1
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Jiang Y, Li S. P450 fatty acid decarboxylase. Methods Enzymol 2023; 693:339-374. [PMID: 37977736 DOI: 10.1016/bs.mie.2023.09.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2023]
Abstract
P450 fatty acid decarboxylases are able to utilize hydrogen peroxide as the sole cofactor to decarboxylate free fatty acids to produce α-olefins with abundant applications as drop-in biofuels and important chemical precursors. In this chapter, we review diverse approaches for discovery, characterization, engineering, and applications of P450 fatty acid decarboxylases. Information gained from structural data has been advancing our understandings of the unique mechanisms underlying alkene production, and providing important insights for exploring new activities. To build an efficient olefin-producing system, various engineering strategies have been proposed and applied to this unusual P450 catalytic system. Furthermore, we highlight a select number of applied examples of P450 fatty acid decarboxylases in enzyme cascades and metabolic engineering.
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Affiliation(s)
- Yuanyuan Jiang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, P.R. China
| | - Shengying Li
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, P.R. China.
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2
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Biosynthesis of alkanes/alkenes from fatty acids or derivatives (triacylglycerols or fatty aldehydes). Biotechnol Adv 2022; 61:108045. [DOI: 10.1016/j.biotechadv.2022.108045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 09/22/2022] [Accepted: 09/24/2022] [Indexed: 11/27/2022]
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3
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Cai P, Li Y, Zhai X, Yao L, Ma X, Jia L, Zhou YJ. Microbial synthesis of long-chain α-alkenes from methanol by engineering Pichia pastoris. BIORESOUR BIOPROCESS 2022; 9:58. [PMID: 38647822 PMCID: PMC10991524 DOI: 10.1186/s40643-022-00551-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 05/12/2022] [Indexed: 11/10/2022] Open
Abstract
α-Alkenes (terminal alkenes) are important fuel and platform chemicals that are mainly produced from petroleum. Microbial synthesis might provide a sustainable approach for α-alkenes. In this work, we engineered the methylotrophic yeast Pichia pastoris to produce long-chain (C15:1, C17:1 and C17:2) α-alkenes via a decarboxylation of fatty acids. Combinatorial engineering, including enzyme selection, expression optimization and peroxisomal compartmentalization, enabled the production of 1.6 mg/L α-alkenes from sole methanol. This study represents the first case of α-alkene biosynthesis from methanol and also provides a reference for the construction of methanol microbial cell factories of other high-value chemicals.
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Affiliation(s)
- Peng Cai
- School of Life Science and Biotechnology, Dalian University of Technology, Dalian, 116024, People's Republic of China
- Division of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, 116023, People's Republic of China
- University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Yunxia Li
- Division of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, 116023, People's Republic of China
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, People's Republic of China
| | - Xiaoxin Zhai
- Division of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, 116023, People's Republic of China
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, People's Republic of China
| | - Lun Yao
- Dalian Key Laboratory of Energy Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, People's Republic of China
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, People's Republic of China
| | - Xiaojun Ma
- Dalian Key Laboratory of Energy Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, People's Republic of China
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, People's Republic of China
| | - Lingyun Jia
- School of Life Science and Biotechnology, Dalian University of Technology, Dalian, 116024, People's Republic of China
| | - Yongjin J Zhou
- Division of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, 116023, People's Republic of China.
- Dalian Key Laboratory of Energy Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, People's Republic of China.
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, People's Republic of China.
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4
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Intasian P, Prakinee K, Phintha A, Trisrivirat D, Weeranoppanant N, Wongnate T, Chaiyen P. Enzymes, In Vivo Biocatalysis, and Metabolic Engineering for Enabling a Circular Economy and Sustainability. Chem Rev 2021; 121:10367-10451. [PMID: 34228428 DOI: 10.1021/acs.chemrev.1c00121] [Citation(s) in RCA: 63] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Since the industrial revolution, the rapid growth and development of global industries have depended largely upon the utilization of coal-derived chemicals, and more recently, the utilization of petroleum-based chemicals. These developments have followed a linear economy model (produce, consume, and dispose). As the world is facing a serious threat from the climate change crisis, a more sustainable solution for manufacturing, i.e., circular economy in which waste from the same or different industries can be used as feedstocks or resources for production offers an attractive industrial/business model. In nature, biological systems, i.e., microorganisms routinely use their enzymes and metabolic pathways to convert organic and inorganic wastes to synthesize biochemicals and energy required for their growth. Therefore, an understanding of how selected enzymes convert biobased feedstocks into special (bio)chemicals serves as an important basis from which to build on for applications in biocatalysis, metabolic engineering, and synthetic biology to enable biobased processes that are greener and cleaner for the environment. This review article highlights the current state of knowledge regarding the enzymatic reactions used in converting biobased wastes (lignocellulosic biomass, sugar, phenolic acid, triglyceride, fatty acid, and glycerol) and greenhouse gases (CO2 and CH4) into value-added products and discusses the current progress made in their metabolic engineering. The commercial aspects and life cycle assessment of products from enzymatic and metabolic engineering are also discussed. Continued development in the field of metabolic engineering would offer diversified solutions which are sustainable and renewable for manufacturing valuable chemicals.
