirable chemical. We previously proposed a multiobjective optimization framework coupled with metabolic flux models to design modular cells and solved it using multiobjective evolutionary algorithms. However, such approach might not achieve solution optimality and hence limits design options for experimental implementation. In this study, we developed the goal attainment formulation compatible with optimization algorithms that guarantee solution optimality. We applied goal attainment to design an Escherichia coli modular cell capable of synthesizing all molecules in a biochemically diverse library at high yields and rates with only a few genetic manipulations. To elucidate modular organization of the designed cells, we developed a flux variance clustering (FVC) method by identifying reactions with high flux variance and clustering them to identify metabolic modules. Using FVC, we identified reaction usage patterns for different modules in the modular cell, revealing that its broad pathway compatibility is enabled by the natural modularity and flexible flux capacity of endogenous core metabolism. Overall, this study not only sheds light on modularity in metabolic networks from their topology and metabolic functions but also presents a useful synthetic biology toolbox to design modular cells with broad applications.
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Affiliation(s)
- Sergio Garcia
- Department of Chemical and Biomolecular Engineering, The University of Tennessee, Knoxville, Tennessee 37996, United States
- Center for Bioenergy Innovation, Oak Ridge National Laboratory Oak Ridge, Tennessee 37830, United States
| | - Cong T. Trinh
- Department of Chemical and Biomolecular Engineering, The University of Tennessee, Knoxville, Tennessee 37996, United States
- Center for Bioenergy Innovation, Oak Ridge National Laboratory Oak Ridge, Tennessee 37830, United States
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69
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Liu Y, Ghosh IN, Martien J, Zhang Y, Amador-Noguez D, Landick R. Regulated redirection of central carbon flux enhances anaerobic production of bioproducts in Zymomonas mobilis. Metab Eng 2020; 61:261-274. [PMID: 32590077 DOI: 10.1016/j.ymben.2020.06.005] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Revised: 06/06/2020] [Accepted: 06/07/2020] [Indexed: 01/25/2023]
Abstract
The microbial production of chemicals and fuels from plant biomass offers a sustainable alternative to fossilized carbon but requires high rates and yields of bioproduct synthesis. Z. mobilis is a promising chassis microbe due to its high glycolytic rate in anaerobic conditions that are favorable for large-scale production. However, diverting flux from its robust ethanol fermentation pathway to nonnative pathways remains a major engineering hurdle. To enable controlled, high-yield synthesis of bioproducts, we implemented a central-carbon metabolism control-valve strategy using regulated, ectopic expression of pyruvate decarboxylase (Pdc) and deletion of chromosomal pdc. Metabolomic and genetic analyses revealed that glycolytic intermediates and NADH accumulate when Pdc is depleted and that Pdc is essential for anaerobic growth of Z. mobilis. Aerobically, all flux can be redirected to a 2,3-butanediol pathway for which respiration maintains redox balance. Anaerobically, flux can be redirected to redox-balanced lactate or isobutanol pathways with ≥65% overall yield from glucose. This strategy provides a promising path for future metabolic engineering of Z. mobilis.
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Affiliation(s)
- Yang Liu
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, 53706, United States; DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, 53726, United States
| | - Indro Neil Ghosh
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, 53726, United States
| | - Julia Martien
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, 53706, United States; DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, 53726, United States
| | - Yaoping Zhang
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, 53726, United States
| | - Daniel Amador-Noguez
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, 53706, United States; DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, 53726, United States
| | - Robert Landick
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, 53706, United States; Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, 53706, United States; DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, 53726, United States.
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70
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Maxel S, Aspacio D, King E, Zhang L, Acosta AP, Li H. A Growth-Based, High-Throughput Selection Platform Enables Remodeling of 4-Hydroxybenzoate Hydroxylase Active Site. ACS Catal 2020; 10:6969-6974. [PMID: 34295569 PMCID: PMC8294663 DOI: 10.1021/acscatal.0c01892] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
We report an aerobic, growth-based selection platform founded on NADP(H) redox balance restoration in Escherichia coli, and we demonstrate its application in the high-throughput evolution of an oxygenase. A single round of selection followed by a facile growth assay enabled Pseudomonas aeruginosa 4-hydroxybenzoate hydroxylase (PobA) to efficiently hydroxylate both 4-hydroxybenzoic acid (4-HBA) and 3,4-dihydroxybenzoic acid (3,4-DHBA), two consecutive steps in gallic acid biosynthesis. Structural modeling suggests precise reorganization of active site hydrogen bond network, which is difficult to obtain without deep navigation of combinatorial sequence space. We envision universal application of this selection platform in engineering NADPH-dependent oxidoreductases.
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Affiliation(s)
- Sarah Maxel
- Department of Chemical and Biomolecular Engineering, University of California, Irvine, Irvine, California 92697, United States
| | - Derek Aspacio
- Department of Chemical and Biomolecular Engineering, University of California, Irvine, Irvine, California 92697, United States
| | - Edward King
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, California 92697, United States
| | - Linyue Zhang
- Department of Chemical and Biomolecular Engineering, University of California, Irvine, Irvine, California 92697, United States
| | - Ana Paula Acosta
- Department of Chemical and Biomolecular Engineering, University of California, Irvine, Irvine, California 92697, United States
| | - Han Li
- Department of Chemical and Biomolecular Engineering, University of California, Irvine, Irvine, California 92697, United States
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71
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Karim AS, Dudley QM, Juminaga A, Yuan Y, Crowe SA, Heggestad JT, Garg S, Abdalla T, Grubbe WS, Rasor BJ, Coar DN, Torculas M, Krein M, Liew F, Quattlebaum A, Jensen RO, Stuart JA, Simpson SD, Köpke M, Jewett MC. In vitro prototyping and rapid optimization of biosynthetic enzymes for cell design. Nat Chem Biol 2020; 16:912-919. [DOI: 10.1038/s41589-020-0559-0] [Citation(s) in RCA: 93] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Revised: 04/10/2020] [Accepted: 05/06/2020] [Indexed: 01/27/2023]
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72
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Kay JE, Jewett MC. A cell-free system for production of 2,3-butanediol is robust to growth-toxic compounds. Metab Eng Commun 2020; 10:e00114. [PMID: 31934547 PMCID: PMC6951449 DOI: 10.1016/j.mec.2019.e00114] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2019] [Revised: 11/14/2019] [Accepted: 11/19/2019] [Indexed: 11/23/2022] Open
Abstract
The need for sustainable, low-cost production of bioenergy and commodity chemicals is increasing. Unfortunately, the engineering potential of whole-cell catalysts to address this need can be hampered by cellular toxicity. When such bottlenecks limit the commercial feasibility of whole-cell fermentation, cell-free, or in vitro, based approaches may offer an alternative. Here, we assess the impact of three classes of growth toxic compounds on crude extract-based, cell-free chemical conversions. As a model system, we test a metabolic pathway for conversion of glucose to 2,3-butanediol (2,3-BDO) in lysates of Escherichia coli. First, we characterized 2,3-BDO production with different classes of antibiotics and found, as expected, that the system is uninhibited by compounds that prevent cell growth by means of cell wall replication and DNA, RNA, and protein synthesis. Second, we considered the impact of polar solvent addition (e.g., methanol, n-butanol). We observed that volumetric productivities (g/L/h) were slowed with increasing hydrophobicity of added alcohols. Finally, we investigated the effects of using pretreated biomass hydrolysate as a feed stock, observing a 25% reduction in 2,3-BDO production as a result of coumaroyl and feruloyl amides. Overall, we find the cell-free system to be robust to working concentrations of antibiotics and other compounds that are toxic to cell growth, but do not denature or inhibit relevant enzymes.
