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Choi SS, Seo SY, Park SO, Lee HN, Song JS, Kim JY, Park JH, Kim S, Lee SJ, Chun GT, Kim ES. Cell Factory Design and Culture Process Optimization for Dehydroshikimate Biosynthesis in Escherichia coli. Front Bioeng Biotechnol 2019; 7:241. [PMID: 31649923 PMCID: PMC6795058 DOI: 10.3389/fbioe.2019.00241] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2019] [Accepted: 09/11/2019] [Indexed: 11/13/2022] Open
Abstract
3-Dehydroshikimate (DHS) is a useful starting metabolite for the biosynthesis of muconic acid (MA) and shikimic acid (SA), which are precursors of various valuable polymers and drugs. Although DHS biosynthesis has been previously reported in several bacteria, the engineered strains were far from satisfactory, due to their low DHS titers. Here, we created an engineered Escherichia coli cell factory to produce a high titer of DHS as well as an efficient system for the conversion DHS into MA. First, the genes showing negative effects on DHS accumulation in E. coli, such as tyrR (tyrosine dependent transcriptional regulator), ptsG (glucose specific sugar: phosphoenolpyruvate phosphotransferase), and pykA (pyruvate kinase 2), were disrupted. In addition, the genes involved in DHS biosynthesis, such as aroB (DHQ synthase), aroD (DHQ dehydratase), ppsA (phosphoenolpyruvate synthase), galP (D-galactose transporter), aroG (DAHP synthase), and aroF (DAHP synthase), were overexpressed to increase the glucose uptake and flux of intermediates. The redesigned DHS-overproducing E. coli strain grown in an optimized medium produced ~117 g/L DHS in 7-L fed-batch fermentation, which is the highest level of DHS production demonstrated in E. coli. To accomplish the DHS-to-MA conversion, which is originally absent in E. coli, a codon-optimized heterologous gene cassette containing asbF, aroY, and catA was expressed as a single operon under a strong promoter in a DHS-overproducing E. coli strain. This redesigned E. coli grown in an optimized medium produced about 64.5 g/L MA in 7-L fed-batch fermentation, suggesting that the rational cell factory design of DHS and MA biosynthesis could be a feasible way to complement petrochemical-based chemical processes.
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Affiliation(s)
- Si-Sun Choi
- Department of Biological Engineering, Inha University, Incheon, South Korea
| | - Seung-Yeul Seo
- STR Biotech Co., Ltd., Chuncheon-si, South Korea.,Department of Molecular Bio-Science, Kangwon National University, Chuncheon-si, South Korea
| | - Sun-Ok Park
- STR Biotech Co., Ltd., Chuncheon-si, South Korea
| | - Han-Na Lee
- Department of Biological Engineering, Inha University, Incheon, South Korea.,STR Biotech Co., Ltd., Chuncheon-si, South Korea
| | - Ji-Soo Song
- Department of Biological Engineering, Inha University, Incheon, South Korea
| | - Ji-Yeon Kim
- Department of Biological Engineering, Inha University, Incheon, South Korea
| | - Ji-Hoon Park
- Department of Biological Engineering, Inha University, Incheon, South Korea
| | - Sangyong Kim
- Green Chemistry and Materials Group, Korea Institute of Industrial Technology, Cheonan-si, South Korea.,Green Process and System Engineering Major, Korea University of Science and Technology (UST), Daejeon, South Korea
| | | | - Gie-Taek Chun
- Department of Molecular Bio-Science, Kangwon National University, Chuncheon-si, South Korea
| | - Eung-Soo Kim
- Department of Biological Engineering, Inha University, Incheon, South Korea
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52
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Kildegaard KR, Tramontin LRR, Chekina K, Li M, Goedecke TJ, Kristensen M, Borodina I. CRISPR/Cas9-RNA interference system for combinatorial metabolic engineering of Saccharomyces cerevisiae. Yeast 2019; 36:237-247. [PMID: 30953378 PMCID: PMC6619288 DOI: 10.1002/yea.3390] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2018] [Revised: 03/08/2019] [Accepted: 03/28/2019] [Indexed: 12/11/2022] Open
Abstract
The yeast Saccharomyces cerevisiae is widely used in industrial biotechnology for the production of fuels, chemicals, food ingredients, food and beverages, and pharmaceuticals. To obtain high-performing strains for such bioprocesses, it is often necessary to test tens or even hundreds of metabolic engineering targets, preferably in combinations, to account for synergistic and antagonistic effects. Here, we present a method that allows simultaneous perturbation of multiple selected genetic targets by combining the advantage of CRISPR/Cas9, in vivo recombination, USER assembly and RNA interference. CRISPR/Cas9 introduces a double-strand break in a specific genomic region, where multiexpression constructs combined with the knockdown constructs are simultaneously integrated by homologous recombination. We show the applicability of the method by improving cis,cis-muconic acid production in S. cerevisiae through simultaneous manipulation of several metabolic engineering targets. The method can accelerate metabolic engineering efforts for the construction of future cell factories.
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Affiliation(s)
| | | | - Ksenia Chekina
- The Novo Nordisk Foundation Center for BiosustainabilityTechnical University of DenmarkKongens LyngbyDenmark
| | - Mingji Li
- The Novo Nordisk Foundation Center for BiosustainabilityTechnical University of DenmarkKongens LyngbyDenmark
| | - Tobias Justus Goedecke
- The Novo Nordisk Foundation Center for BiosustainabilityTechnical University of DenmarkKongens LyngbyDenmark
| | - Mette Kristensen
- The Novo Nordisk Foundation Center for BiosustainabilityTechnical University of DenmarkKongens LyngbyDenmark
| | - Irina Borodina
- The Novo Nordisk Foundation Center for BiosustainabilityTechnical University of DenmarkKongens LyngbyDenmark
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53
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Amin SA, Endalur Gopinarayanan V, Nair NU, Hassoun S. Establishing synthesis pathway-host compatibility via enzyme solubility. Biotechnol Bioeng 2019; 116:1405-1416. [PMID: 30802311 DOI: 10.1002/bit.26959] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Revised: 12/18/2018] [Accepted: 02/21/2019] [Indexed: 12/12/2022]
Abstract
Current pathway synthesis tools identify possible pathways that can be added to a host to produce the desired target molecule through the exploration of abstract metabolic and reaction network space. However, not many of these tools explore gene-level information required to physically realize the identified synthesis pathways, and none explore enzyme-host compatibility. Developing tools that address this disconnect between abstract reactions/metabolic design space and physical genetic sequence design space will enable expedited experimental efforts that avoid exploring unprofitable synthesis pathways. This work describes a workflow, termed Probabilistic Pathway Assembly with Solubility Confidence Scores (ProPASS), which links synthesis pathway construction with the exploration of the physical design space as imposed by the availability of enzymes with predicted characterized activities within the host. Predicted protein solubility propensity scores are used as a confidence level to quantify the compatibility of each pathway enzyme with the host Escherichia coli (E. coli). This study also presents a database, termed Protein Solubility Database (ProSol DB), which provides solubility confidence scores in E. coli for 240,016 characterized enzymes obtained from UniProtKB/Swiss-Prot. The utility of ProPASS is demonstrated by generating genetic implementations of heterologous synthesis pathways in E. coli that target several commercially useful biomolecules.
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Affiliation(s)
- Sara A Amin
- Department of Computer Science, Tufts University, Medford, Massachusetts
| | | | - Nikhil U Nair
- Department of Chemical and Biological Engineering, Tufts University, Medford, Massachusetts
| | - Soha Hassoun
- Department of Computer Science, Tufts University, Medford, Massachusetts.,Department of Chemical and Biological Engineering, Tufts University, Medford, Massachusetts
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54
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Huccetogullari D, Luo ZW, Lee SY. Metabolic engineering of microorganisms for production of aromatic compounds. Microb Cell Fact 2019; 18:41. [PMID: 30808357 PMCID: PMC6390333 DOI: 10.1186/s12934-019-1090-4] [Citation(s) in RCA: 111] [Impact Index Per Article: 22.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 02/19/2019] [Indexed: 01/09/2023] Open
Abstract
Metabolic engineering has been enabling development of high performance microbial strains for the efficient production of natural and non-natural compounds from renewable non-food biomass. Even though microbial production of various chemicals has successfully been conducted and commercialized, there are still numerous chemicals and materials that await their efficient bio-based production. Aromatic chemicals, which are typically derived from benzene, toluene and xylene in petroleum industry, have been used in large amounts in various industries. Over the last three decades, many metabolically engineered microorganisms have been developed for the bio-based production of aromatic chemicals, many of which are derived from aromatic amino acid pathways. This review highlights the latest metabolic engineering strategies and tools applied to the biosynthesis of aromatic chemicals, many derived from shikimate and aromatic amino acids, including L-phenylalanine, L-tyrosine and L-tryptophan. It is expected that more and more engineered microorganisms capable of efficiently producing aromatic chemicals will be developed toward their industrial-scale production from renewable biomass.
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Affiliation(s)
- Damla Huccetogullari
- Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering (BK21 Plus Program) and Institute for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
- Systems Metabolic Engineering and Systems Healthcare Cross-Generation Collaborative Laboratory, KAIST, Daejeon, 34141, Republic of Korea
| | - Zi Wei Luo
- Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering (BK21 Plus Program) and Institute for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
- Systems Metabolic Engineering and Systems Healthcare Cross-Generation Collaborative Laboratory, KAIST, Daejeon, 34141, Republic of Korea
| | - Sang Yup Lee
- Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering (BK21 Plus Program) and Institute for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea.
- Systems Metabolic Engineering and Systems Healthcare Cross-Generation Collaborative Laboratory, KAIST, Daejeon, 34141, Republic of Korea.
- BioProcess Engineering Research Center and Bioinformatics Research Center, KAIST, Daejeon, 34141, Republic of Korea.