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Affiliation(s)
- Pattarawan Intasian
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Wangchan Valley, Rayong 21210, Thailand
| | - Kridsadakorn Prakinee
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Wangchan Valley, Rayong 21210, Thailand
| | - Aisaraphon Phintha
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Wangchan Valley, Rayong 21210, Thailand.,Department of Biochemistry and Center for Excellence in Protein and Enzyme Technology, Faculty of Science, Mahidol University, Bangkok 10400, Thailand
| | - Duangthip Trisrivirat
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Wangchan Valley, Rayong 21210, Thailand
| | - Nopphon Weeranoppanant
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Wangchan Valley, Rayong 21210, Thailand.,Department of Chemical Engineering, Faculty of Engineering, Burapha University, 169, Long-hard Bangsaen, Saensook, Muang, Chonburi 20131, Thailand
| | - Thanyaporn Wongnate
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Wangchan Valley, Rayong 21210, Thailand
| | - Pimchai Chaiyen
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Wangchan Valley, Rayong 21210, Thailand
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5
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Pereira R, Ishchuk OP, Li X, Liu Q, Liu Y, Otto M, Chen Y, Siewers V, Nielsen J. Metabolic Engineering of Yeast. Metab Eng 2021. [DOI: 10.1002/9783527823468.ch18] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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6
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Zhang J, Zhang C, Xin X, Liu D, Zhang W. Comparative Analysis of Traditional and Modern Fermentation for Xuecai and Correlations Between Volatile Flavor Compounds and Bacterial Community. Front Microbiol 2021; 12:631054. [PMID: 33995294 PMCID: PMC8118120 DOI: 10.3389/fmicb.2021.631054] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Accepted: 04/07/2021] [Indexed: 01/28/2023] Open
Abstract
Differences in flavor compounds and bacterial communities of Xuecai by traditional and modern fermentation are poorly understood. Allyl isothiocyanate (E9), ethyl acetate (E1), 3-butenenitrile (N1), phenol (P1), ethanol (A1), and 3-(2,6,6-trimethyl-1-cyclohexen-1-yl) acrylaldehyde (L11) were the main flavor compounds that differed between Xuecai produced by traditional and modern fermentation. Among these compounds, the contents of N1 and E9 were higher in modern fermentation Xuecai. Traditional fermentation Xuecai possessed higher contents of A1, P1, E1, and L11. High-throughput sequencing showed that Lactobacillus-related genera was the most abundant genus (50%) in modern fermentation Xuecai. However, in traditional fermentation Xuecai, Halanaerobium (29.06%) and Halomonas (12.96%) were the dominant genera. Halophilic bacteria (HB) positively contribute to the flavor of Xuecai. Carbohydrate metabolism and amino acid metabolism were the most abundant pathways associated with the bacterial communities of the Xuecai. This indicated that Xuecai flavor formation is mainly dependent on protein and carbohydrate degradation. This study provides a novel insight that HB may be important for flavor formation of Xuecai.
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Affiliation(s)
- Jianming Zhang
- Institute of Food Science, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Chengcheng Zhang
- Institute of Food Science, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Xiaoting Xin
- Institute of Food Science, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Daqun Liu
- Institute of Food Science, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Wenwu Zhang
- Hangzhou Trendbiotech Co., Ltd, Hangzhou, China
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7
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Sharma A, Yazdani SS. Microbial engineering to produce fatty alcohols and alkanes. J Ind Microbiol Biotechnol 2021; 48:6169711. [PMID: 33713132 DOI: 10.1093/jimb/kuab011] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Accepted: 11/18/2020] [Indexed: 11/14/2022]
Abstract
Owing to their high energy density and composition, fatty acid-derived chemicals possess a wide range of applications such as biofuels, biomaterials, and other biochemical, and as a consequence, the global annual demand for products has surpassed 2 million tons. With the exhausting petroleum reservoirs and emerging environmental concerns on using petroleum feedstock, it has become indispensable to shift to a renewable-based industry. With the advancement in the field of synthetic biology and metabolic engineering, the use of microbes as factories for the production of fatty acid-derived chemicals is becoming a promising alternative approach for the production of these derivatives. Numerous metabolic approaches have been developed for conditioning the microbes to improve existing or develop new methodologies capable of efficient oleochemical production. However, there still exist several limitations that need to be addressed for the commercial viability of the microbial cell factory production. Though substantial advancement has been made toward successfully producing these fatty acids derived chemicals, a considerable amount of work needs to be done for improving the titers. In the present review, we aim to address the roadblocks impeding the heterologous production, the engineering pathway strategies implemented across the range of microbes in a detailed manner, and the commercial readiness of these molecules of immense application.