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Affiliation(s)
- Jennifer E. Kay
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, 60208, USA
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL, 60208, USA
- Center for Synthetic Biology, Northwestern University, Evanston, IL, 60208, USA
| | - Michael C. Jewett
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, 60208, USA
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL, 60208, USA
- Center for Synthetic Biology, Northwestern University, Evanston, IL, 60208, USA
- Robert H. Lurie Comprehensive Cancer Center and Northwestern University, Chicago, IL, 60611, USA
- Simpson Querrey Institute, Northwestern University, Chicago, IL, 60611, USA
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73
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Li A, Wen Z, Fang D, Lu M, Ma Y, Xie Q, Jin M. Developing Clostridium diolis as a biorefinery chassis by genetic manipulation. BIORESOURCE TECHNOLOGY 2020; 305:123066. [PMID: 32114307 DOI: 10.1016/j.biortech.2020.123066] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 02/17/2020] [Accepted: 02/18/2020] [Indexed: 06/10/2023]
Abstract
Clostridium diolis can efficiently utilize various inexpensive, renewable resources such as crude glycerol and lignocellulosic biomass hydrolysate to produce bulk chemicals and fuels. However, its study has been impeded by the lack of efficient plasmids electro-transformation techniques. In this study, an efficient electroporation protocol for C. diolis was developed and two replicons functional in C. diolis were identified. After optimizing parameters, the electro-transformation efficiency was enhanced from 5 to 692 transformants/ug DNA. Moreover, metabolic engineering of C. diolis was performed as proof of concept for the first time. By simply overexpressing heterologous genes based on the replicable plasmids, the strain was engineered to improve productions of diol (1,3-propanediol) and n-alcohol (butanol), and to enable butyl acetate synthesis in vivo, respectively under different culture conditions. This work represented a milestone of breeding C. diolis using metabolic engineering, and paved the way for studying C. diolis on the molecular level.
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Affiliation(s)
- Ang Li
- School of Environmental and Biological Engineering, Nanjing University of Science & Technology, Nanjing 210094, China
| | - Zhiqiang Wen
- School of Environmental and Biological Engineering, Nanjing University of Science & Technology, Nanjing 210094, China
| | - Dahui Fang
- School of Environmental and Biological Engineering, Nanjing University of Science & Technology, Nanjing 210094, China
| | - Minrui Lu
- School of Environmental and Biological Engineering, Nanjing University of Science & Technology, Nanjing 210094, China
| | - Yuheng Ma
- School of Environmental and Biological Engineering, Nanjing University of Science & Technology, Nanjing 210094, China
| | - Qian Xie
- School of Environmental and Biological Engineering, Nanjing University of Science & Technology, Nanjing 210094, China
| | - Mingjie Jin
- School of Environmental and Biological Engineering, Nanjing University of Science & Technology, Nanjing 210094, China.
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74
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Laviña WA, Sakurai SSM, Pontrelli S, Putri SP, Fukusaki E. Metabolomics Analysis Reveals Global Metabolic Changes in the Evolved E. coli Strain with Improved Growth and 1-Butanol Production in Minimal Medium. Metabolites 2020; 10:metabo10050192. [PMID: 32414016 PMCID: PMC7281505 DOI: 10.3390/metabo10050192] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 04/29/2020] [Accepted: 05/07/2020] [Indexed: 11/30/2022] Open
Abstract
Production of 1-butanol from microorganisms has garnered significant interest due to its prospect as a drop-in biofuel and precursor for a variety of commercially relevant chemicals. Previously, high 1-butanol titer has been reported in Escherichia coli strain JCL166, which contains a modified clostridial 1-butanol pathway. Although conventional and metabolomics-based strain improvement strategies of E. coli strain JCL166 have been successful in improving production in rich medium, 1-butanol titer was severely limited in minimal medium. To further improve growth and consequently 1-butanol production in minimal medium, adaptive laboratory evolution (ALE) using mutD5 mutator plasmid was done on JCL166. Comparative metabolomics analysis of JCL166 and BP1 revealed global perturbations in the evolved strain BP1 compared to JCL166 (44 out of 64 metabolites), encompassing major metabolic pathways such as glycolysis, nucleotide biosynthesis, and CoA-related processes. Collectively, these metabolic changes in BP1 result in improved growth and, consequently, 1-butanol production in minimal medium. Furthermore, we found that the mutation in ihfB caused by ALE had a significant effect on the metabolome profile of the evolved strain. This study demonstrates how metabolomics was utilized for characterization of ALE-developed strains to understand the overall effect of mutations acquired through evolution.
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Affiliation(s)
- Walter A. Laviña
- Microbiology Division, Institute of Biological Sciences, University of the Philippines Los Baños, Los Baños, Laguna 4031, Philippines;
| | - Sana Subhan Memon Sakurai
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan; (S.S.M.S.); (S.P.P.)
| | - Sammy Pontrelli
- Institute of Molecular Systems Biology, D-BIOL, ETH Zurich, 8092 Zurich, Switzerland;
| | - Sastia Prama Putri
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan; (S.S.M.S.); (S.P.P.)
| | - Eiichiro Fukusaki
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan; (S.S.M.S.); (S.P.P.)
- Correspondence: ; Tel.: +81-6-6879-7416
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75
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Ferreira S, Pereira R, Wahl SA, Rocha I. Metabolic engineering strategies for butanol production in Escherichia coli. Biotechnol Bioeng 2020; 117:2571-2587. [PMID: 32374413 DOI: 10.1002/bit.27377] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Revised: 04/03/2020] [Accepted: 05/04/2020] [Indexed: 11/06/2022]
Abstract
The global market of butanol is increasing due to its growing applications as solvent, flavoring agent, and chemical precursor of several other compounds. Recently, the superior properties of n-butanol as a biofuel over ethanol have stimulated even more interest. (Bio)butanol is natively produced together with ethanol and acetone by Clostridium species through acetone-butanol-ethanol fermentation, at noncompetitive, low titers compared to petrochemical production. Different butanol production pathways have been expressed in Escherichia coli, a more accessible host compared to Clostridium species, to improve butanol titers and rates. The bioproduction of butanol is here reviewed from a historical and theoretical perspective. All tested rational metabolic engineering strategies in E. coli to increase butanol titers are reviewed: manipulation of central carbon metabolism, elimination of competing pathways, cofactor balancing, development of new pathways, expression of homologous enzymes, consumption of different substrates, and molecular biology strategies. The progress in the field of metabolic modeling and pathway generation algorithms and their potential application to butanol production are also summarized here. The main goals are to gather all the strategies, evaluate the respective progress obtained, identify, and exploit the outstanding challenges.