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55
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Saccharoquinoline, a Cytotoxic Alkaloidal Meroterpenoid from Marine-Derived Bacterium Saccharomonospora sp. Mar Drugs 2019; 17:md17020098. [PMID: 30717397 PMCID: PMC6410326 DOI: 10.3390/md17020098] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2018] [Revised: 01/25/2019] [Accepted: 01/29/2019] [Indexed: 12/17/2022] Open
Abstract
A cytotoxic alkaloidal meroterpenoid, saccharoquinoline (1), has been isolated from the fermentation broth of the marine-derived bacterium Saccharomonospora sp. CNQ-490. The planar structure of 1 was elucidated by 1D, 2D NMR, and MS spectroscopic data analyzes, while the relative configuration of 1 was defined through the interpretation of NOE spectroscopic data. Saccharoquinoline (1) is composed of a drimane-type sesquiterpene unit in combination with an apparent 6,7,8-trihydroxyquinoline-2-carboxylic acid. This combination of biosynthetic pathways was observed for the first time in natural microbial products. Saccharoquinoline (1) was found to have cytotoxicity against the HCT-116 cancer cell line by inducing G1 arrest, which leads to cell growth inhibition.
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56
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Gottardi M, Grün P, Bode HB, Hoffmann T, Schwab W, Oreb M, Boles E. Optimisation of trans-cinnamic acid and hydrocinnamyl alcohol production with recombinant Saccharomyces cerevisiae and identification of cinnamyl methyl ketone as a by-product. FEMS Yeast Res 2019; 17:4654848. [PMID: 29186481 DOI: 10.1093/femsyr/fox091] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Accepted: 11/22/2017] [Indexed: 01/08/2023] Open
Abstract
Trans-cinnamic acid (tCA) and hydrocinnamyl alcohol (HcinOH) are valuable aromatic compounds with applications in the flavour, fragrance and cosmetic industry. They can be produced with recombinant yeasts from sugars via phenylalanine after expression of a phenylalanine ammonia lyase (PAL) and an aryl carboxylic acid reductase. Here, we show that in Saccharomyces cerevisiae a PAL enzyme from the bacterium Photorhabdus luminescens was superior to a previously used plant PAL enzyme for the production of tCA. Moreover, after expression of a UDP-glucose:cinnamate glucosyltransferase (FaGT2) from Fragaria x ananassa, tCA could be converted to cinnamoyl-D-glucose which is expected to be less toxic to the yeast cells. Production of tCA and HcinOH from glucose could be increased by eliminating feedback-regulated steps of aromatic amino acid biosynthesis and diminishing the decarboxylation step of the competing Ehrlich pathway. Finally, an unknown by-product resulting from further metabolisation of a carboligation product of cinnamaldehyde (cinALD) with activated acetaldehyde, mediated by pyruvate decarboxylases, could be identified as cinnamyl methyl ketone providing a new route for the biosynthesis of precursors, such as (2S,3R) 5-phenylpent-4-ene-2,3-diol, necessary for the chemical synthesis of specific biologically active drugs such as daunomycin.
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Affiliation(s)
- Manuela Gottardi
- Institute of Molecular Biosciences, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
| | - Peter Grün
- Merck-Stiftungsprofessur für Molekulare Biotechnologie, Fachbereich Biowissenschaften, Goethe Universität Frankfurt, 60438 Frankfurt am Main, Germany
| | - Helge B Bode
- Merck-Stiftungsprofessur für Molekulare Biotechnologie, Fachbereich Biowissenschaften, Goethe Universität Frankfurt, 60438 Frankfurt am Main, Germany.,Buchmann Institute for Molecular Life Sciences (BMLS), Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
| | - Thomas Hoffmann
- Biotechnology of Natural Products, Technische Universität München, 85354 Freising, Germany
| | - Wilfried Schwab
- Biotechnology of Natural Products, Technische Universität München, 85354 Freising, Germany
| | - Mislav Oreb
- Institute of Molecular Biosciences, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
| | - Eckhard Boles
- Institute of Molecular Biosciences, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
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57
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Anthony WE, Carr RR, DeLorenzo DM, Campbell TP, Shang Z, Foston M, Moon TS, Dantas G. Development of Rhodococcus opacus as a chassis for lignin valorization and bioproduction of high-value compounds. BIOTECHNOLOGY FOR BIOFUELS 2019; 12:192. [PMID: 31404385 PMCID: PMC6683499 DOI: 10.1186/s13068-019-1535-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Accepted: 07/24/2019] [Indexed: 05/09/2023]
Abstract
The current extraction and use of fossil fuels has been linked to extensive negative health and environmental outcomes. Lignocellulosic biomass-derived biofuels and bioproducts are being actively considered as renewable alternatives to the fuels, chemicals, and materials produced from fossil fuels. A major challenge limiting large-scale, economic deployment of second-generation biorefineries is the insufficient product yield, diversity, and value that current conversion technologies can extract from lignocellulose, in particular from the underutilized lignin fraction. Rhodococcus opacus PD630 is an oleaginous gram-positive bacterium with innate catabolic pathways and tolerance mechanisms for the inhibitory aromatic compounds found in depolymerized lignin, as well as native or engineered pathways for hexose and pentose sugars found in the carbohydrate fractions of biomass. As a result, R. opacus holds potential as a biological chassis for the conversion of lignocellulosic biomass into biodiesel precursors and other value-added products. This review begins by examining the important role that lignin utilization will play in the future of biorefineries and by providing a concise survey of the current lignin conversion technologies. The genetic machinery and capabilities of R. opacus that allow the bacterium to tolerate and metabolize aromatic compounds and depolymerized lignin are also discussed, along with a synopsis of the genetic toolbox and synthetic biology methods now available for engineering this organism. Finally, we summarize the different feedstocks that R. opacus has been demonstrated to consume, and the high-value products that it has been shown to produce. Engineered R. opacus will enable lignin valorization over the coming years, leading to cost-effective conversion of lignocellulose into fuels, chemicals, and materials.
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Affiliation(s)
- Winston E. Anthony
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University in St. Louis School of Medicine, St. Louis, MO 63110 USA
| | - Rhiannon R. Carr
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, St. Louis, MO 63130 USA
| | - Drew M. DeLorenzo
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, St. Louis, MO 63130 USA
| | - Tayte P. Campbell
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University in St. Louis School of Medicine, St. Louis, MO 63110 USA
| | - Zeyu Shang
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, St. Louis, MO 63130 USA
| | - Marcus Foston
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, St. Louis, MO 63130 USA
| | - Tae Seok Moon
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, St. Louis, MO 63130 USA
| | - Gautam Dantas
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University in St. Louis School of Medicine, St. Louis, MO 63110 USA
- Department of Pathology and Immunology, Washington University in St. Louis School of Medicine, St. Louis, MO 63108 USA
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, MO 63130 USA
- Department of Molecular Microbiology, Washington University in St. Louis School of Medicine, St. Louis, MO 63108 USA
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58
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Corynebacterium Cell Factory Design and Culture Process Optimization for Muconic Acid Biosynthesis. Sci Rep 2018; 8:18041. [PMID: 30575781 PMCID: PMC6303301 DOI: 10.1038/s41598-018-36320-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Accepted: 11/13/2018] [Indexed: 12/03/2022] Open
Abstract
Muconic acid (MA) is a valuable compound for adipic acid production, which is a precursor for the synthesis of various polymers such as plastics, coatings, and nylons. Although MA biosynthesis has been previously reported in several bacteria, the engineered strains were not satisfactory owing to low MA titers. Here, we generated an engineered Corynebacterium cell factory to produce a high titer of MA through 3-dehydroshikimate (DHS) conversion to MA, with heterologous expression of foreign protocatechuate (PCA) decarboxylase genes. To accumulate key intermediates in the MA biosynthetic pathway, aroE (shikimate dehydrogenase gene), pcaG/H (PCA dioxygenase alpha/beta subunit genes) and catB (chloromuconate cycloisomerase gene) were disrupted. To accomplish the conversion of PCA to catechol (CA), a step that is absent in Corynebacterium, a codon-optimized heterologous PCA decarboxylase gene was expressed as a single operon under the strong promoter in a aroE-pcaG/H-catB triple knock-out Corynebacterium strain. This redesigned Corynebacterium, grown in an optimized medium, produced about 38 g/L MA and 54 g/L MA in 7-L and 50-L fed-batch fermentations, respectively. These results show highest levels of MA production demonstrated in Corynebacterium, suggesting that the rational cell factory design of MA biosynthesis could be an alternative way to complement petrochemical-based chemical processes.
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59
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Skoog E, Shin JH, Saez-Jimenez V, Mapelli V, Olsson L. Biobased adipic acid – The challenge of developing the production host. Biotechnol Adv 2018; 36:2248-2263. [DOI: 10.1016/j.biotechadv.2018.10.012] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Revised: 10/18/2018] [Accepted: 10/27/2018] [Indexed: 11/28/2022]
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Wang S, Fu C, Bilal M, Hu H, Wang W, Zhang X. Enhanced biosynthesis of arbutin by engineering shikimate pathway in Pseudomonas chlororaphis P3. Microb Cell Fact 2018; 17:174. [PMID: 30414616 PMCID: PMC6230248 DOI: 10.1186/s12934-018-1022-8] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Accepted: 11/03/2018] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Arbutin is a plant-derived glycoside with potential antioxidant, antibacterial and anti-inflammatory activities. Currently, it is mainly produced by plant extraction or enzymatic processes, which suffers from expensive processing cost and low product yield. Metabolic engineering of microbes is an increasingly powerful method for the high-level production of valuable biologicals. Since Pseudomonas chlororaphis has been widely engineered as a phenazine-producing platform organism due to its well-characterized genetics and physiology, and faster growth rate using glycerol as a renewable carbon source, it can also be engineered as the cell factory using strong shikimate pathway on the basis of synthetic biology. RESULTS In this work, a plasmid-free biosynthetic pathway was constructed in P. chlororaphis P3 for elevated biosynthesis of arbutin from sustainable carbon sources. The arbutin biosynthetic pathway was expressed under the native promoter Pphz using chromosomal integration. Instead of being plasmid and inducer dependent, the metabolic engineering approach used to fine-tune the biosynthetic pathway significantly enhanced the arbutin production with a 22.4-fold increase. On the basis of medium factor optimization and mixed fed-batch fermentation of glucose and 4-hydroxybenzoic acid, the engineered P. chlororaphis P3-Ar5 strain led to the highest arbutin production of 6.79 g/L with the productivity of 0.094 g/L/h, with a 54-fold improvement over the initial strain. CONCLUSIONS The results suggested that the construction of plasmid-free synthetic pathway displays a high potential for improved biosynthesis of arbutin and other shikimate pathway derived biologicals in P. chlororaphis.