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Affiliation(s)
- Ashima Sharma
- Microbial Engineering Group, International Centre for Genetic Engineering and Biotechnology, New Delhi 110067, India.,DBT-ICGEB Centre for Advanced Bioenergy Research, International Centre for Genetic Engineering and Biotechnology, New Delhi 110067, India
| | - Syed Shams Yazdani
- Microbial Engineering Group, International Centre for Genetic Engineering and Biotechnology, New Delhi 110067, India.,DBT-ICGEB Centre for Advanced Bioenergy Research, International Centre for Genetic Engineering and Biotechnology, New Delhi 110067, India
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8
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Bauer D, Zachos I, Sieber V. Production of Propene from n-Butanol: A Three-Step Cascade Utilizing the Cytochrome P450 Fatty Acid Decarboxylase OleT JE. Chembiochem 2020; 21:3273-3281. [PMID: 32656928 PMCID: PMC7754297 DOI: 10.1002/cbic.202000378] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 07/09/2020] [Indexed: 11/22/2022]
Abstract
Propene is one of the most important starting materials in the chemical industry. Herein, we report an enzymatic cascade reaction for the biocatalytic production of propene starting from n-butanol, thus offering a biobased production from glucose. In order to create an efficient system, we faced the issue of an optimal cofactor supply for the fatty acid decarboxylase OleTJE , which is said to be driven by either NAD(P)H or H2 O2 . In the first system, we used an alcohol and aldehyde dehydrogenase coupled to OleTJE by the electron-transfer complex putidaredoxin reductase/putidaredoxin, allowing regeneration of the NAD+ cofactor. With the second system, we intended full oxidation of n-butanol to butyric acid, generating one equivalent of H2 O2 that can be used for the oxidative decarboxylation. As the optimal substrate is a long-chain fatty acid, we also tried to create an improved variant for the decarboxylation of butyric acid by using rational protein design. Within a mutational study with 57 designed mutants, we generated the mutant OleTV292I , which showed a 2.4-fold improvement in propene production in our H2 O2 -driven cascade system and reached total turnover numbers >1000.
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Affiliation(s)
- Daniel Bauer
- Chair of Chemistry of Biogenic ResourcesCampus Straubing for Biotechnology and SustainabilityTechnical University of MunichSchulgasse 1694315StraubingGermany
| | - Ioannis Zachos
- Chair of Chemistry of Biogenic ResourcesCampus Straubing for Biotechnology and SustainabilityTechnical University of MunichSchulgasse 1694315StraubingGermany
| | - Volker Sieber
- Chair of Chemistry of Biogenic ResourcesCampus Straubing for Biotechnology and SustainabilityTechnical University of MunichSchulgasse 1694315StraubingGermany
- TUM Catalysis Research CenterTechnical University of MunichErnst-Otto-Fischer-Straße 185748GarchingGermany
- Bio, Electro and Chemocatalysis BioCat, Straubing BranchFraunhofer Institute for Interfacial Engineering and Biotechnology IGBSchulgasse 11a94315StraubingGermany
- School of Chemistry and Molecular Biosciences, Chemistry Building 68The University of QueenslandCooper RoadSt. Lucia4072QueenslandAustralia
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9
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Foo JL, Rasouliha BH, Susanto AV, Leong SSJ, Chang MW. Engineering an Alcohol-Forming Fatty Acyl-CoA Reductase for Aldehyde and Hydrocarbon Biosynthesis in Saccharomyces cerevisiae. Front Bioeng Biotechnol 2020; 8:585935. [PMID: 33123518 PMCID: PMC7573125 DOI: 10.3389/fbioe.2020.585935] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Accepted: 09/08/2020] [Indexed: 11/19/2022] Open
Abstract
Aldehydes are a class of highly versatile chemicals that can undergo a wide range of chemical reactions and are in high demand as starting materials for chemical manufacturing. Biologically, fatty aldehydes can be produced from fatty acyl-CoA by the action of fatty acyl-CoA reductases. The aldehydes produced can be further converted enzymatically to other valuable derivatives. Thus, metabolic engineering of microorganisms for biosynthesizing aldehydes and their derivatives could provide an economical and sustainable platform for key aldehyde precursor production and subsequent conversion to various value-added chemicals. Saccharomyces cerevisiae is an excellent host for this purpose because it is a robust organism that has been used extensively for industrial biochemical production. However, fatty acyl-CoA-dependent aldehyde-forming enzymes expressed in S. cerevisiae thus far have extremely low activities, hence limiting direct utilization of fatty acyl-CoA as substrate for aldehyde biosynthesis. Toward overcoming this challenge, we successfully engineered an alcohol-forming fatty acyl-CoA reductase for aldehyde production through rational design. We further improved aldehyde production through strain engineering by deleting competing pathways and increasing substrate availability. Subsequently, we demonstrated alkane and alkene production as one of the many possible applications of the aldehyde-producing strain. Overall, by protein engineering of a fatty acyl-CoA reductase to alter its activity and metabolic engineering of S. cerevisiae, we generated strains with the highest reported cytosolic aliphatic aldehyde and alkane/alkene production to date in S. cerevisiae from fatty acyl-CoA.