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Affiliation(s)
- Sofia Ferreira
- CEB-Centre of Biological Engineering, University of Minho, Campus de Gualtar, Braga, Portugal.,Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB-NOVA), Oeiras, Portugal
| | - Rui Pereira
- SilicoLife Lda, Braga, Portugal.,Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - S A Wahl
- Department of Biotechnology, Delft University of Technology, Delft, The Netherlands
| | - Isabel Rocha
- CEB-Centre of Biological Engineering, University of Minho, Campus de Gualtar, Braga, Portugal.,Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB-NOVA), Oeiras, Portugal
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76
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Chen AY, Lan EI. Chemical Production from Methanol Using Natural and Synthetic Methylotrophs. Biotechnol J 2020; 15:e1900356. [DOI: 10.1002/biot.201900356] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2019] [Revised: 03/03/2020] [Indexed: 12/27/2022]
Affiliation(s)
- Arvin Y. Chen
- Institute of Molecular Medicine and BioengineeringNational Chiao Tung University Hsinchu 30010 Taiwan
| | - Ethan I. Lan
- Department of Biological Science and TechnologyNational Chiao Tung University Hsinchu 30010 Taiwan
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77
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Ku JT, Chen AY, Lan EI. Metabolic Engineering Design Strategies for Increasing Acetyl-CoA Flux. Metabolites 2020; 10:metabo10040166. [PMID: 32340392 PMCID: PMC7240943 DOI: 10.3390/metabo10040166] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 04/19/2020] [Accepted: 04/21/2020] [Indexed: 01/18/2023] Open
Abstract
Acetyl-CoA is a key metabolite precursor for the biosynthesis of lipids, polyketides, isoprenoids, amino acids, and numerous other bioproducts which are used in various industries. Metabolic engineering efforts aim to increase carbon flux towards acetyl-CoA in order to achieve higher productivities of its downstream products. In this review, we summarize the strategies that have been implemented for increasing acetyl-CoA flux and concentration, and discuss their effects. Furthermore, recent works have developed synthetic acetyl-CoA biosynthesis routes that achieve higher stoichiometric yield of acetyl-CoA from glycolytic substrates.
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Affiliation(s)
- Jason T. Ku
- Institute of Molecular Medicine and Bioengineering, National Chiao Tung University, Hsinchu City 300, Taiwan; (J.T.K.); (A.Y.C.)
| | - Arvin Y. Chen
- Institute of Molecular Medicine and Bioengineering, National Chiao Tung University, Hsinchu City 300, Taiwan; (J.T.K.); (A.Y.C.)
| | - Ethan I. Lan
- Department of Biological Science and Technology, National Chiao Tung University, Hsinchu City 300, Taiwan
- Correspondence:
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Ma Y, Deng Q, Du Y, Ren J, Chen Y, Liu X, Guo X, Xiao D. Biosynthetic Pathway for Ethyl Butyrate Production in Saccharomyces cerevisiae. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:4252-4260. [PMID: 32186186 DOI: 10.1021/acs.jafc.0c00750] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Ethyl butyrate is one of the most important flavor substances in Chinese Baijiu and is also an ingredient in various daily-use chemical essences and food flavorings. In this study, to produce ethyl butyrate, we first introduced a butyryl-CoA synthesis pathway into Saccharomyces cerevisiae. Subsequently, three different alcohol acyltransferases, SAAT, VAAT, and CmAAT, were separately introduced into S. cerevisiae to catalyze the reaction of butyryl-CoA with ethanol to produce ethyl butyrate, and the results showed that strain EBS with SAAT produced the most ethyl butyrate (20.06 ± 2.23 mg/L). Furthermore, as the reaction catalyzed by Bcd to produce butyryl-CoA from crotonyl-CoA is a rate-limiting step, we replaced Bcd with Ter, and the modified strain EST produced 77.33 ± 4.79 mg/L ethyl butyrate. Finally, the copy numbers of Ter and SAAT were further increased, and the resulting modified strain EST-dST produced 99.65 ± 7.32 mg/L ethyl butyrate.
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Affiliation(s)
- Yanrui Ma
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Industrial Microbiology Key Laboratory, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, People's Republic of China
| | - Qingbo Deng
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Industrial Microbiology Key Laboratory, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, People's Republic of China
| | - Yongjing Du
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Industrial Microbiology Key Laboratory, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, People's Republic of China
| | - Jinying Ren
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Industrial Microbiology Key Laboratory, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, People's Republic of China
| | - Yefu Chen
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Industrial Microbiology Key Laboratory, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, People's Republic of China
| | - Xiaohang Liu
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Industrial Microbiology Key Laboratory, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, People's Republic of China
| | - Xuewu Guo
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Industrial Microbiology Key Laboratory, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, People's Republic of China
| | - Dongguang Xiao
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Industrial Microbiology Key Laboratory, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, People's Republic of China
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79
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Nawab S, Wang N, Ma X, Huo YX. Genetic engineering of non-native hosts for 1-butanol production and its challenges: a review. Microb Cell Fact 2020; 19:79. [PMID: 32220254 PMCID: PMC7099781 DOI: 10.1186/s12934-020-01337-w] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Accepted: 03/18/2020] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND Owing to the increase in energy consumption, fossil fuel resources are gradually depleting which has led to the growing environmental concerns; therefore, scientists are being urged to produce sustainable and ecofriendly fuels. Thus, there is a growing interest in the generation of biofuels from renewable energy resources using microbial fermentation. MAIN TEXT Butanol is a promising biofuel that can substitute for gasoline; unfortunately, natural microorganisms pose challenges for the economical production of 1-butanol at an industrial scale. The availability of genetic and molecular tools to engineer existing native pathways or create synthetic pathways have made non-native hosts a good choice for the production of 1-butanol from renewable resources. Non-native hosts have several distinct advantages, including using of cost-efficient feedstock, solvent tolerant and reduction of contamination risk. Therefore, engineering non-native hosts to produce biofuels is a promising approach towards achieving sustainability. This paper reviews the currently employed strategies and synthetic biology approaches used to produce 1-butanol in non-native hosts over the past few years. In addition, current challenges faced in using non-native hosts and the possible solutions that can help improve 1-butanol production are also discussed. CONCLUSION Non-native organisms have the potential to realize commercial production of 1- butanol from renewable resources. Future research should focus on substrate utilization, cofactor imbalance, and promoter selection to boost 1-butanol production in non-native hosts. Moreover, the application of robust genetic engineering approaches is required for metabolic engineering of microorganisms to make them industrially feasible for 1-butanol production.