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Affiliation(s)
- Songwei Wang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Cong Fu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Muhammad Bilal
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Hongbo Hu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China.,National Experimental, Teaching Center for Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Wei Wang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Xuehong Zhang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China.
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61
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Luo ZW, Kim WJ, Lee SY. Metabolic Engineering of Escherichia coli for Efficient Production of 2-Pyrone-4,6-dicarboxylic Acid from Glucose. ACS Synth Biol 2018; 7:2296-2307. [PMID: 30096230 DOI: 10.1021/acssynbio.8b00281] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
2-Pyrone-4,6-dicarboxylic acid (PDC) is a pseudoaromatic dicarboxylic acid and is a promising biobased building block chemical that can be used to make diverse polyesters with novel functionalities. In this study, Escherichia coli was metabolically engineered to produce PDC from glucose. First, an efficient biosynthetic pathway for PDC production from glucose was suggested by in silico metabolic flux simulation. This best pathway employs a single-step biosynthetic route to protocatechuic acid (PCA), a metabolic precursor for PDC biosynthesis. On the basis of the selected PDC biosynthetic pathway, a shikimate dehydrogenase (encoded by aroE)-deficient E. coli strain was engineered by introducing heterologous genes of different microbial origin encoding enzymes responsible for converting 3-dehydroshikimate (DHS) to PDC, which allowed de novo biosynthesis of PDC from glucose. Next, production of PDC was further improved by applying stepwise rational metabolic engineering strategies. These include elimination of feedback inhibition on 3-deoxy-d-arabino-heptulosonate-7-phosphate synthase (encoded by aroG) by overexpressing a feedback-resistant variant, enhancement of the precursor phosphoenolpyruvate supply by changing the native promoter of the ppsA gene with the strong trc promoter, and reducing accumulation of the major byproduct DHS by overexpression of a DHS importer (encoded by shiA). Furthermore, cofactor (NADP+/NADPH) utilization was manipulated through genetic modifications of the E. coli soluble pyridine nucleotide transhydrogenase (encoded by sthA), and the resultant impact on PDC production was investigated. Fed-batch fermentation of the final engineered E. coli strain allowed production of 16.72 g/L of PDC from glucose with the yield and productivity of 0.201 g/g and 0.172 g/L/h, respectively, representing the highest PDC production performance indices reported to date.
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Affiliation(s)
- Zi Wei Luo
- Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering (BK21 Plus Program), Institute for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
- Systems Metabolic Engineering and Systems Healthcare Cross-Generation Collaborative Laboratory, KAIST, Daejeon 34141, Republic of Korea
| | - Won Jun Kim
- Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering (BK21 Plus Program), Institute for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
- Systems Metabolic Engineering and Systems Healthcare Cross-Generation Collaborative Laboratory, KAIST, Daejeon 34141, Republic of Korea
| | - Sang Yup Lee
- Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering (BK21 Plus Program), Institute for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
- Systems Metabolic Engineering and Systems Healthcare Cross-Generation Collaborative Laboratory, KAIST, Daejeon 34141, Republic of Korea
- BioProcess Engineering Research Center and BioInformatics Research Center, KAIST, Daejeon 34141, Republic of Korea
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62
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Pyne ME, Narcross L, Melgar M, Kevvai K, Mookerjee S, Leite GB, Martin VJJ. An Engineered Aro1 Protein Degradation Approach for Increased cis,cis-Muconic Acid Biosynthesis in Saccharomyces cerevisiae. Appl Environ Microbiol 2018; 84:e01095-18. [PMID: 29934332 PMCID: PMC6102976 DOI: 10.1128/aem.01095-18] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Accepted: 06/16/2018] [Indexed: 12/11/2022] Open
Abstract
Muconic acid (MA) is a chemical building block and precursor to adipic and terephthalic acids used in the production of nylon and polyethylene terephthalate polymer families. Global demand for these important materials, coupled to their dependence on petrochemical resources, provides substantial motivation for the microbial synthesis of MA and its derivatives. In this context, the Saccharomyces cerevisiae yeast shikimate pathway can be sourced as a precursor for the formation of MA. Here we report a novel strategy to balance MA pathway performance with aromatic amino acid prototrophy by destabilizing Aro1 through C-terminal degron tagging. Coupling of a composite MA production pathway to degron-tagged Aro1 in an aro3Δ aro4Δ mutant background led to the accumulation of 5.6 g/liter protocatechuic acid (PCA). However, metabolites downstream of PCA were not detected, despite the inclusion of genes mediating their biosynthesis. Because CEN.PK family strains of S. cerevisiae lack the activity of Pad1, a key enzyme supporting PCA decarboxylase activity, chromosomal expression of intact PAD1 alleviated this bottleneck, resulting in nearly stoichiometric conversion (95%) of PCA to downstream products. In a fed-batch bioreactor, the resulting strain produced 1.2 g/liter MA under prototrophic conditions and 5.1 g/liter MA when supplemented with amino acids, corresponding to a yield of 58 mg/g sugar.IMPORTANCE Previous efforts to engineer a heterologous MA pathway in Saccharomyces cerevisiae have been hindered by a bottleneck at the PCA decarboxylation step and the creation of aromatic amino acid auxotrophy through deleterious manipulation of the pentafunctional Aro1 protein. In light of these studies, this work was undertaken with the central objective of preserving amino acid prototrophy, which we achieved by employing an Aro1 degradation strategy. Moreover, resolution of the key PCA decarboxylase bottleneck, as detailed herein, advances our understanding of yeast MA biosynthesis and will guide future strain engineering efforts. These strategies resulted in the highest titer reported to date for muconic acid produced in yeast. Overall, our study showcases the effectiveness of careful tuning of yeast Aro1 activity and the importance of host-pathway dynamics.
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Affiliation(s)
- Michael E Pyne
- Department of Biology, Concordia University, Montréal, Québec, Canada
- Centre for Applied Synthetic Biology, Concordia University, Montréal, Québec, Canada
| | - Lauren Narcross
- Department of Biology, Concordia University, Montréal, Québec, Canada
- Centre for Applied Synthetic Biology, Concordia University, Montréal, Québec, Canada
| | - Mindy Melgar
- Department of Biology, Concordia University, Montréal, Québec, Canada
- Centre for Applied Synthetic Biology, Concordia University, Montréal, Québec, Canada
| | - Kaspar Kevvai
- Department of Biology, Concordia University, Montréal, Québec, Canada
- Centre for Applied Synthetic Biology, Concordia University, Montréal, Québec, Canada
| | - Shoham Mookerjee
- Department of Biology, Concordia University, Montréal, Québec, Canada
- Centre for Applied Synthetic Biology, Concordia University, Montréal, Québec, Canada
| | - Gustavo B Leite
- Department of Biology, Concordia University, Montréal, Québec, Canada
- Centre for Applied Synthetic Biology, Concordia University, Montréal, Québec, Canada
| | - Vincent J J Martin
- Department of Biology, Concordia University, Montréal, Québec, Canada
- Centre for Applied Synthetic Biology, Concordia University, Montréal, Québec, Canada
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63
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Recent advances in metabolic engineering of Corynebacterium glutamicum for bioproduction of value-added aromatic chemicals and natural products. Appl Microbiol Biotechnol 2018; 102:8685-8705. [DOI: 10.1007/s00253-018-9289-6] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Revised: 07/30/2018] [Accepted: 07/31/2018] [Indexed: 02/06/2023]
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64
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Shih PM. Towards a sustainable bio-based economy: Redirecting primary metabolism to new products with plant synthetic biology. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2018; 273:84-91. [PMID: 29907312 PMCID: PMC6005202 DOI: 10.1016/j.plantsci.2018.03.012] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Revised: 02/28/2018] [Accepted: 03/10/2018] [Indexed: 05/23/2023]
Abstract
Humans have domesticated many plant species as indispensable sources of food, materials, and medicines. The dawning era of synthetic biology represents a means to further refine, redesign, and engineer crops to meet various societal and industrial needs. Current and future endeavors will utilize plants as the foundation of a bio-based economy through the photosynthetic production of carbohydrate feedstocks for the microbial fermentation of biofuels and bioproducts, with the end goal of decreasing our dependence on petrochemicals. As our technological capabilities improve, metabolic engineering efforts may expand the utility of plants beyond sugar feedstocks through the direct production of target compounds, including pharmaceuticals, renewable fuels, and commodity chemicals. However, relatively little work has been done to fully realize the potential in redirecting central carbon metabolism in plants for the engineering of novel bioproducts. Although our ability to rationally engineer and manipulate plant metabolism is in its infancy, I highlight some of the opportunities and challenges in applying synthetic biology towards engineering plant primary metabolism.
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Affiliation(s)
- Patrick M Shih
- Joint BioEnergy Institute, 5885 Hollis St, Emeryville, CA, 94608, United States; Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, One Cyclotron Rd, Berkeley, CA, 94720, United States; Department of Chemical Engineering, Stanford University, Stanford, CA, 94305, United States.