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Affiliation(s)
- Jee Loon Foo
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, Singapore, Singapore
| | - Bahareh Haji Rasouliha
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, Singapore, Singapore
| | - Adelia Vicanatalita Susanto
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, Singapore, Singapore
| | - Susanna Su Jan Leong
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, Singapore, Singapore.,Singapore Institute of Technology, Singapore, Singapore
| | - Matthew Wook Chang
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, Singapore, Singapore
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10
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Chen B, Foo JL, Ling H, Chang MW. Mechanism-Driven Metabolic Engineering for Bio-Based Production of Free R-Lipoic Acid in Saccharomyces cerevisiae Mitochondria. Front Bioeng Biotechnol 2020; 8:965. [PMID: 32974306 PMCID: PMC7468506 DOI: 10.3389/fbioe.2020.00965] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Accepted: 07/24/2020] [Indexed: 01/28/2023] Open
Abstract
Lipoic acid is a valuable organosulfur compound used as an antioxidant for dietary supplementation, and potentially anti-diabetic and anti-cancer. Currently, lipoic acid is obtained mainly through chemical synthesis, which requires toxic reagents and organic solvents, thus causing environmental issues. Moreover, chemically synthesized lipoic acid is conventionally a racemic mixture. To obtain enantiomerically pure R-lipoic acid, which has superior bioactivity than the S form, chiral resolution and asymmetric synthesis methods require additional reagents and solvents, and often lead to wastage of S-lipoic acid or precursors with undesired chirality. Toward sustainable production of R-lipoic acid, we aim to develop a synthetic biology-based method using engineered yeast. Here, we deepened mechanistic understanding of lipoic acid biosynthesis and protein lipoylation in the model yeast Saccharomyces cerevisiae to facilitate metabolic engineering of the microbe for producing free R-lipoic acid. In brief, we studied the biosynthesis and confirmed the availability of protein-bound lipoate in yeast cells through LC-MS/MS. We then characterized in vitro the activity of a lipoamidase from Enterococcus faecalis for releasing free R-lipoic acid from lipoate-modified yeast proteins. Overexpression of the lipoamidase in yeast mitochondria enabled de novo free R-lipoic acid production in vivo. By overexpressing pathway enzymes and regenerating the cofactor, the production titer was increased ∼2.9-fold. This study represents the first report of free R-lipoic acid biosynthesis in S. cerevisiae. We envision that these results could provide insights into lipoic acid biosynthesis in eukaryotic cells and drive development of sustainable R-lipoic acid production.