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Affiliation(s)
- Said Nawab
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, 5 South Zhongguancun Street, Haidian District, Beijing, 100081, People's Republic of China
| | - Ning Wang
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, 5 South Zhongguancun Street, Haidian District, Beijing, 100081, People's Republic of China.
| | - Xiaoyan Ma
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, 5 South Zhongguancun Street, Haidian District, Beijing, 100081, People's Republic of China.
| | - Yi-Xin Huo
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, 5 South Zhongguancun Street, Haidian District, Beijing, 100081, People's Republic of China
- Biology Institute, Shandong Province Key Laboratory for Biosensors, Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250103, China
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80
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Li S, Huang L, Ke C, Pang Z, Liu L. Pathway dissection, regulation, engineering and application: lessons learned from biobutanol production by solventogenic clostridia. BIOTECHNOLOGY FOR BIOFUELS 2020; 13:39. [PMID: 32165923 PMCID: PMC7060580 DOI: 10.1186/s13068-020-01674-3] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Accepted: 02/04/2020] [Indexed: 06/01/2023]
Abstract
The global energy crisis and limited supply of petroleum fuels have rekindled the interest in utilizing a sustainable biomass to produce biofuel. Butanol, an advanced biofuel, is a superior renewable resource as it has a high energy content and is less hygroscopic than other candidates. At present, the biobutanol route, employing acetone-butanol-ethanol (ABE) fermentation in Clostridium species, is not economically competitive due to the high cost of feedstocks, low butanol titer, and product inhibition. Based on an analysis of the physiological characteristics of solventogenic clostridia, current advances that enhance ABE fermentation from strain improvement to product separation were systematically reviewed, focusing on: (1) elucidating the metabolic pathway and regulation mechanism of butanol synthesis; (2) enhancing cellular performance and robustness through metabolic engineering, and (3) optimizing the process of ABE fermentation. Finally, perspectives on engineering and exploiting clostridia as cell factories to efficiently produce various chemicals and materials are also discussed.
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Affiliation(s)
- Shubo Li
- College of Light Industry and Food Engineering, Guangxi University, Nanning, 530004 China
| | - Li Huang
- College of Light Industry and Food Engineering, Guangxi University, Nanning, 530004 China
| | - Chengzhu Ke
- College of Light Industry and Food Engineering, Guangxi University, Nanning, 530004 China
| | - Zongwen Pang
- College of Life Science and Technology, Guangxi University, Nanning, 530005 China
| | - Liming Liu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122 China
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81
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Cao M, Gao M, Suástegui M, Mei Y, Shao Z. Building microbial factories for the production of aromatic amino acid pathway derivatives: From commodity chemicals to plant-sourced natural products. Metab Eng 2020; 58:94-132. [DOI: 10.1016/j.ymben.2019.08.008] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 08/03/2019] [Accepted: 08/07/2019] [Indexed: 01/23/2023]
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82
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Wen Z, Ledesma-Amaro R, Lu M, Jin M, Yang S. Metabolic Engineering of Clostridium cellulovorans to Improve Butanol Production by Consolidated Bioprocessing. ACS Synth Biol 2020; 9:304-315. [PMID: 31940438 DOI: 10.1021/acssynbio.9b00331] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Clostridium cellulovorans DSM 743B can produce butyrate when grown on lignocellulose, but it can hardly synthesize butanol. In a previous study, C. cellulovorans was successfully engineered to switch the metabolism from butyryl-CoA to butanol by overexpressing an alcohol aldehyde dehydrogenase gene adhE1 from Clostridium acetobutylicum ATCC 824; however, its full potential in butanol production is still unexplored. In the study, a metabolic engineering approach based on a push-pull strategy was developed to further enhance cellulosic butanol production. In order to accomplish this, the carbon flux from acetyl-CoA to butyryl-CoA was pulled by overexpressing a trans-enoyl-coenzyme A reductase gene (ter), which can irreversibly catalyze crotonyl-CoA to butyryl-CoA. Then an acid reassimilation pathway uncoupled with acetone production was introduced to redirect the carbon flow from butyrate and acetate toward butyryl-CoA. Finally, xylose metabolism engineering was implemented by inactivating xylR (Clocel_0594) and araR (Clocel_1253), as well as overexpressing xylT (CA_C1345), which is expected to supply additional carbon and reducing power for CoA and butanol synthesis pathways. The final engineered strain produced 4.96 g/L of n-butanol from alkali extracted corn cobs (AECC), increasing by 235-fold compared to that of the wild type. It serves as a promising butanol producer by consolidated bioprocessing.
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Affiliation(s)
- Zhiqiang Wen
- School of Environmental and Biological Engineering, Nanjing University of Science & Technology, Nanjing 210094, China
| | | | - Minrui Lu
- School of Environmental and Biological Engineering, Nanjing University of Science & Technology, Nanjing 210094, China
| | - Mingjie Jin
- School of Environmental and Biological Engineering, Nanjing University of Science & Technology, Nanjing 210094, China
| | - Sheng Yang
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
- Huzhou Center of Industrial Biotechnology, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
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83
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Mazzoli R, Olson D. Clostridium thermocellum: A microbial platform for high-value chemical production from lignocellulose. ADVANCES IN APPLIED MICROBIOLOGY 2020; 113:111-161. [PMID: 32948265 DOI: 10.1016/bs.aambs.2020.07.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Second generation biorefining, namely fermentation processes based on lignocellulosic feedstocks, has attracted tremendous interest (owing to the large availability and low cost of this biomass) as a strategy to produce biofuels and commodity chemicals that is an alternative to oil refining. However, the innate recalcitrance of lignocellulose has slowed progress toward economically viable processes. Consolidated bioprocessing (CBP), i.e., single-step fermentation of lignocellulose may dramatically reduce the current costs of 2nd generation biorefining. Metabolic engineering has been used as a tool to develop improved microbial strains supporting CBP. Clostridium thermocellum is among the most efficient cellulose degraders isolated so far and one of the most promising host organisms for application of CBP. The development of efficient and reliable genetic tools has allowed significant progress in metabolic engineering of this strain aimed at expanding the panel of growth substrates and improving the production of a number of commodity chemicals of industrial interest such as ethanol, butanol, isobutanol, isobutyl acetate and lactic acid. The present review aims to summarize recent developments in metabolic engineering of this organism which currently represents a reference model for the development of biocatalysts for 2nd generation biorefining.
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84
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Karim AS, Rasor BJ, Jewett MC. Enhancing control of cell-free metabolism through pH modulation. Synth Biol (Oxf) 2019. [DOI: 10.1093/synbio/ysz027] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Abstract
Engineering metabolism for the synthesis of bio-based products in non-model organisms can be challenging. One specific challenge is that biosynthetic pathways are often built from enzyme candidates sourced from diverse organisms, which can prove difficult to implement in recombinant hosts due to differences in their cellular environments (e.g. pH, cofactor balance). To address this problem, we report a cell-free synthetic biology approach for understanding metabolism in a range of environmental conditions, specifically under varied pH. The key idea is to control the pH of Escherichia coli-based cell-free systems for assessing pathway performance using enzymes sourced from organisms other than E. coli. As a model, we apply this approach to study the impact of pH on the n-butanol biosynthesis pathway derived from clostridia in E. coli lysates. Specifically, we exploit the open, cell-free reaction environment to explore pH outside the habitable range of E. coli, revealing insights into how chemical context impacts the interaction between native metabolism and heterologous enzymes. We find that the pH optimum for butanol production from acetyl-CoA is substantially lower than the optimal pH of glycolysis in E. coli-based crude lysates. In addition, pH is an essential factor to consider when activating metabolic pathways in the cell-free environment due to its effect on reaction yield or enzyme activity, the latter of which is demonstrated in this work for alcohol dehydrogenases from a range of extremophiles. Ultimately, altering metabolism through pH control will allow cell-free systems to be used in studying the metabolic state of organisms and identify suitable enzymes for pathway engineering.