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65
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Kallscheuer N, Marienhagen J. Corynebacterium glutamicum as platform for the production of hydroxybenzoic acids. Microb Cell Fact 2018; 17:70. [PMID: 29753327 PMCID: PMC5948850 DOI: 10.1186/s12934-018-0923-x] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Accepted: 05/05/2018] [Indexed: 11/10/2022] Open
Abstract
Background Hydroxybenzoic acids are industrially relevant aromatic compounds, which also play key roles in the microbial carbon metabolism, e.g., as precursors for the synthesis of cofactors or metal-chelating molecules. Due to its pronounced resistance to aromatics Corynebacterium glutamicum represents an interesting platform for production of these compounds. Unfortunately, a complex catabolic network for aromatic molecules prevents application of C. glutamicum for microbial production of aromatic compounds other than aromatic amino acids, which cannot be metabolized by this microorganism. Results We completed the construction of the platform strain C. glutamicum DelAro5, in which the deletion of altogether 27 genes in five gene clusters abolished most of the peripheral and central catabolic pathways for aromatic compounds known in this microorganism. The obtained strain was subsequently applied for the production of 2-hydroxybenzoate (salicylate), 3-hydroxybenzoate, 4-hydroxybenzoate and protocatechuate, which all derive from intermediates of the aromatic amino acid-forming shikimate pathway. For an optimal connection of the designed hydroxybenzoate production pathways to the host metabolism, C. glutamicum was additionally engineered towards increased supply of the shikimate pathway substrates erythrose-4-phosphate and phosphoenolpyruvate by manipulation of the glucose transport and key enzymatic activities of the central carbon metabolism. With an optimized genetic background the constructed strains produced 0.01 g/L (0.07 mM) 2-hydroxybenzoate, 0.3 g/L (2.2 mM) 3-hydroxybenzoate, 2.0 g/L (13.0 mM) protocatechuate and 3.3 g/L (23.9 mM) 4-hydroxybenzoate in shaking flasks. Conclusion By abolishing its natural catabolic network for aromatic compounds, C. glutamicum was turned into a versatile microbial platform for aromatics production, which could be exemplarily demonstrated by rapidly engineering this platform organism towards producing four biotechnologically interesting hydroxybenzoates. Production of these compounds was optimized following different metabolic engineering strategies leading to increased precursor availability. The constructed C. glutamicum strains are promising hosts for the production of hydroxybenzoates and other aromatic compounds at larger scales. Electronic supplementary material The online version of this article (10.1186/s12934-018-0923-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Nicolai Kallscheuer
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany.,Bioeconomy Science Center (BioSC), Forschungszentrum Jülich GmbH, 52425, Jülich, Germany
| | - Jan Marienhagen
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany. .,Bioeconomy Science Center (BioSC), Forschungszentrum Jülich GmbH, 52425, Jülich, Germany.
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66
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Zhao M, Huang D, Zhang X, Koffas MA, Zhou J, Deng Y. Metabolic engineering of Escherichia coli for producing adipic acid through the reverse adipate-degradation pathway. Metab Eng 2018; 47:254-262. [DOI: 10.1016/j.ymben.2018.04.002] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Revised: 03/19/2018] [Accepted: 04/01/2018] [Indexed: 12/25/2022]
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67
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Hanson PK. Saccharomyces cerevisiae: A Unicellular Model Genetic Organism of Enduring Importance. ACTA ACUST UNITED AC 2018. [DOI: 10.1002/cpet.21] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Pamela K. Hanson
- Department of Biology, Birmingham-Southern College; Birmingham Alabama
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68
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Snoek T, Romero-Suarez D, Zhang J, Ambri F, Skjoedt ML, Sudarsan S, Jensen MK, Keasling JD. An Orthogonal and pH-Tunable Sensor-Selector for Muconic Acid Biosynthesis in Yeast. ACS Synth Biol 2018; 7:995-1003. [PMID: 29613773 DOI: 10.1021/acssynbio.7b00439] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Microbes offer enormous potential for production of industrially relevant chemicals and therapeutics, yet the rapid identification of high-producing microbes from large genetic libraries is a major bottleneck in modern cell factory development. Here, we develop and apply a synthetic selection system in Saccharomyces cerevisiae that couples the concentration of muconic acid, a plastic precursor, to cell fitness by using the prokaryotic transcriptional regulator BenM driving an antibiotic resistance gene. We show that the sensor-selector does not affect production nor fitness, and find that tuning pH of the cultivation medium limits the rise of nonproducing cheaters. We apply the sensor-selector to selectively enrich for best-producing variants out of a large library of muconic acid production strains, and identify an isolate that produces more than 2 g/L muconic acid in a bioreactor. We expect that this sensor-selector can aid the development of other synthetic selection systems based on allosteric transcription factors.
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Affiliation(s)
- Tim Snoek
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - David Romero-Suarez
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Jie Zhang
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Francesca Ambri
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Mette L. Skjoedt
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Suresh Sudarsan
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Michael K. Jensen
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Jay D. Keasling
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
- Joint BioEnergy Institute, Emeryville, California 94608, United States
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- Department of Chemical and Biomolecular Engineering & Department of Bioengineering, University of California, Berkeley, California 94720, United States
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69
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Turner TL, Kim H, Kong II, Liu JJ, Zhang GC, Jin YS. Engineering and Evolution of Saccharomyces cerevisiae to Produce Biofuels and Chemicals. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2018; 162:175-215. [PMID: 27913828 DOI: 10.1007/10_2016_22] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
To mitigate global climate change caused partly by the use of fossil fuels, the production of fuels and chemicals from renewable biomass has been attempted. The conversion of various sugars from renewable biomass into biofuels by engineered baker's yeast (Saccharomyces cerevisiae) is one major direction which has grown dramatically in recent years. As well as shifting away from fossil fuels, the production of commodity chemicals by engineered S. cerevisiae has also increased significantly. The traditional approaches of biochemical and metabolic engineering to develop economic bioconversion processes in laboratory and industrial settings have been accelerated by rapid advancements in the areas of yeast genomics, synthetic biology, and systems biology. Together, these innovations have resulted in rapid and efficient manipulation of S. cerevisiae to expand fermentable substrates and diversify value-added products. Here, we discuss recent and major advances in rational (relying on prior experimentally-derived knowledge) and combinatorial (relying on high-throughput screening and genomics) approaches to engineer S. cerevisiae for producing ethanol, butanol, 2,3-butanediol, fatty acid ethyl esters, isoprenoids, organic acids, rare sugars, antioxidants, and sugar alcohols from glucose, xylose, cellobiose, galactose, acetate, alginate, mannitol, arabinose, and lactose.
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Affiliation(s)
- Timothy L Turner
- Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Heejin Kim
- Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - In Iok Kong
- Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Jing-Jing Liu
- Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Guo-Chang Zhang
- Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Yong-Su Jin
- Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA. .,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
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70
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Averesch NJH, Krömer JO. Metabolic Engineering of the Shikimate Pathway for Production of Aromatics and Derived Compounds-Present and Future Strain Construction Strategies. Front Bioeng Biotechnol 2018; 6:32. [PMID: 29632862 PMCID: PMC5879953 DOI: 10.3389/fbioe.2018.00032] [Citation(s) in RCA: 103] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Accepted: 03/12/2018] [Indexed: 11/25/2022] Open
Abstract
The aromatic nature of shikimate pathway intermediates gives rise to a wealth of potential bio-replacements for commonly fossil fuel-derived aromatics, as well as naturally produced secondary metabolites. Through metabolic engineering, the abundance of certain intermediates may be increased, while draining flux from other branches off the pathway. Often targets for genetic engineering lie beyond the shikimate pathway, altering flux deep in central metabolism. This has been extensively used to develop microbial production systems for a variety of compounds valuable in chemical industry, including aromatic and non-aromatic acids like muconic acid, para-hydroxybenzoic acid, and para-coumaric acid, as well as aminobenzoic acids and aromatic α-amino acids. Further, many natural products and secondary metabolites that are valuable in food- and pharma-industry are formed outgoing from shikimate pathway intermediates. (Re)construction of such routes has been shown by de novo production of resveratrol, reticuline, opioids, and vanillin. In this review, strain construction strategies are compared across organisms and put into perspective with requirements by industry for commercial viability. Focus is put on enhancing flux to and through shikimate pathway, and engineering strategies are assessed in order to provide a guideline for future optimizations.
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Affiliation(s)
- Nils J H Averesch
- Universities Space Research Association at NASA Ames Research Center, Moffett Field, CA, United States
| | - Jens O Krömer
- Department of Solar Materials, Helmholtz Centre for Environmental Research, Leipzig, Germany
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71
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Wang S, Bilal M, Hu H, Wang W, Zhang X. 4-Hydroxybenzoic acid-a versatile platform intermediate for value-added compounds. Appl Microbiol Biotechnol 2018. [PMID: 29516141 DOI: 10.1007/s00253-018-8815-x] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
4-Hydroxybenzoic acid (4-HBA) has recently emerged as a promising intermediate for several value-added bioproducts with potential biotechnological applications in food, cosmetics, pharmacy, fungicides, etc. Over the past years, a variety of biosynthetic techniques have been developed for producing the 4-HBA and 4-HBA-based products. At this juncture, synthetic biology and metabolic engineering approaches enabled the biosynthesis of 4-HBA to address the increasing demand for high-value bioproducts. This review summarizes the biosynthesis of a variety of industrially pertinent compounds such as resveratrol, muconic acid, gastrodin, xiamenmycin, and vanillyl alcohol using 4-HBA as the starting feedstock. Moreover, potential research activities with a close-up look at the future perspectives to produce new compounds using 4-HBA have also been discussed.
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Affiliation(s)
- Songwei Wang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Muhammad Bilal
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Hongbo Hu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Wei Wang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Xuehong Zhang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China.
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72
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A protocatechuate biosensor for Pseudomonas putida KT2440 via promoter and protein evolution. Metab Eng Commun 2018; 6:33-38. [PMID: 29765865 PMCID: PMC5949891 DOI: 10.1016/j.meteno.2018.03.001] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Revised: 03/03/2018] [Accepted: 03/03/2018] [Indexed: 11/27/2022] Open
Abstract
Robust fluorescence-based biosensors are emerging as critical tools for high-throughput strain improvement in synthetic biology. Many biosensors are developed in model organisms where sophisticated synthetic biology tools are also well established. However, industrial biochemical production often employs microbes with phenotypes that are advantageous for a target process, and biosensors may fail to directly transition outside the host in which they are developed. In particular, losses in sensitivity and dynamic range of sensing often occur, limiting the application of a biosensor across hosts. Here we demonstrate the optimization of an Escherichia coli-based biosensor in a robust microbial strain for the catabolism of aromatic compounds, Pseudomonas putida KT2440, through a generalizable approach of modulating interactions at the protein-DNA interface in the promoter and the protein-protein dimer interface. The high-throughput biosensor optimization approach demonstrated here is readily applicable towards other allosteric regulators. A biosensor optimized for a robust, industrially useful P. putida strain. Modulation of protein-DNA and protein-protein interactions pursued. Offers a generalized optimization protocol for transcription factor-based sensors. Intracellular metabolite production and detection made possible in P. putida. Functional biosensor in P. putida will allow high throughput strain evolution.