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Affiliation(s)
- Binbin Chen
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, Singapore, Singapore
| | - Jee Loon Foo
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, Singapore, Singapore
| | - Hua Ling
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, Singapore, Singapore
| | - Matthew Wook Chang
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, Singapore, Singapore
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11
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Dutta S. Hydro(deoxygenation) Reaction Network of Lignocellulosic Oxygenates. CHEMSUSCHEM 2020; 13:2894-2915. [PMID: 32134557 DOI: 10.1002/cssc.202000247] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Revised: 02/27/2020] [Indexed: 06/10/2023]
Abstract
Hydrodeoxygenation (HDO) is a key transformation step to convert lignocellulosic oxygenates into drop-in and functional high-value hydrocarbons through controlled oxygen removal. Nevertheless, the mechanistic insights of HDO chemistry have been scarcely investigated as opposed to a significant extent of hydrodesulfurization chemistry. Current requirements emphasize certain underexplored events of HDO of oxygenates, which include 1) interactions of oxygenates of varied molecular size with active sites of the catalysts, 2) determining the conformation of oxygenates on the active site at the point of interaction, and 3) effects of oxygen contents of oxygenates on the reaction rate of HDO. It is realized that the molecular interactions of oxygenates with the surface of the catalyst dominates the degree and nature of deoxygenation to derive products with desired selectivity by overcoming complex separation processes in a biorefinery. Those oxygenates with high carbon numbers (>C10), multiple furan rings, and branched architectures are even more complex to understand. This article aims to focus on concise mechanistic analysis of biorefinery oxygenates (C10-35 ) for their deoxygenation processes, with a special emphasis on their interactions with active sites in a complex chemical environment. This article also addresses differentiation of the mode of interactions based on the molecular size of oxygenates. Deoxygenation processes coupled with or without ring opening of furan-based oxygenates and site-substrate cooperativity dictate the formation of diverse value-added products. Oxygen removal has been the key step for microbial deoxygenation by the use of oxygen-removing decarbonylase enzymes. However, challenges to obtain branched and long-chain hydrocarbons remain, which require special attention, including the invention of newer techniques to upgrade the process for combined depolymerization-HDO from real biomass.
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Affiliation(s)
- Saikat Dutta
- Molecular Catalysis & Energy (MCR) Laboratory, Amity Institute Click Chemistry Research & Studies (AICCRS), Amity University, Sector 125, Noida, 201303, India
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12
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Hu Y, Zhu Z, Nielsen J, Siewers V. Engineering Saccharomyces cerevisiae cells for production of fatty acid-derived biofuels and chemicals. Open Biol 2020; 9:190049. [PMID: 31088249 PMCID: PMC6544985 DOI: 10.1098/rsob.190049] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The yeast Saccharomyces cerevisiae is a widely used cell factory for the production of fuels and chemicals, in particular ethanol, a biofuel produced in large quantities. With a need for high-energy-density fuels for jets and heavy trucks, there is, however, much interest in the biobased production of hydrocarbons that can be derived from fatty acids. Fatty acids also serve as precursors to a number of oleochemicals and hence provide interesting platform chemicals. Here, we review the recent strategies applied to metabolic engineering of S. cerevisiae for the production of fatty acid-derived biofuels and for improvement of the titre, rate and yield (TRY). This includes, for instance, redirection of the flux towards fatty acids through engineering of the central carbon metabolism, balancing the redox power and varying the chain length of fatty acids by enzyme engineering. We also discuss the challenges that currently hinder further TRY improvements and the potential solutions in order to meet the requirements for commercial application.
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Affiliation(s)
- Yating Hu
- 1 Department of Biology and Biological Engineering, Chalmers University of Technology , 41296 Gothenburg , Sweden.,2 Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology , 41296 Gothenburg , Sweden
| | - Zhiwei Zhu
- 1 Department of Biology and Biological Engineering, Chalmers University of Technology , 41296 Gothenburg , Sweden.,2 Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology , 41296 Gothenburg , Sweden
| | - Jens Nielsen
- 1 Department of Biology and Biological Engineering, Chalmers University of Technology , 41296 Gothenburg , Sweden.,2 Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology , 41296 Gothenburg , Sweden.,3 Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark , 2800 Kgs Lyngby , Denmark.,4 BioInnovation Institute , Ole Måløes Vej, 2200 Copenhagen N , Denmark
| | - Verena Siewers
- 1 Department of Biology and Biological Engineering, Chalmers University of Technology , 41296 Gothenburg , Sweden.,2 Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology , 41296 Gothenburg , Sweden
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13
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Building cell factories for the production of advanced fuels. Biochem Soc Trans 2020; 47:1701-1714. [PMID: 31803925 DOI: 10.1042/bst20190168] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Revised: 11/13/2019] [Accepted: 11/15/2019] [Indexed: 12/31/2022]
Abstract
Synthetic biology-based engineering strategies are being extensively employed for microbial production of advanced fuels. Advanced fuels, being comparable in energy efficiency and properties to conventional fuels, have been increasingly explored as they can be directly incorporated into the current fuel infrastructure without the need for reconstructing the pre-existing set-up rendering them economically viable. Multiple metabolic engineering approaches have been used for rewiring microbes to improve existing or develop newly programmed cells capable of efficient fuel production. The primary challenge in using these approaches is improving the product yield for the feasibility of the commercial processes. Some of the common roadblocks towards enhanced fuel production include - limited availability of flux towards precursors and desired pathways due to presence of competing pathways, limited cofactor and energy supply in cells, the low catalytic activity of pathway enzymes, obstructed product transport, and poor tolerance of host cells for end products. Consequently, despite extensive studies on the engineering of microbial hosts, the costs of industrial-scale production of most of these heterologously produced fuel compounds are still too high. Though considerable progress has been made towards successfully producing some of these biofuels, a substantial amount of work needs to be done for improving the titers of others. In this review, we have summarized the different engineering strategies that have been successfully used for engineering pathways into commercial hosts for the production of advanced fuels and different approaches implemented for tuning host strains and pathway enzymes for scaling up production levels.