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Affiliation(s)
- Ashty S Karim
- Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Tech E-136, Evanston, IL, 60208, USA
- Chemistry of Life Processes Institute, Northwestern University, 2145 Sheridan Road, Tech E-136, Evanston, IL, 60208, USA
- Center for Synthetic Biology, Northwestern University, 2145 Sheridan Road, Tech E-136, Evanston, IL, 60208, USA
| | - Blake J Rasor
- Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Tech E-136, Evanston, IL, 60208, USA
- Chemistry of Life Processes Institute, Northwestern University, 2145 Sheridan Road, Tech E-136, Evanston, IL, 60208, USA
- Center for Synthetic Biology, Northwestern University, 2145 Sheridan Road, Tech E-136, Evanston, IL, 60208, USA
| | - Michael C Jewett
- Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Tech E-136, Evanston, IL, 60208, USA
- Chemistry of Life Processes Institute, Northwestern University, 2145 Sheridan Road, Tech E-136, Evanston, IL, 60208, USA
- Center for Synthetic Biology, Northwestern University, 2145 Sheridan Road, Tech E-136, Evanston, IL, 60208, USA
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL, 60611, USA
- Simpson Querrey Institute, Northwestern University, Chicago, IL, 60611, USA
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85
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Becker J, Wittmann C. A field of dreams: Lignin valorization into chemicals, materials, fuels, and health-care products. Biotechnol Adv 2019; 37:107360. [DOI: 10.1016/j.biotechadv.2019.02.016] [Citation(s) in RCA: 207] [Impact Index Per Article: 41.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Revised: 02/18/2019] [Accepted: 02/22/2019] [Indexed: 02/07/2023]
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86
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Chen W, Chen R, Wang H, Li Y, Zhang Y, Li S. Tuning chromosomal gene expression in Escherichia coli by combining single-stranded oligonucleotides mediated recombination and kil counter selection system. J Biotechnol 2019; 307:63-68. [PMID: 31678458 DOI: 10.1016/j.jbiotec.2019.10.014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Revised: 10/03/2019] [Accepted: 10/21/2019] [Indexed: 10/25/2022]
Abstract
Extensively modulating gene expression to achieve optimal flux is a critical step in metabolic engineering. Gene expression is usually modulated at the transcriptional level by controlling the strength of a promoter. However, this type of modulation is often hampered by its inability to fully sample the complete continuum of transcriptional control. In Escherichia coli, this limitation can be solved by constructing promoters with a wide range of strengths. In this study, a highly efficient method was developed to modulate a particular chromosomal gene of E. coli at a wide range of expression levels. This was achieved by combining highly efficient single-stranded oligonucleotide-mediated recombination and a stringent counter selection system kil. Using this strategy, a chromosomal library, with a range from 0.3% to 388% relative to the wild lac promoter, was easily obtained. The strength of our chromosomal promoter library was approximately 5-60 times wider in range than those of libraries reported before.
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Affiliation(s)
- Wei Chen
- Guangdong Province Key Laboratory for Biotechnology Drug Candidates, School of Biosciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou 510006, China.
| | - Ruyi Chen
- Guangdong Province Key Laboratory for Biotechnology Drug Candidates, School of Biosciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou 510006, China
| | - Hui Wang
- School of Biological Medicine, Beijing City University, Beijing, 10084, China
| | - Yujuan Li
- Guangdong Province Key Laboratory for Biotechnology Drug Candidates, School of Biosciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou 510006, China
| | - Yunyi Zhang
- Guangdong Province Key Laboratory for Biotechnology Drug Candidates, School of Biosciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou 510006, China
| | - Shanhu Li
- Beijing Institute of Biotechnology, Beijing 100850, China.
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87
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Zhao C, Zhang Y, Li Y. Production of fuels and chemicals from renewable resources using engineered Escherichia coli. Biotechnol Adv 2019; 37:107402. [DOI: 10.1016/j.biotechadv.2019.06.001] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2018] [Revised: 05/23/2019] [Accepted: 06/02/2019] [Indexed: 02/06/2023]
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88
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Mahajan D, Sengupta S, Sen S. Strategies to improve microbial lipid production: Optimization techniques. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2019. [DOI: 10.1016/j.bcab.2019.101321] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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89
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Ferreira S, Pereira R, Liu F, Vilaça P, Rocha I. Discovery and implementation of a novel pathway for n-butanol production via 2-oxoglutarate. BIOTECHNOLOGY FOR BIOFUELS 2019; 12:230. [PMID: 31583016 PMCID: PMC6767645 DOI: 10.1186/s13068-019-1565-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Accepted: 09/07/2019] [Indexed: 05/12/2023]
Abstract
BACKGROUND One of the European Union directives indicates that 10% of all fuels must be bio-synthesized by 2020. In this regard, biobutanol-natively produced by clostridial strains-poses as a promising alternative biofuel. One possible approach to overcome the difficulties of the industrial exploration of the native producers is the expression of more suitable pathways in robust microorganisms such as Escherichia coli. The enumeration of novel pathways is a powerful tool, allowing to identify non-obvious combinations of enzymes to produce a target compound. RESULTS This work describes the in silico driven design of E. coli strains able to produce butanol via 2-oxoglutarate by a novel pathway. This butanol pathway was generated by a hypergraph algorithm and selected from an initial set of 105,954 different routes by successively applying different filters, such as stoichiometric feasibility, size and novelty. The implementation of this pathway involved seven catalytic steps and required the insertion of nine heterologous genes from various sources in E. coli distributed in three plasmids. Expressing butanol genes in E. coli K12 and cultivation in High-Density Medium formulation seem to favor butanol accumulation via the 2-oxoglutarate pathway. The maximum butanol titer obtained was 85 ± 1 mg L-1 by cultivating the cells in bioreactors. CONCLUSIONS In this work, we were able to successfully translate the computational analysis into in vivo applications, designing novel strains of E. coli able to produce n-butanol via an innovative pathway. Our results demonstrate that enumeration algorithms can broad the spectrum of butanol producing pathways. This validation encourages further research to other target compounds.