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73
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Saraçi E, Wang L, Theopold KH, Lobo RF. Bioderived Muconates by Cross-Metathesis and Their Conversion into Terephthalates. CHEMSUSCHEM 2018; 11:773-780. [PMID: 29159887 DOI: 10.1002/cssc.201701874] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Revised: 10/23/2017] [Indexed: 06/07/2023]
Abstract
Polyethylene terephthalate that is 100 % bioderived is in high demand in the market guided by the ever-more exigent sustainability regulations with the challenge of producing renewable terephthalic acid remaining. Renewable terephthalic acid or its precursors can be obtained by Diels-Alder cycloaddition and further dehydrogenation of biomass-derived muconic acid. The cis,cis isomer of the dicarboxylic acid is typically synthesized by fermentation with genetically modified microorganisms, a process that requires complex separations to obtain a high yield of the pure product. Furthermore, the cis isomer has to be transformed into the trans,trans form and has to be esterified before it is suitable for terephthalate synthesis. To overcome these challenges, we investigated the synthesis of dialkyl muconates by cross-metathesis. The Ru-catalyzed cross-coupling of sorbates with acrylates, which can be bioderived, proceeded selectively to yield diester muconates in up to 41 % yield by using very low catalyst amounts (0.5-3.0 mol %) and no solvent. In the optimized procedure, the muconate precipitated as a solid and was easily recovered from the reaction medium. Analysis by GC-MS and NMR spectroscopy showed that this method delivered exclusively the trans,trans isomer of dimethyl muconate. The Diels-Alder reaction of dimethyl muconate with ethylene was studied in various solvents to obtain 1,4-bis(carbomethoxy)cyclohexene. The cycloaddition proceeded with very high conversions (77-100 %) and yields (70-98 %) in all of the solvents investigated, and methanol and tetrahydrofuran were the best choices. Next, the aromatization of 1,4-bis(carbomethoxy)cyclohexene to dimethyl terephthalate over a Pd/C catalyst resulted in up to 70 % yield in tetrahydrofuran under an air atmosphere. Owing to the high yield of the reaction of dimethyl muconate to 1,4-bis(carbomethoxy)cyclohexene, no separation step was needed before the aromatization. This is the first time that cross-metathesis is used to produce bioderived trans,trans-muconates as precursors to renewable terephthalates, important building blocks in the polymer industry.
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Affiliation(s)
- Erisa Saraçi
- Catalysis Center for Energy Innovation, U.S. Department of Energy, Energy Frontier Research Center, University of Delaware, 221 Academy St., Newark, DE, 19716, USA
- Department of Chemical and Biomolecular Engineering, University of Delaware, 150 Academy St., Newark, DE, 19716, USA
| | - Lan Wang
- Catalysis Center for Energy Innovation, U.S. Department of Energy, Energy Frontier Research Center, University of Delaware, 221 Academy St., Newark, DE, 19716, USA
- Department of Chemistry and Biochemistry, University of Delaware, 102 Brown Laboratory, Newark, DE, 19716, USA
| | - Klaus H Theopold
- Catalysis Center for Energy Innovation, U.S. Department of Energy, Energy Frontier Research Center, University of Delaware, 221 Academy St., Newark, DE, 19716, USA
- Department of Chemistry and Biochemistry, University of Delaware, 102 Brown Laboratory, Newark, DE, 19716, USA
| | - Raul F Lobo
- Catalysis Center for Energy Innovation, U.S. Department of Energy, Energy Frontier Research Center, University of Delaware, 221 Academy St., Newark, DE, 19716, USA
- Department of Chemical and Biomolecular Engineering, University of Delaware, 150 Academy St., Newark, DE, 19716, USA
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74
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Thompson B, Pugh S, Machas M, Nielsen DR. Muconic Acid Production via Alternative Pathways and a Synthetic "Metabolic Funnel". ACS Synth Biol 2018; 7:565-575. [PMID: 29053259 DOI: 10.1021/acssynbio.7b00331] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Muconic acid is a promising platform biochemical and precursor to adipic acid, which can be used to synthesize various plastics and polymers. In this study, the systematic construction and comparative evaluation of a modular network of non-natural pathways for muconic acid biosynthesis was investigated in Escherichia coli, including via three distinct and novel pathways proceeding via phenol as a common intermediate. However, poor recombinant activity and high promiscuity of phenol hydroxylase ultimately limited "phenol-dependent" muconic acid production. A fourth pathway proceeding via p-hydroxybenzoate, protocatechuate, and catechol was accordingly developed, though with muconic acid titers by this route reaching just 819 mg/L, its performance lagged behind that of the established, "3-dehydroshikimiate-derived" route. Finally, these two most promising pathways were coexpressed in parallel to create a synthetic "metabolic funnel" that, by enabling maximal net precursor assimilation and flux while preserving native chorismate biosynthesis, nearly doubled muconic acid production to up to >3.1 g/L at a glucose yield of 158 mg/g while introducing only a single auxotrophy. This generalizable, "funneling" strategy is expected to have broad applications in metabolic engineering for further enhancing production of muconic acid, as well as other important bioproducts of interest.
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Affiliation(s)
- Brian Thompson
- Chemical Engineering, School for Engineering
of Matter, Transport, and Energy, Arizona State University, Tempe, Arizona 85287, United States
| | - Shawn Pugh
- Chemical Engineering, School for Engineering
of Matter, Transport, and Energy, Arizona State University, Tempe, Arizona 85287, United States
| | - Michael Machas
- Chemical Engineering, School for Engineering
of Matter, Transport, and Energy, Arizona State University, Tempe, Arizona 85287, United States
| | - David R. Nielsen
- Chemical Engineering, School for Engineering
of Matter, Transport, and Energy, Arizona State University, Tempe, Arizona 85287, United States
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75
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Averesch NJH, Martínez VS, Nielsen LK, Krömer JO. Toward Synthetic Biology Strategies for Adipic Acid Production: An in Silico Tool for Combined Thermodynamics and Stoichiometric Analysis of Metabolic Networks. ACS Synth Biol 2018; 7:490-509. [PMID: 29237121 DOI: 10.1021/acssynbio.7b00304] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Adipic acid, a nylon-6,6 precursor, has recently gained popularity in synthetic biology. Here, 16 different production routes to adipic acid were evaluated using a novel tool for network-embedded thermodynamic analysis of elementary flux modes. The tool distinguishes between thermodynamically feasible and infeasible modes under determined metabolite concentrations, allowing the thermodynamic feasibility of theoretical yields to be assessed. Further, patterns that always caused infeasible flux distributions were identified, which will aid the development of tailored strain design. A review of cellular efflux mechanisms revealed that significant accumulation of extracellular product is only possible if coupled with ATP hydrolysis. A stoichiometric analysis demonstrated that the maximum theoretical product carbon yield heavily depends on the metabolic route, ranging from 32 to 99% on glucose and/or palmitate in Escherichia coli and Saccharomyces cerevisiae metabolic models. Equally important, metabolite concentrations appeared to be thermodynamically restricted in several pathways. Consequently, the number of thermodynamically feasible flux distributions was reduced, in some cases even rendering whole pathways infeasible, highlighting the importance of pathway choice. Only routes based on the shikimate pathway were thermodynamically favorable over a large concentration and pH range. The low pH capability of S. cerevisiae shifted the thermodynamic equilibrium of some pathways toward product formation. One identified infeasible-pattern revealed that the reversibility of the mitochondrial malate dehydrogenase contradicted the current state of knowledge, which imposes a major restriction on the metabolism of S. cerevisiae. Finally, the evaluation of industrially relevant constraints revealed that two shikimate pathway-based routes in E. coli were the most robust.