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14
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Jaroensuk J, Intasian P, Wattanasuepsin W, Akeratchatapan N, Kesornpun C, Kittipanukul N, Chaiyen P. Enzymatic reactions and pathway engineering for the production of renewable hydrocarbons. J Biotechnol 2020; 309:1-19. [DOI: 10.1016/j.jbiotec.2019.12.010] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Revised: 12/14/2019] [Accepted: 12/15/2019] [Indexed: 01/23/2023]
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15
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Jiang Y, Li Z, Zheng S, Xu H, Zhou YJ, Gao Z, Meng C, Li S. Establishing an enzyme cascade for one-pot production of α-olefins from low-cost triglycerides and oils without exogenous H 2O 2 addition. BIOTECHNOLOGY FOR BIOFUELS 2020; 13:52. [PMID: 32190117 PMCID: PMC7075034 DOI: 10.1186/s13068-020-01684-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Accepted: 02/21/2020] [Indexed: 05/04/2023]
Abstract
BACKGROUND Biological α-olefins can be used as both biofuels and high value-added chemical precursors to lubricants, polymers, and detergents. The prototypic CYP152 peroxygenase family member OleTJE from Jeotgalicoccus sp. ATCC 8456 catalyzes a single-step decarboxylation of free fatty acids (FFAs) to form α-olefins using H2O2 as a cofactor, thus attracting much attention since its discovery. To improve the productivity of α-olefins, significant efforts on protein engineering, electron donor engineering, and metabolic engineering of OleTJE have been made. However, little success has been achieved in obtaining α-olefin high-producer microorganisms due to multiple reasons such as the tight regulation of FFA biosynthesis, the difficulty of manipulating multi-enzyme metabolic network, and the poor catalytic performance of OleTJE. RESULTS In this study, a novel enzyme cascade was developed for one-pot production of α-olefins from low-cost triacylglycerols (TAGs) and natural oils without exogenous H2O2 addition. This artificial biocatalytic route consists of a lipase (CRL, AOL or Lip2) for TAG hydrolysis to produce glycerol and free fatty acids (FFAs), an alditol oxidase (AldO) for H2O2 generation upon glycerol oxidation, and the P450 fatty acid decarboxylase OleTJE for FFA decarboxylation using H2O2 generated in situ. The multi-enzyme system was systematically optimized leading to the production of α-olefins with the conversion rates ranging from 37.2 to 68.5%. Furthermore, a reaction using lyophilized CRL/OleTJE/AldO enzymes at an optimized ratio (5 U/6 μM/30 μM) gave a promising α-olefin yield of 0.53 g/L from 1500 μM (~1 g/L) coconut oil. CONCLUSIONS The one-pot enzyme cascade was successfully established and applied to prepare high value-added α-olefins from low-cost and renewable TAGs/natural oils. This system is independent of exogenous addition of H2O2, thus not only circumventing the detrimental effect of H2O2 on the stability and activity of involved enzymes, but also lower the overall costs on the TAG-to-olefin transformation. It is anticipated that this biotransformation system will become industrially relevant in the future upon more engineering efforts based on this proof-of-concept work.