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Affiliation(s)
- Sofia Ferreira
- CEB-Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
| | - Rui Pereira
- SilicoLife Lda, Rua do Canastreiro 15, 4715-387 Braga, Portugal
- Present Address: Department of Biology and Biological Engineering, Chalmers University of Technology, 412 96 Gothenburg, Sweden
| | - Filipe Liu
- CEB-Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
- Present Address: Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, IL USA
| | - Paulo Vilaça
- SilicoLife Lda, Rua do Canastreiro 15, 4715-387 Braga, Portugal
| | - Isabel Rocha
- CEB-Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB-NOVA), Oeiras, Portugal
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90
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A Feasibility Study of Cellulosic Isobutanol Production—Process Simulation and Economic Analysis. Processes (Basel) 2019. [DOI: 10.3390/pr7100667] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Renewable liquid biofuels for transportation have recently attracted enormous global attention due to their potential to provide a sustainable alternative to fossil fuels. In recent years, the attention has shifted from first-generation bioethanol to the production of higher molecular weight alcohols, such as biobutanol, from cellulosic feedstocks. The economic feasibility of such processes depends on several parameters such as the cost of raw materials, the fermentation performance and the energy demand for the pretreatment of biomass and downstream processing. In this work, two conceptual process scenarios for isobutanol production, one with and one without integrated product removal from the fermentor by vacuum stripping, were developed and evaluated using SuperPro Designer®. In agreement with previous publications, it was concluded that the fermentation titer is a crucial parameter for the economic competitiveness of the process as it is closely related to the energy requirements for product purification. In the first scenario where the product titer was 22 g/L, the energy demand for downstream processing was 15.8 MJ/L isobutanol and the unit production cost of isobutanol was $2.24/L. The integrated product removal by vacuum stripping implemented in the second scenario was assumed to improve the isobutanol titer to 50 g/L. In this case, the energy demand for the product removal (electricity) and downstream processing were 1.8 MJ/L isobutanol and 10 MJ/L isobutanol, respectively, and the unit production cost was reduced to $1.42/L. The uncertainty associated with the choice of modeling and economic parameters was investigated by Monte Carlo simulation sensitivity analysis.
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91
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The significance of aspartate on NAD(H) biosynthesis and ABE fermentation in Clostridium acetobutylicum ATCC 824. AMB Express 2019; 9:142. [PMID: 31506849 PMCID: PMC6737123 DOI: 10.1186/s13568-019-0874-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Accepted: 09/05/2019] [Indexed: 01/25/2023] Open
Abstract
The co-factor NADH plays an important role in butanol biosynthesis. In this study, we found that aspartate could effectively improve the butanol production of Clostridium acetobutylicum ATCC 824. Further study showed that aspartate could be used as the precursor of NADH de novo synthesis in C. acetobutylicum ATCC 824. When 2 g/L aspartate was added, the transcription levels of essential genes (nadA, nadB and nadC) for NADH de novo synthesis were significantly higher than that of without aspartate addition. The levels of intracellular NAD+, NADH, total NAD(H) and the ratio of NADH/NAD+ were also significantly increased, which were 63.9 ± 8.0%, 85.0 ± %, 77.7 ± 8.0% and 12.7 ± 2.9% higher than those of without aspartate addition, respectively. Furthermore, the butanol production was improved by overexpressing the NADH de novo synthesis genes, and the fermentation performance could be further enhanced by strengthening the VB1 biosynthesis and NADH de novo synthesis pathway simultaneously. As a result, the butanol titer of the engineered strain 824(thiCGE–nadC) reached 13.96 ± 0.11 g/L, 7.2 ± 0.4%, 18.1 ± 0.1%, 34.1 ± 0.1% higher than that of 824(thiCGE), 824(nadC) and the wild type strain, respectively. This study has a reference value for the NADH related researches of other microbes, and the engineering strategy used in this study provides a new idea for construction of efficient fuel-producing strains.
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92
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Zhao C, Sinumvayo JP, Zhang Y, Li Y. Design and development of a “Y-shaped” microbial consortium capable of simultaneously utilizing biomass sugars for efficient production of butanol. Metab Eng 2019; 55:111-119. [DOI: 10.1016/j.ymben.2019.06.012] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2019] [Revised: 06/18/2019] [Accepted: 06/22/2019] [Indexed: 10/26/2022]
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93
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Li W, Ma L, Shen X, Wang J, Feng Q, Liu L, Zheng G, Yan Y, Sun X, Yuan Q. Targeting metabolic driving and intermediate influx in lysine catabolism for high-level glutarate production. Nat Commun 2019; 10:3337. [PMID: 31350399 PMCID: PMC6659618 DOI: 10.1038/s41467-019-11289-4] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2019] [Accepted: 07/03/2019] [Indexed: 11/09/2022] Open
Abstract
Various biosynthetic pathways have been designed to explore sustainable production of glutarate, an attractive C5 building block of polyesters and polyamides. However, its efficient production has not been achieved in Escherichia coli. Here, we use E. coli native lysine catabolic machinery for glutarate biosynthesis. This endogenous genes-only design can generate strong metabolic driving force to maximize carbon flux toward glutarate biosynthesis by replenishing glutamate and NAD(P)H for lysine biosynthesis, releasing lysine feedback inhibition, and boosting oxaloacetate supply. We use native transporters to overcome extracellular accumulation of cadaverine and 5-aminovalerate. With these efforts, both high titer (54.5 g L-1) and high yield (0.54 mol mol-1 glucose) of glutarate production are achieved under fed-batch conditions. This work demonstrates the power of redirecting carbon flux and the role of transporters to decrease intermediate accumulation.
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Affiliation(s)
- Wenna Li
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Lin Ma
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Xiaolin Shen
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Jia Wang
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Qi Feng
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Lexuan Liu
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Guojun Zheng
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Yajun Yan
- School of Chemical, Materials and Biomedical Engineering, College of Engineering, The University of Georgia, Athens, GA, 30602, USA
| | - Xinxiao Sun
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing, 100029, China.
| | - Qipeng Yuan
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing, 100029, China.
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94
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Tian L, Conway PM, Cervenka ND, Cui J, Maloney M, Olson DG, Lynd LR. Metabolic engineering of Clostridium thermocellum for n-butanol production from cellulose. BIOTECHNOLOGY FOR BIOFUELS 2019; 12:186. [PMID: 31367231 PMCID: PMC6652007 DOI: 10.1186/s13068-019-1524-6] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 07/05/2019] [Indexed: 05/15/2023]
Abstract
BACKGROUND Biofuel production from plant cell walls offers the potential for sustainable and economically attractive alternatives to petroleum-based products. In particular, Clostridium thermocellum is a promising host for consolidated bioprocessing (CBP) because of its strong native ability to ferment cellulose. RESULTS We tested 12 different enzyme combinations to identify an n-butanol pathway with high titer and thermostability in C. thermocellum. The best producing strain contained the thiolase-hydroxybutyryl-CoA dehydrogenase-crotonase (Thl-Hbd-Crt) module from Thermoanaerobacter thermosaccharolyticum, the trans-enoyl-CoA reductase (Ter) enzyme from Spirochaeta thermophila and the butyraldehyde dehydrogenase and alcohol dehydrogenase (Bad-Bdh) module from Thermoanaerobacter sp. X514 and was able to produce 88 mg/L n-butanol. The key enzymes from this combination were further optimized by protein engineering. The Thl enzyme was engineered by introducing homologous mutations previously identified in Clostridium acetobutylicum. The Hbd and Ter enzymes were engineered for changes in cofactor specificity using the CSR-SALAD algorithm to guide the selection of mutations. The cofactor engineering of Hbd had the unexpected side effect of also increasing activity by 50-fold. CONCLUSIONS Here we report engineering C. thermocellum to produce n-butanol. Our initial pathway designs resulted in low levels (88 mg/L) of n-butanol production. By engineering the protein sequence of key enzymes in the pathway, we increased the n-butanol titer by 2.2-fold. We further increased n-butanol production by adding ethanol to the growth media. By combining all these improvements, the engineered strain was able to produce 357 mg/L of n-butanol from cellulose within 120 h.