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Affiliation(s)
- Nils J. H. Averesch
- Centre
for Microbial Electrochemical Systems (CEMES), Advanced Water Management
Centre (AWMC), The University of Queensland, Brisbane 4072, Australia
- Universities Space Research Association at NASA Ames Research Center, Moffett Field, California 94035, United States
| | - Verónica S. Martínez
- Systems
and Synthetic Biology Group, Australian Institute for Bioengineering
and Nanotechnology (AIBN), The University of Queensland, Brisbane 4072, Australia
- ARC
Training Centre for Biopharmaceutical Innovation (CBI), Australian
Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane 4072, Australia
| | - Lars K. Nielsen
- Systems
and Synthetic Biology Group, Australian Institute for Bioengineering
and Nanotechnology (AIBN), The University of Queensland, Brisbane 4072, Australia
- DTU
BIOSUSTAIN, Novo Nordisk Foundation Center for Biosustainability, Danmarks Tekniske Universitet, Kemitorvet, 2800 Kongens Lyngby, Denmark
| | - Jens O. Krömer
- Centre
for Microbial Electrochemical Systems (CEMES), Advanced Water Management
Centre (AWMC), The University of Queensland, Brisbane 4072, Australia
- Department
for Solar Materials, Helmholtz Centre of Environmental Research−UFZ, 04318 Leipzig, Germany
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76
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Brückner C, Oreb M, Kunze G, Boles E, Tripp J. An expanded enzyme toolbox for production of cis, cis-muconic acid and other shikimate pathway derivatives in Saccharomyces cerevisiae. FEMS Yeast Res 2018; 18:4862472. [DOI: 10.1093/femsyr/foy017] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Accepted: 02/14/2018] [Indexed: 11/14/2022] Open
Affiliation(s)
- Christine Brückner
- Institute of Molecular Biosciences, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
| | - Mislav Oreb
- Institute of Molecular Biosciences, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
| | - Gotthard Kunze
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstraße 3, 06466 Gatersleben, Germany
| | - Eckhard Boles
- Institute of Molecular Biosciences, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
| | - Joanna Tripp
- Institute of Molecular Biosciences, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
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77
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The UbiX-UbiD system: The biosynthesis and use of prenylated flavin (prFMN). Arch Biochem Biophys 2017; 632:209-221. [DOI: 10.1016/j.abb.2017.07.014] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Revised: 07/19/2017] [Accepted: 07/24/2017] [Indexed: 12/17/2022]
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78
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Biotechnological production of aromatic compounds of the extended shikimate pathway from renewable biomass. J Biotechnol 2017; 257:211-221. [DOI: 10.1016/j.jbiotec.2016.11.016] [Citation(s) in RCA: 75] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Revised: 11/17/2016] [Accepted: 11/17/2016] [Indexed: 01/17/2023]
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79
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Leavitt JM, Wagner JM, Tu CC, Tong A, Liu Y, Alper HS. Biosensor-Enabled Directed Evolution to Improve Muconic Acid Production in Saccharomyces cerevisiae. Biotechnol J 2017; 12. [PMID: 28296355 DOI: 10.1002/biot.201600687] [Citation(s) in RCA: 82] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Revised: 01/28/2017] [Indexed: 12/12/2022]
Abstract
Muconic acid is a valuable platform chemical with potential applications in the production of polymers such as nylon and polyethylene terephthalate (PET). The conjugate base, muconate, has been previously biosynthesized in the bacterial host Escherichia coli. Likewise, previous significant pathway engineering lead to the first reported instance of rationally engineered production of muconic acid in the yeast Saccharomyces cerevisiae. To further increase muconic acid production in this host, a combined adaptive laboratory evolution (ALE) strategy and rational metabolic engineering is employed. To this end, a biosensor module that responds to the endogenous aromatic amino acid (AAA) as a surrogate for pathway flux is adapted. Following two rounds of ALE coupled with an anti-metabolite feeding strategy, the strains with improved AAA pathway flux is isolated. Next, it is demonstrated that this increased flux can be redirected into the composite muconic acid pathway with a threefold increase in the total titer of the composite pathway compared to our previously engineered strain. Finally, a truncation of the penta-functional ARO1 protein is complemented and overexpress an endogenous aromatic decarboxylase to establish a final strain capable of producing 0.5 g L-1 muconic acid in shake flasks and 2.1 g L-1 in a fed-batch bioreactor with a yield of 12.9 mg muconic acid/g glucose at the rate of 9.0 mg h-1 . This value represents the highest titer of muconic acid reported to date in S. cerevisiae, in addition to the highest reported titer of a shikimate pathway derivative in this host.
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Affiliation(s)
- John M Leavitt
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, 2500 Speedway Avenue, Austin, TX, 78712, USA
| | - James M Wagner
- McKetta Department of Chemical Engineering, The University of Texas at Austin, 200 E Dean Keeton St. Stop C0400, Austin, TX, 78712, USA
| | - Cuong C Tu
- McKetta Department of Chemical Engineering, The University of Texas at Austin, 200 E Dean Keeton St. Stop C0400, Austin, TX, 78712, USA
| | - Alice Tong
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, 2500 Speedway Avenue, Austin, TX, 78712, USA
| | - Yanyi Liu
- McKetta Department of Chemical Engineering, The University of Texas at Austin, 200 E Dean Keeton St. Stop C0400, Austin, TX, 78712, USA
| | - Hal S Alper
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, 2500 Speedway Avenue, Austin, TX, 78712, USA.,McKetta Department of Chemical Engineering, The University of Texas at Austin, 200 E Dean Keeton St. Stop C0400, Austin, TX, 78712, USA
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80
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Lignin Valorization: Two Hybrid Biochemical Routes for the Conversion of Polymeric Lignin into Value-added Chemicals. Sci Rep 2017; 7:8420. [PMID: 28827602 PMCID: PMC5566326 DOI: 10.1038/s41598-017-07895-1] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Accepted: 07/06/2017] [Indexed: 11/26/2022] Open
Abstract
Naturally, many aerobic organisms degrade lignin-derived aromatics through conserved intermediates including protocatechuate and catechol. Employing this microbial approach offers a potential solution for valorizing lignin into valuable chemicals for a potential lignocellulosic biorefinery and enabling bioeconomy. In this study, two hybrid biochemical routes combining lignin chemical depolymerization, plant metabolic engineering, and synthetic pathway reconstruction were demonstrated for valorizing lignin into value-added products. In the biochemical route 1, alkali lignin was chemically depolymerized into vanillin and syringate as major products, which were further bio-converted into cis, cis-muconic acid (ccMA) and pyrogallol, respectively, using engineered Escherichia coli strains. In the second biochemical route, the shikimate pathway of Tobacco plant was engineered to accumulate protocatechuate (PCA) as a soluble intermediate compound. The PCA extracted from the engineered Tobacco was further converted into ccMA using the engineered E. coli strain. This study reports a direct process for converting lignin into ccMA and pyrogallol as value-added chemicals, and more importantly demonstrates benign methods for valorization of polymeric lignin that is inherently heterogeneous and recalcitrant. Our approach also validates the promising combination of plant engineering with microbial chassis development for the production of value added and speciality chemicals.
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81
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Suástegui M, Yu Ng C, Chowdhury A, Sun W, Cao M, House E, Maranas CD, Shao Z. Multilevel engineering of the upstream module of aromatic amino acid biosynthesis in Saccharomyces cerevisiae for high production of polymer and drug precursors. Metab Eng 2017. [DOI: 10.1016/j.ymben.2017.06.008] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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82
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Abstract
Along with the development of metabolic engineering and synthetic biology tools, various microbes are being used to produce aromatic chemicals. In microbes, aromatics are mainly produced via a common important precursor, chorismate, in the shikimate pathway. Natural or non-natural aromatics have been produced by engineering metabolic pathways involving chorismate. In the past decade, novel approaches have appeared to produce various aromatics or to increase their productivity, whereas previously, the targets were mainly aromatic amino acids and the strategy was deregulating feedback inhibition. In this review, we summarize recent studies of microbial production of aromatics based on metabolic engineering approaches. In addition, future perspectives and challenges in this research area are discussed.
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Affiliation(s)
- Shuhei Noda
- Center for Sustainable Resource Science, RIKEN, 1-7-22, Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Akihiko Kondo
- Center for Sustainable Resource Science, RIKEN, 1-7-22, Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan; Department of Chemical Science and Engineering, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan.
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83
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Gottardi M, Reifenrath M, Boles E, Tripp J. Pathway engineering for the production of heterologous aromatic chemicals and their derivatives in Saccharomyces cerevisiae: bioconversion from glucose. FEMS Yeast Res 2017; 17:3861259. [DOI: 10.1093/femsyr/fox035] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Accepted: 06/01/2017] [Indexed: 12/30/2022] Open
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84
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Requirement of a Functional Flavin Mononucleotide Prenyltransferase for the Activity of a Bacterial Decarboxylase in a Heterologous Muconic Acid Pathway in Saccharomyces cerevisiae. Appl Environ Microbiol 2017; 83:AEM.03472-16. [PMID: 28283523 DOI: 10.1128/aem.03472-16] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Accepted: 03/05/2017] [Indexed: 01/26/2023] Open
Abstract
Biotechnological production of cis,cis-muconic acid from renewable feedstocks is an environmentally sustainable alternative to conventional, petroleum-based methods. Even though a heterologous production pathway for cis,cis-muconic acid has already been established in the host organism Saccharomyces cerevisiae, the generation of industrially relevant amounts of cis,cis-muconic acid is hampered by the low activity of the bacterial protocatechuic acid (PCA) decarboxylase AroY isomeric subunit Ciso (AroY-Ciso), leading to secretion of large amounts of the intermediate PCA into the medium. In the present study, we show that the activity of AroY-Ciso in S. cerevisiae strongly depends on the strain background. We could demonstrate that the strain dependency is caused by the presence or absence of an intact genomic copy of PAD1, which encodes a mitochondrial enzyme responsible for the biosynthesis of a prenylated form of the cofactor flavin mononucleotide (prFMN). The inactivity of AroY-Ciso in strain CEN.PK2-1 could be overcome by plasmid-borne expression of Pad1 or its bacterial homologue AroY subunit B (AroY-B). Our data reveal that the two enzymes perform the same function in decarboxylation of PCA by AroY-Ciso, although coexpression of Pad1 led to higher decarboxylase activity. Conversely, AroY-B can replace Pad1 in its function in decarboxylation of phenylacrylic acids by ferulic acid decarboxylase Fdc1. Targeting of the majority of AroY-B to mitochondria by fusion to a heterologous mitochondrial targeting signal did not improve decarboxylase activity of AroY-Ciso, suggesting that mitochondrial localization has no major impact on cofactor biosynthesis.IMPORTANCE In Saccharomyces cerevisiae, the decarboxylation of protocatechuic acid (PCA) to catechol is the bottleneck reaction in the heterologous biosynthetic pathway for production of cis,cis-muconic acid, a valuable precursor for the production of bulk chemicals. In our work, we demonstrate the importance of the strain background for the activity of a bacterial PCA decarboxylase in S. cerevisiae Inactivity of the decarboxylase is due to a nonsense mutation in a gene encoding a mitochondrial enzyme involved in the biosynthesis of a cofactor required for decarboxylase function. Our study reveals functional interchangeability of Pad1 and a bacterial homologue, irrespective of their intracellular localization. Our results open up new possibilities to improve muconic acid production by engineering cofactor supply. Furthermore, the results have important implications for the choice of the production strain.
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85
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Metabolic engineering strategies to bio-adipic acid production. Curr Opin Biotechnol 2017; 45:136-143. [PMID: 28365404 DOI: 10.1016/j.copbio.2017.03.006] [Citation(s) in RCA: 72] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2017] [Revised: 03/08/2017] [Accepted: 03/09/2017] [Indexed: 11/21/2022]
Abstract
Adipic acid is the most industrially important dicarboxylic acid as it is a key monomer in the synthesis of nylon. Today, adipic acid is obtained via a chemical process that relies on petrochemical precursors and releases large quantities of greenhouse gases. In the last two years, significant progress has been made in engineering microbes for the production of adipic acid and its immediate precursors, muconic acid and glucaric acid. Not only have the microbial substrates expanded beyond glucose and glycerol to include lignin monomers and hemicellulose components, but the number of microbial chassis now goes further than Escherichia coli and Saccharomyces cerevisiae to include microbes proficient in aromatic degradation, cellulose secretion and degradation of multiple carbon sources. Here, we review the metabolic engineering and nascent protein engineering strategies undertaken in each of these chassis to convert different feedstocks to adipic, muconic and glucaric acid. We also highlight near term prospects and challenges for each of the metabolic routes discussed.