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Affiliation(s)
- Yuanyuan Jiang
- Shandong Provincial Key Laboratory of Synthetic Biology, CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Qingdao, 266101 Shandong China
- University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Zhong Li
- Shandong Provincial Key Laboratory of Synthetic Biology, CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Qingdao, 266101 Shandong China
- University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Shanmin Zheng
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237 Shandong China
- School of Life Sciences, Shandong University of Technology, Zibo, 255000 Shandong China
| | - Huifang Xu
- Shandong Provincial Key Laboratory of Synthetic Biology, CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Qingdao, 266101 Shandong China
| | - Yongjin J. Zhou
- Division of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023 Liaoning China
| | - Zhengquan Gao
- School of Life Sciences, Shandong University of Technology, Zibo, 255000 Shandong China
| | - Chunxiao Meng
- School of Life Sciences, Shandong University of Technology, Zibo, 255000 Shandong China
| | - Shengying Li
- Shandong Provincial Key Laboratory of Synthetic Biology, CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Qingdao, 266101 Shandong China
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237 Shandong China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237 Shandong China
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16
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Engineering Yarrowia lipolytica towards food waste bioremediation: Production of fatty acid ethyl esters from vegetable cooking oil. J Biosci Bioeng 2020; 129:31-40. [DOI: 10.1016/j.jbiosc.2019.06.009] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Revised: 06/06/2019] [Accepted: 06/12/2019] [Indexed: 11/22/2022]
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17
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Continuous photoproduction of hydrocarbon drop-in fuel by microbial cell factories. Sci Rep 2019; 9:13713. [PMID: 31548626 PMCID: PMC6757031 DOI: 10.1038/s41598-019-50261-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Accepted: 09/09/2019] [Indexed: 11/20/2022] Open
Abstract
Use of microbes to produce liquid transportation fuels is not yet economically viable. A key point to reduce production costs is the design a cell factory that combines the continuous production of drop-in fuel molecules with the ability to recover products from the cell culture at low cost. Medium-chain hydrocarbons seem ideal targets because they can be produced from abundant fatty acids and, due to their volatility, can be easily collected in gas phase. However, pathways used to produce hydrocarbons from fatty acids require two steps, low efficient enzymes and/or complex electron donors. Recently, a new hydrocarbon-forming route involving a single enzyme called fatty acid photodecarboxylase (FAP) was discovered in microalgae. Here, we show that in illuminated E. coli cultures coexpression of FAP and a medium-chain fatty acid thioesterase results in continuous release of volatile hydrocarbons. Maximum hydrocarbon productivity was reached under low/medium light while higher irradiance resulted in decreased amounts of FAP. It was also found that the production rate of hydrocarbons was constant for at least 5 days and that 30% of total hydrocarbons could be collected in the gas phase of the culture. This work thus demonstrates that the photochemistry of the FAP can be harnessed to design a simple cell factory that continuously produces hydrocarbons easy to recover and in pure form.
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18
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Yang K, Qiao Y, Li F, Xu Y, Yan Y, Madzak C, Yan J. Subcellular engineering of lipase dependent pathways directed towards lipid related organelles for highly effectively compartmentalized biosynthesis of triacylglycerol derived products in Yarrowia lipolytica. Metab Eng 2019; 55:231-238. [DOI: 10.1016/j.ymben.2019.08.001] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Revised: 07/11/2019] [Accepted: 08/02/2019] [Indexed: 11/25/2022]
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19
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Bruder S, Moldenhauer EJ, Lemke RD, Ledesma-Amaro R, Kabisch J. Drop-in biofuel production using fatty acid photodecarboxylase from Chlorella variabilis in the oleaginous yeast Yarrowia lipolytica. BIOTECHNOLOGY FOR BIOFUELS 2019; 12:202. [PMID: 31462926 PMCID: PMC6708191 DOI: 10.1186/s13068-019-1542-4] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Accepted: 08/10/2019] [Indexed: 05/14/2023]
Abstract
BACKGROUND Oleaginous yeasts are potent hosts for the renewable production of lipids and harbor great potential for derived products, such as biofuels. Several promising processes have been described that produce hydrocarbon drop-in biofuels based on fatty acid decarboxylation and fatty aldehyde decarbonylation. Unfortunately, besides fatty aldehyde toxicity and high reactivity, the most investigated enzyme, aldehyde-deformylating oxygenase, shows unfavorable catalytic properties which hindered high yields in previous metabolic engineering approaches. RESULTS To demonstrate an alternative alkane production pathway for oleaginous yeasts, we describe the production of diesel-like, odd-chain alkanes and alkenes, by heterologously expressing a recently discovered light-driven oxidase from Chlorella variabilis (CvFAP) in Yarrowia lipolytica. Initial experiments showed that only strains engineered to have an increased pool of free fatty acids were susceptible to sufficient decarboxylation. Providing these strains with glucose and light in a synthetic medium resulted in titers of 10.9 mg/L of hydrocarbons. Using custom 3D printed labware for lighting bioreactors, and an automated pulsed glycerol fed-batch strategy, intracellular titers of 58.7 mg/L were achieved. The production of odd-numbered alkanes and alkenes with a length of 17 and 15 carbons shown in previous studies could be confirmed. CONCLUSIONS Oleaginous yeasts such as Yarrowia lipolytica can transform renewable resources such as glycerol into fatty acids and lipids. By heterologously expressing a fatty acid photodecarboxylase from the algae Chlorella variabilis hydrocarbons were produced in several scales from microwell plate to 400 mL bioreactors. The lighting turned out to be a crucial factor in terms of growth and hydrocarbon production, therefore, the evaluation of different conditions was an important step towards a tailor-made process. In general, the developed bioprocess shows a route to the renewable production of hydrocarbons for a variety of applications ranging from being substrates for further enzymatic or chemical modification or as a drop-in biofuel blend.