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Affiliation(s)
- Liang Tian
- Thayer School of Engineering, Dartmouth College, Hanover, NH 03755 USA
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37830 USA
| | | | | | - Jingxuan Cui
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37830 USA
- Department of Biological Sciences, Dartmouth College, Hanover, NH 03755 USA
| | - Marybeth Maloney
- Thayer School of Engineering, Dartmouth College, Hanover, NH 03755 USA
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37830 USA
| | - Daniel G. Olson
- Thayer School of Engineering, Dartmouth College, Hanover, NH 03755 USA
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37830 USA
| | - Lee R. Lynd
- Thayer School of Engineering, Dartmouth College, Hanover, NH 03755 USA
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37830 USA
- Department of Biological Sciences, Dartmouth College, Hanover, NH 03755 USA
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95
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Wang J, Zhang R, Zhang Y, Yang Y, Lin Y, Yan Y. Developing a pyruvate-driven metabolic scenario for growth-coupled microbial production. Metab Eng 2019; 55:191-200. [PMID: 31348998 DOI: 10.1016/j.ymben.2019.07.011] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Revised: 07/17/2019] [Accepted: 07/20/2019] [Indexed: 11/17/2022]
Abstract
Microbial-based chemical synthesis serves as a promising approach for sustainable production of industrially important products. However, limited production performance caused by metabolic burden or genetic variations poses one of the major challenges in achieving an economically viable biomanufacturing process. To address this issue, one superior strategy is to couple the product synthesis with cellular growth, which renders production obligatory for cell survival. Here we create a pyruvate-driven metabolic scenario in engineered Escherichia coli for growth-coupled bioproduction, with which we demonstrate its application in boosting production of anthranilate and its derivatives. Deletion of a minimal set of endogenous pyruvate-releasing pathways engenders anthranilate synthesis as the salvage route for pyruvate generation to support cell growth, concomitant with simultaneous anthranilate production. Further introduction of native and non-native downstream pathways affords production enhancement of two anthranilate-derived high-value products including L-tryptophan and cis, cis-muconic acid from different carbon sources. The work reported here presents a new growth-coupled strategy with demonstrated feasibility for promoting microbial production.
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Affiliation(s)
- Jian Wang
- School of Chemical, Materials and Biomedical Engineering, College of Engineering, The University of Georgia, Athens, GA, 30602, USA
| | - Ruihua Zhang
- School of Chemical, Materials and Biomedical Engineering, College of Engineering, The University of Georgia, Athens, GA, 30602, USA
| | - Yan Zhang
- School of Chemical, Materials and Biomedical Engineering, College of Engineering, The University of Georgia, Athens, GA, 30602, USA
| | - Yaping Yang
- School of Chemical, Materials and Biomedical Engineering, College of Engineering, The University of Georgia, Athens, GA, 30602, USA
| | - Yuheng Lin
- BiotecEra Inc., 220 Riverbend Rd., Athens, GA, 30602, USA
| | - Yajun Yan
- School of Chemical, Materials and Biomedical Engineering, College of Engineering, The University of Georgia, Athens, GA, 30602, USA.
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96
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Chacón MG, Kendrick EG, Leak DJ. Engineering Escherichia coli for the production of butyl octanoate from endogenous octanoyl-CoA. PeerJ 2019; 7:e6971. [PMID: 31304053 PMCID: PMC6610577 DOI: 10.7717/peerj.6971] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Accepted: 04/18/2019] [Indexed: 11/20/2022] Open
Abstract
Medium chain esters produced from fruits and flowering plants have a number of commercial applications including use as flavour and fragrance ingredients, biofuels, and in pharmaceutical formulations. These esters are typically made via the activity of an alcohol acyl transferase (AAT) enzyme which catalyses the condensation of an alcohol and an acyl-CoA. Developing a microbial platform for medium chain ester production using AAT activity presents several obstacles, including the low product specificity of these enzymes for the desired ester and/or low endogenous substrate availability. In this study, we engineered Escherichia coli for the production of butyl octanoate from endogenously produced octanoyl-CoA. This was achieved through rational protein engineering of an AAT enzyme from Actinidia chinensis for improved octanoyl-CoA substrate specificity and metabolic engineering of E. coli fatty acid metabolism for increased endogenous octanoyl-CoA availability. This resulted in accumulation of 3.3 + 0.1 mg/L butyl octanoate as the sole product from E. coli after 48 h. This study represents a preliminary examination of the feasibility of developing E. coli platforms for the synthesis single medium chain esters from endogenous fatty acids.
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Affiliation(s)
- Micaela G Chacón
- Department of Biology and Biochemistry, University of Bath, Bath, England
| | | | - David J Leak
- Department of Biology and Biochemistry, University of Bath, Bath, England
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97
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Naseri G, Behrend J, Rieper L, Mueller-Roeber B. COMPASS for rapid combinatorial optimization of biochemical pathways based on artificial transcription factors. Nat Commun 2019; 10:2615. [PMID: 31197154 PMCID: PMC6565718 DOI: 10.1038/s41467-019-10224-x] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Accepted: 04/26/2019] [Indexed: 02/08/2023] Open
Abstract
Balanced expression of multiple genes is central for establishing new biosynthetic pathways or multiprotein cellular complexes. Methods for efficient combinatorial assembly of regulatory sequences (promoters) and protein coding sequences are therefore highly wanted. Here, we report a high-throughput cloning method, called COMPASS for COMbinatorial Pathway ASSembly, for the balanced expression of multiple genes in Saccharomyces cerevisiae. COMPASS employs orthogonal, plant-derived artificial transcription factors (ATFs) and homologous recombination-based cloning for the generation of thousands of individual DNA constructs in parallel. The method relies on a positive selection of correctly assembled pathway variants from both, in vivo and in vitro cloning procedures. To decrease the turnaround time in genomic engineering, COMPASS is equipped with multi-locus CRISPR/Cas9-mediated modification capacity. We demonstrate the application of COMPASS by generating cell libraries producing β-carotene and co-producing β-ionone and biosensor-responsive naringenin. COMPASS will have many applications in synthetic biology projects that require gene expression balancing. Metabolic engineering requires the balancing of gene expression to obtain optimal output. Here the authors present COMPASS – COMbinatorial Pathway ASSembly – which uses plant-derived artificial transcription factors and cloning of thousands of DNA constructs in parallel to rapidly optimise pathways.
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Affiliation(s)
- Gita Naseri
- University of Potsdam, Cell2Fab Research Unit, Karl-Liebknecht-Str. 24-25, 14476, Potsdam, Germany.,University of Potsdam, Department Molecular Biology, Karl-Liebknecht-Str. 24-25, House 20, 14476, Potsdam, Germany
| | - Jessica Behrend
- University of Potsdam, Cell2Fab Research Unit, Karl-Liebknecht-Str. 24-25, 14476, Potsdam, Germany
| | - Lisa Rieper
- University of Potsdam, Cell2Fab Research Unit, Karl-Liebknecht-Str. 24-25, 14476, Potsdam, Germany
| | - Bernd Mueller-Roeber
- University of Potsdam, Department Molecular Biology, Karl-Liebknecht-Str. 24-25, House 20, 14476, Potsdam, Germany. .,Max-Planck Institute of Molecular Plant Physiology, Plant Signalling Group, Am Mühlenberg 1, D-14476, Potsdam-Golm, Germany. .,Center of Plant Systems Biology and Biotechnology (CPSBB), Department Plant Development, Ruski Blvd. 139, 4000, Plovdiv, Bulgaria.