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86
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Opportunities and challenges in biological lignin valorization. Curr Opin Biotechnol 2016; 42:40-53. [DOI: 10.1016/j.copbio.2016.02.030] [Citation(s) in RCA: 420] [Impact Index Per Article: 52.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Revised: 02/15/2016] [Accepted: 02/24/2016] [Indexed: 02/08/2023]
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87
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Walter JM, Chandran SS, Horwitz AA. CRISPR-Cas-Assisted Multiplexing (CAM): Simple Same-Day Multi-Locus Engineering in Yeast. J Cell Physiol 2016; 231:2563-9. [PMID: 26991244 DOI: 10.1002/jcp.25375] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Accepted: 03/11/2016] [Indexed: 01/21/2023]
Abstract
Demands on the industrial and academic yeast strain engineer have increased significantly in the era of synthetic biology. Installing complex biosynthetic pathways and combining point mutations are tedious and time-consuming using traditional methods. With multiplex engineering tools, these tasks can be completed in a single step, typically achieving up to sixfold compression in strain engineering timelines. To capitalize on this potential, a variety of yeast CRISPR-Cas methods have been developed, differing largely in how the guide RNA (gRNA) reagents that direct the Cas9 nuclease are delivered. However, in nearly all reported protocols, the time savings of multiplexing is offset by multiple days of cloning to prepare the required reagents. Here, we discuss the advantages and opportunities of CRISPR-Cas-assisted multiplexing (CAM), a same-day, cloning-free method for multi-locus engineering in yeast. J. Cell. Physiol. 231: 2563-2569, 2016. © 2016 Wiley Periodicals, Inc.
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88
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Yu S, Plan MR, Winter G, Krömer JO. Metabolic Engineering of Pseudomonas putida KT2440 for the Production of para-Hydroxy Benzoic Acid. Front Bioeng Biotechnol 2016; 4:90. [PMID: 27965953 PMCID: PMC5124731 DOI: 10.3389/fbioe.2016.00090] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Accepted: 11/10/2016] [Indexed: 11/13/2022] Open
Abstract
para-Hydroxy benzoic acid (PHBA) is the key component for preparing parabens, a common preservatives in food, drugs, and personal care products, as well as high-performance bioplastics such as liquid crystal polymers. Pseudomonas putida KT2440 was engineered to produce PHBA from glucose via the shikimate pathway intermediate chorismate. To obtain the PHBA production strain, chorismate lyase UbiC from Escherichia coli and a feedback resistant 3-deoxy-d-arabino-heptulosonate-7-phosphate synthase encoded by gene aroGD146N were overexpressed individually and simultaneously. In addition, genes related to product degradation (pobA) or competing for the precursor chorismate (pheA and trpE) were deleted from the genome. To further improve PHBA production, the glucose metabolism repressor hexR was knocked out in order to increase erythrose 4-phosphate and NADPH supply. The best strain achieved a maximum titer of 1.73 g L−1 and a carbon yield of 18.1% (C-mol C-mol−1) in a non-optimized fed-batch fermentation. This is to date the highest PHBA concentration produced by P. putida using a chorismate lyase.
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Affiliation(s)
- Shiqin Yu
- Centre for Microbial Electrochemical Systems (CEMES), The University of Queensland, Brisbane, QLD, Australia; Advanced Water Management Centre (AWMC), The University of Queensland, Brisbane, QLD, Australia
| | - Manuel R Plan
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, QLD, Australia; Metabolomics Australia (Queensland Node), The University of Queensland, Brisbane, QLD, Australia
| | - Gal Winter
- Centre for Microbial Electrochemical Systems (CEMES), The University of Queensland, Brisbane, QLD, Australia; Advanced Water Management Centre (AWMC), The University of Queensland, Brisbane, QLD, Australia; School of Science and Technology, The University of New England, Armidale, NSW, Australia
| | - Jens O Krömer
- Centre for Microbial Electrochemical Systems (CEMES), The University of Queensland, Brisbane, QLD, Australia; Advanced Water Management Centre (AWMC), The University of Queensland, Brisbane, QLD, Australia
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89
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Peek J, Roman J, Moran GR, Christendat D. Structurally diverse dehydroshikimate dehydratase variants participate in microbial quinate catabolism. Mol Microbiol 2016; 103:39-54. [DOI: 10.1111/mmi.13542] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/21/2016] [Indexed: 11/30/2022]
Affiliation(s)
- James Peek
- Department of Cell and Systems BiologyUniversity of Toronto25 Willcocks StreetToronto, Ontario CanadaM5S 3B2
| | - Joseph Roman
- Department of Chemistry and BiochemistryUniversity of Wisconsin‐Milwaukee3210 North Cramer StreetMilwaukee WI53211‐3209 USA
| | - Graham R. Moran
- Department of Chemistry and BiochemistryUniversity of Wisconsin‐Milwaukee3210 North Cramer StreetMilwaukee WI53211‐3209 USA
| | - Dinesh Christendat
- Department of Cell and Systems BiologyUniversity of Toronto25 Willcocks StreetToronto, Ontario CanadaM5S 3B2
- Centre for the Analysis of Genome Evolution and FunctionUniversity of TorontoToronto, Ontario CanadaM5S 3B2
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90
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Johnson CW, Salvachúa D, Khanna P, Smith H, Peterson DJ, Beckham GT. Enhancing muconic acid production from glucose and lignin-derived aromatic compounds via increased protocatechuate decarboxylase activity. Metab Eng Commun 2016; 3:111-119. [PMID: 29468118 PMCID: PMC5779730 DOI: 10.1016/j.meteno.2016.04.002] [Citation(s) in RCA: 125] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Revised: 04/01/2016] [Accepted: 04/21/2016] [Indexed: 11/28/2022] Open
Abstract
The conversion of biomass-derived sugars and aromatic molecules to cis,cis-muconic acid (referred to hereafter as muconic acid or muconate) has been of recent interest owing to its facile conversion to adipic acid, an important commodity chemical. Metabolic routes to produce muconate from both sugars and many lignin-derived aromatic compounds require the use of a decarboxylase to convert protocatechuate (PCA, 3,4-dihydroxybenzoate) to catechol (1,2-dihydroxybenzene), two central aromatic intermediates in this pathway. Several studies have identified the PCA decarboxylase as a metabolic bottleneck, causing an accumulation of PCA that subsequently reduces muconate production. A recent study showed that activity of the PCA decarboxylase is enhanced by co-expression of two genetically associated proteins, one of which likely produces a flavin-derived cofactor utilized by the decarboxylase. Using entirely genome-integrated gene expression, we have engineered Pseudomonas putida KT2440-derived strains to produce muconate from either aromatic molecules or sugars and demonstrate in both cases that co-expression of these decarboxylase associated proteins reduces PCA accumulation and enhances muconate production relative to strains expressing the PCA decarboxylase alone. In bioreactor experiments, co-expression increased the specific productivity (mg/g cells/h) of muconate from the aromatic lignin monomer p-coumarate by 50% and resulted in a titer of >15 g/L. In strains engineered to produce muconate from glucose, co-expression more than tripled the titer, yield, productivity, and specific productivity, with the best strain producing 4.92±0.48 g/L muconate. This study demonstrates that overcoming the PCA decarboxylase bottleneck can increase muconate yields from biomass-derived sugars and aromatic molecules in industrially relevant strains and cultivation conditions. We engineered Pseudomonas putida to produce muconate from p-coumarate and glucose. A protocatechuate decarboxylase was expressed with two associated proteins. Co-expression of these proteins reduced protocatechuate accumulation. Co-expression of these proteins reduced enhanced muconate production up to 3X. 15.6 g/L muconate was produced from p-coumarate and 4.92 g/L from glucose
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Affiliation(s)
- Christopher W Johnson
- National Bioenergy Center, National Renewable Energy Laboratory, Golden, CO 80401, United States
| | - Davinia Salvachúa
- National Bioenergy Center, National Renewable Energy Laboratory, Golden, CO 80401, United States
| | - Payal Khanna
- National Bioenergy Center, National Renewable Energy Laboratory, Golden, CO 80401, United States
| | - Holly Smith
- National Bioenergy Center, National Renewable Energy Laboratory, Golden, CO 80401, United States
| | - Darren J Peterson
- National Bioenergy Center, National Renewable Energy Laboratory, Golden, CO 80401, United States
| | - Gregg T Beckham
- National Bioenergy Center, National Renewable Energy Laboratory, Golden, CO 80401, United States
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91
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Genetically encoded sensors enable real-time observation of metabolite production. Proc Natl Acad Sci U S A 2016; 113:2388-93. [PMID: 26858408 DOI: 10.1073/pnas.1600375113] [Citation(s) in RCA: 133] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Engineering cells to produce valuable metabolic products is hindered by the slow and laborious methods available for evaluating product concentration. Consequently, many designs go unevaluated, and the dynamics of product formation over time go unobserved. In this work, we develop a framework for observing product formation in real time without the need for sample preparation or laborious analytical methods. We use genetically encoded biosensors derived from small-molecule responsive transcription factors to provide a fluorescent readout that is proportional to the intracellular concentration of a target metabolite. Combining an appropriate biosensor with cells designed to produce a metabolic product allows us to track product formation by observing fluorescence. With individual cells exhibiting fluorescent intensities proportional to the amount of metabolite they produce, high-throughput methods can be used to rank the quality of genetic variants or production conditions. We observe production of several renewable plastic precursors with fluorescent readouts and demonstrate that higher fluorescence is indeed an indicator of higher product titer. Using fluorescence as a guide, we identify process parameters that produce 3-hydroxypropionate at 4.2 g/L, 23-fold higher than previously reported. We also report, to our knowledge, the first engineered route from glucose to acrylate, a plastic precursor with global sales of $14 billion. Finally, we monitor the production of glucarate, a replacement for environmentally damaging detergents, and muconate, a renewable precursor to polyethylene terephthalate and nylon with combined markets of $51 billion, in real time, demonstrating that our method is applicable to a wide range of molecules.