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98
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Comparison of Multi-Objective Evolutionary Algorithms to Solve the Modular Cell Design Problem for Novel Biocatalysis. Processes (Basel) 2019. [DOI: 10.3390/pr7060361] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
A large space of chemicals with broad industrial and consumer applications could be synthesized by engineered microbial biocatalysts. However, the current strain optimization process is prohibitively laborious and costly to produce one target chemical and often requires new engineering efforts to produce new molecules. To tackle this challenge, modular cell design based on a chassis strain that can be combined with different product synthesis pathway modules has recently been proposed. This approach seeks to minimize unexpected failure and avoid task repetition, leading to a more robust and faster strain engineering process. In our previous study, we mathematically formulated the modular cell design problem based on the multi-objective optimization framework. In this study, we evaluated a library of state-of-the-art multi-objective evolutionary algorithms (MOEAs) to identify the most effective method to solve the modular cell design problem. Using the best MOEA, we found better solutions for modular cells compatible with many product synthesis modules. Furthermore, the best performing algorithm could provide better and more diverse design options that might help increase the likelihood of successful experimental implementation. We identified key parameter configurations to overcome the difficulty associated with multi-objective optimization problems with many competing design objectives. Interestingly, we found that MOEA performance with a real application problem, e.g., the modular strain design problem, does not always correlate with artificial benchmarks. Overall, MOEAs provide powerful tools to solve the modular cell design problem for novel biocatalysis.
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99
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Stella RG, Wiechert J, Noack S, Frunzke J. Evolutionary engineering of
Corynebacterium glutamicum. Biotechnol J 2019; 14:e1800444. [DOI: 10.1002/biot.201800444] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Revised: 01/23/2019] [Indexed: 01/02/2023]
Affiliation(s)
- Roberto G. Stella
- Institute of Bio‐ and Geosciences, IBG‐1: Biotechnology, Forschungszentrum Jülich Wilhelm‐Johnen‐Straße 52428 Jülich Germany
| | - Johanna Wiechert
- Institute of Bio‐ and Geosciences, IBG‐1: Biotechnology, Forschungszentrum Jülich Wilhelm‐Johnen‐Straße 52428 Jülich Germany
| | - Stephan Noack
- Institute of Bio‐ and Geosciences, IBG‐1: Biotechnology, Forschungszentrum Jülich Wilhelm‐Johnen‐Straße 52428 Jülich Germany
| | - Julia Frunzke
- Institute of Bio‐ and Geosciences, IBG‐1: Biotechnology, Forschungszentrum Jülich Wilhelm‐Johnen‐Straße 52428 Jülich Germany
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100
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Sevilla E, Bes MT, González A, Peleato ML, Fillat MF. Redox-Based Transcriptional Regulation in Prokaryotes: Revisiting Model Mechanisms. Antioxid Redox Signal 2019; 30:1651-1696. [PMID: 30073850 DOI: 10.1089/ars.2017.7442] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
SIGNIFICANCE The successful adaptation of microorganisms to ever-changing environments depends, to a great extent, on their ability to maintain redox homeostasis. To effectively maintain the redox balance, cells have developed a variety of strategies mainly coordinated by a battery of transcriptional regulators through diverse mechanisms. Recent Advances: This comprehensive review focuses on the main mechanisms used by major redox-responsive regulators in prokaryotes and their relationship with the different redox signals received by the cell. An overview of the corresponding regulons is also provided. CRITICAL ISSUES Some regulators are difficult to classify since they may contain several sensing domains and respond to more than one signal. We propose a classification of redox-sensing regulators into three major groups. The first group contains one-component or direct regulators, whose sensing and regulatory domains are in the same protein. The second group comprises the classical two-component systems involving a sensor kinase that transduces the redox signal to its DNA-binding partner. The third group encompasses a heterogeneous group of flavin-based photosensors whose mechanisms are not always fully understood and are often involved in more complex regulatory networks. FUTURE DIRECTIONS Redox-responsive transcriptional regulation is an intricate process as identical signals may be sensed and transduced by different transcription factors, which often interplay with other DNA-binding proteins with or without regulatory activity. Although there is much information about some key regulators, many others remain to be fully characterized due to the instability of their clusters under oxygen. Understanding the mechanisms and the regulatory networks operated by these regulators is essential for the development of future applications in biotechnology and medicine.
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Affiliation(s)
- Emma Sevilla
- 1 Departamento de Bioquímica y Biología Molecular y Celular, Universidad de Zaragoza, Zaragoza, Spain.,2 Instituto de Biocomputación y Física de Sistemas Complejos (BIFI), Universidad de Zaragoza, Zaragoza, Spain.,3 Grupo de Bioquímica, Biofísica y Biología Computacional (BIFI, UNIZAR), Unidad Asociada al CSIC, Zaragoza, Spain
| | - María Teresa Bes
- 1 Departamento de Bioquímica y Biología Molecular y Celular, Universidad de Zaragoza, Zaragoza, Spain.,2 Instituto de Biocomputación y Física de Sistemas Complejos (BIFI), Universidad de Zaragoza, Zaragoza, Spain.,3 Grupo de Bioquímica, Biofísica y Biología Computacional (BIFI, UNIZAR), Unidad Asociada al CSIC, Zaragoza, Spain
| | - Andrés González
- 2 Instituto de Biocomputación y Física de Sistemas Complejos (BIFI), Universidad de Zaragoza, Zaragoza, Spain.,3 Grupo de Bioquímica, Biofísica y Biología Computacional (BIFI, UNIZAR), Unidad Asociada al CSIC, Zaragoza, Spain.,4 Instituto de Investigación Sanitaria Aragón (IIS Aragón), Zaragoza, Spain
| | - María Luisa Peleato
- 1 Departamento de Bioquímica y Biología Molecular y Celular, Universidad de Zaragoza, Zaragoza, Spain.,2 Instituto de Biocomputación y Física de Sistemas Complejos (BIFI), Universidad de Zaragoza, Zaragoza, Spain.,3 Grupo de Bioquímica, Biofísica y Biología Computacional (BIFI, UNIZAR), Unidad Asociada al CSIC, Zaragoza, Spain
| | - María F Fillat
- 1 Departamento de Bioquímica y Biología Molecular y Celular, Universidad de Zaragoza, Zaragoza, Spain.,2 Instituto de Biocomputación y Física de Sistemas Complejos (BIFI), Universidad de Zaragoza, Zaragoza, Spain.,3 Grupo de Bioquímica, Biofísica y Biología Computacional (BIFI, UNIZAR), Unidad Asociada al CSIC, Zaragoza, Spain
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