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92
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Suastegui M, Matthiesen JE, Carraher JM, Hernandez N, Rodriguez Quiroz N, Okerlund A, Cochran EW, Shao Z, Tessonnier J. Combining Metabolic Engineering and Electrocatalysis: Application to the Production of Polyamides from Sugar. Angew Chem Int Ed Engl 2016; 55:2368-73. [DOI: 10.1002/anie.201509653] [Citation(s) in RCA: 94] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Indexed: 12/18/2022]
Affiliation(s)
- Miguel Suastegui
- Department of Chemical and Biological Engineering Iowa State University Ames IA 50011 USA
- NSF Engineering Research Center for Biorenewable Chemicals (CBiRC) Ames IA 50011 USA
| | - John E. Matthiesen
- Department of Chemical and Biological Engineering Iowa State University Ames IA 50011 USA
- NSF Engineering Research Center for Biorenewable Chemicals (CBiRC) Ames IA 50011 USA
- US Department of Energy Ames Laboratory Ames IA 50011 USA
| | - Jack M. Carraher
- Department of Chemical and Biological Engineering Iowa State University Ames IA 50011 USA
- NSF Engineering Research Center for Biorenewable Chemicals (CBiRC) Ames IA 50011 USA
| | - Nacu Hernandez
- Department of Chemical and Biological Engineering Iowa State University Ames IA 50011 USA
| | | | - Adam Okerlund
- NSF Engineering Research Center for Biorenewable Chemicals (CBiRC) Ames IA 50011 USA
| | - Eric W. Cochran
- Department of Chemical and Biological Engineering Iowa State University Ames IA 50011 USA
| | - Zengyi Shao
- Department of Chemical and Biological Engineering Iowa State University Ames IA 50011 USA
- NSF Engineering Research Center for Biorenewable Chemicals (CBiRC) Ames IA 50011 USA
| | - Jean‐Philippe Tessonnier
- Department of Chemical and Biological Engineering Iowa State University Ames IA 50011 USA
- NSF Engineering Research Center for Biorenewable Chemicals (CBiRC) Ames IA 50011 USA
- US Department of Energy Ames Laboratory Ames IA 50011 USA
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93
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Combining Metabolic Engineering and Electrocatalysis: Application to the Production of Polyamides from Sugar. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201509653] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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94
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Deng Y, Ma L, Mao Y. Biological production of adipic acid from renewable substrates: Current and future methods. Biochem Eng J 2016. [DOI: 10.1016/j.bej.2015.08.015] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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95
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Sengupta S, Jonnalagadda S, Goonewardena L, Juturu V. Metabolic engineering of a novel muconic acid biosynthesis pathway via 4-hydroxybenzoic acid in Escherichia coli. Appl Environ Microbiol 2015; 81:8037-43. [PMID: 26362984 PMCID: PMC4651072 DOI: 10.1128/aem.01386-15] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2015] [Accepted: 09/10/2015] [Indexed: 11/20/2022] Open
Abstract
cis,cis-Muconic acid (MA) is a commercially important raw material used in pharmaceuticals, functional resins, and agrochemicals. MA is also a potential platform chemical for the production of adipic acid (AA), terephthalic acid, caprolactam, and 1,6-hexanediol. A strain of Escherichia coli K-12, BW25113, was genetically modified, and a novel nonnative metabolic pathway was introduced for the synthesis of MA from glucose. The proposed pathway converted chorismate from the aromatic amino acid pathway to MA via 4-hydroxybenzoic acid (PHB). Three nonnative genes, pobA, aroY, and catA, coding for 4-hydroxybenzoate hydrolyase, protocatechuate decarboxylase, and catechol 1,2-dioxygenase, respectively, were functionally expressed in E. coli to establish the MA biosynthetic pathway. E. coli native genes ubiC, aroF(FBR), aroE, and aroL were overexpressed and the genes ptsH, ptsI, crr, and pykF were deleted from the E. coli genome in order to increase the precursors of the proposed MA pathway. The final engineered E. coli strain produced nearly 170 mg/liter of MA from simple carbon sources in shake flask experiments. The proposed pathway was proved to be functionally active, and the strategy can be used for future metabolic engineering efforts for production of MA from renewable sugars.
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Affiliation(s)
- Sudeshna Sengupta
- Institute of Chemical and Engineering Sciences, Agency for Science, Technology and Research, Singapore, Republic of Singapore
| | - Sudhakar Jonnalagadda
- Institute of Chemical and Engineering Sciences, Agency for Science, Technology and Research, Singapore, Republic of Singapore
| | - Lakshani Goonewardena
- Institute of Chemical and Engineering Sciences, Agency for Science, Technology and Research, Singapore, Republic of Singapore
| | - Veeresh Juturu
- Institute of Chemical and Engineering Sciences, Agency for Science, Technology and Research, Singapore, Republic of Singapore
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96
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Babu T, Yun EJ, Kim S, Kim DH, Liu KH, Kim SR, Kim KH. Engineering Escherichia coli for the production of adipic acid through the reversed β-oxidation pathway. Process Biochem 2015. [DOI: 10.1016/j.procbio.2015.09.018] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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97
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Top value platform chemicals: bio-based production of organic acids. Curr Opin Biotechnol 2015; 36:168-75. [DOI: 10.1016/j.copbio.2015.08.022] [Citation(s) in RCA: 193] [Impact Index Per Article: 21.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Revised: 08/11/2015] [Accepted: 08/18/2015] [Indexed: 11/19/2022]
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98
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Sonoki T, Morooka M, Sakamoto K, Otsuka Y, Nakamura M, Jellison J, Goodell B. Enhancement of protocatechuate decarboxylase activity for the effective production of muconate from lignin-related aromatic compounds. J Biotechnol 2015; 192 Pt A:71-7. [PMID: 25449108 DOI: 10.1016/j.jbiotec.2014.10.027] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2014] [Revised: 10/20/2014] [Accepted: 10/21/2014] [Indexed: 10/24/2022]
Abstract
The decarboxylation reaction of protocatechuate has been described as a bottleneck and a rate-limiting step in cis,cis-muconate (ccMA) bioproduction from renewable feedstocks such as sugar. Because sugars are already in high demand in the development of many bio-based products, our work focuses on improving protocatechuate decarboxylase (Pdc) activity and ccMA production in particular, from lignin-related aromatic compounds. We previously had transformed an Escherichia coli strain using aroY, which had been used as a protocatechuate decarboxylase encoding gene from Klebsiella pneumoniae subsp. pneumoniae A170-40, and inserted other required genes from Pseudomonas putida KT2440, to allow the production of ccMA from vanillin. This recombinant strain produced ccMA from vanillin, however the Pdc reaction step remained a bottleneck during incubation. In the current study, we identify a way to increase protocatechuate decarboxylase activity in E. coli through enzyme production involving both aroY and kpdB; the latter which encodes for the B subunit of 4-hydroxybenzoate decarboxylase. This permits expression of Pdc activity at a level approximately 14-fold greater than the strain with aroY only. The expression level of AroY increased, apparently as a function of the co-expression of AroY and KpdB. Our results also imply that ccMA may inhibit vanillate demethylation, a reaction step that is rate limiting for efficient ccMA production from lignin-related aromatic compounds, so even though ccMA production may be enhanced, other challenges to overcome vanilate demethylation inhibition still remain.
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Production of protocatechuic acid by Corynebacterium glutamicum expressing chorismate-pyruvate lyase from Escherichia coli. Appl Microbiol Biotechnol 2015; 100:135-45. [DOI: 10.1007/s00253-015-6976-4] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2015] [Revised: 08/19/2015] [Accepted: 09/01/2015] [Indexed: 10/23/2022]
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100
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Zhang H, Li Z, Pereira B, Stephanopoulos G. Engineering E. coli-E. coli cocultures for production of muconic acid from glycerol. Microb Cell Fact 2015; 14:134. [PMID: 26369810 PMCID: PMC4570557 DOI: 10.1186/s12934-015-0319-0] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Accepted: 08/20/2015] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND cis, cis-Muconic acid is an important chemical that can be biosynthesized from simple substrates in engineered microorganisms. Recently, it has been shown that engineering microbial cocultures is an emerging and promising approach for biochemical production. In this study, we aim to explore the potential of the E. coli-E. coli coculture system to use a single renewable carbon source, glycerol, for the production of value-added product cis, cis-muconic acid. RESULTS Two coculture engineering strategies were investigated. In the first strategy, an E. coli strain containing the complete biosynthesis pathway was co-cultivated with another E. coli strain containing only a heterologous intermediate-to-product biosynthetic pathway. In the second strategy, the upstream and downstream pathways were accommodated in two separate E. coli strains, each of which was dedicated to one portion of the biosynthesis process. Compared with the monoculture approach, both coculture engineering strategies improved the production significantly. Using a batch bioreactor, the engineered coculture achieved a 2 g/L muconic acid production with a yield of 0.1 g/g. CONCLUSIONS Our results demonstrate that coculture engineering is a viable option for producing muconic acid from glycerol. Moreover, microbial coculture systems are shown to have the potential for converting single carbon source to value-added products.
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Affiliation(s)
- Haoran Zhang
- Chemical Engineering Department, Massachusetts Institute of Technology, 77 Massachusetts Ave, Cambridge, MA, 02139, USA.
| | - Zhengjun Li
- Chemical Engineering Department, Massachusetts Institute of Technology, 77 Massachusetts Ave, Cambridge, MA, 02139, USA. .,Beijing Key Laboratory of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, People's Republic of China.
| | - Brian Pereira
- Chemical Engineering Department, Massachusetts Institute of Technology, 77 Massachusetts Ave, Cambridge, MA, 02139, USA.
| | - Gregory Stephanopoulos
- Chemical Engineering Department, Massachusetts Institute of Technology, 77 Massachusetts Ave, Cambridge, MA, 02139, USA.
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