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Affiliation(s)
- Stefan Bruder
- Computer-Aided Synthetic Biology, Technische Universität Darmstadt, Schnittspahnstr. 12, 64287 Darmstadt, Germany
| | - Eva Johanna Moldenhauer
- Computer-Aided Synthetic Biology, Technische Universität Darmstadt, Schnittspahnstr. 12, 64287 Darmstadt, Germany
| | - Robert Denis Lemke
- Computer-Aided Synthetic Biology, Technische Universität Darmstadt, Schnittspahnstr. 12, 64287 Darmstadt, Germany
| | - Rodrigo Ledesma-Amaro
- Department of Bioengineering and Imperial College Centre for Synthetic Biology, Imperial College London, London, UK
| | - Johannes Kabisch
- Computer-Aided Synthetic Biology, Technische Universität Darmstadt, Schnittspahnstr. 12, 64287 Darmstadt, Germany
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20
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Yan Q, Pfleger BF. Revisiting metabolic engineering strategies for microbial synthesis of oleochemicals. Metab Eng 2019; 58:35-46. [PMID: 31022535 DOI: 10.1016/j.ymben.2019.04.009] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Revised: 04/20/2019] [Accepted: 04/21/2019] [Indexed: 02/06/2023]
Abstract
Microbial production of oleochemicals from renewable feedstocks remains an attractive route to produce high-energy density, liquid transportation fuels and high-value chemical products. Metabolic engineering strategies have been applied to demonstrate production of a wide range of oleochemicals, including free fatty acids, fatty alcohols, esters, olefins, alkanes, ketones, and polyesters in both bacteria and yeast. The majority of these demonstrations synthesized products containing long-chain fatty acids. These successes motivated additional effort to produce analogous molecules comprised of medium-chain fatty acids, molecules that are less common in natural oils and therefore of higher commercial value. Substantial progress has been made towards producing a subset of these chemicals, but significant work remains for most. The other primary challenge to producing oleochemicals in microbes is improving the performance, in terms of yield, rate, and titer, of biocatalysts such that economic large-scale processes are feasible. Common metabolic engineering strategies include blocking pathways that compete with synthesis of oleochemical building blocks and/or consume products, pulling flux through pathways by removing regulatory signals, pushing flux into biosynthesis by overexpressing rate-limiting enzymes, and engineering cells to tolerate the presence of oleochemical products. In this review, we describe the basic fundamentals of oleochemical synthesis and summarize advances since 2013 towards improving performance of heterotrophic microbial cell factories.
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Affiliation(s)
- Qiang Yan
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI 53706, United States; DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Wisconsin-Madison, Madison, WI 53706, United States
| | - Brian F Pfleger
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI 53706, United States; DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Wisconsin-Madison, Madison, WI 53706, United States; Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, WI 53706, United States.
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21
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Synthetic metabolic pathway for the production of 1-alkenes from lignin-derived molecules. Microb Cell Fact 2019; 18:48. [PMID: 30857542 PMCID: PMC6410514 DOI: 10.1186/s12934-019-1097-x] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Accepted: 02/28/2019] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Integration of synthetic metabolic pathways to catabolically diverse chassis provides new opportunities for sustainable production. One attractive scenario is the use of abundant waste material to produce a readily collectable product, which can reduce the production costs. Towards that end, we established a cellular platform for the production of semivolatile medium-chain α-olefins from lignin-derived molecules: we constructed 1-undecene synthesis pathway in Acinetobacter baylyi ADP1 using ferulate, a lignin-derived model compound, as the sole carbon source for both cell growth and product synthesis. RESULTS In order to overcome the toxicity of ferulate, we first applied adaptive laboratory evolution to A. baylyi ADP1, resulting in a highly ferulate-tolerant strain. The adapted strain exhibited robust growth in 100 mM ferulate while the growth of the wild type strain was completely inhibited. Next, we expressed two heterologous enzymes in the wild type strain to confer 1-undecene production from glucose: a fatty acid decarboxylase UndA from Pseudomonas putida, and a thioesterase 'TesA from Escherichia coli. Finally, we constructed the 1-undecene synthesis pathway in the ferulate-tolerant strain. The engineered cells were able to produce biomass and 1-undecene solely from ferulate, and excreted the product directly to the culture headspace. CONCLUSIONS In this study, we employed a bacterium Acinetobacter baylyi ADP1 to integrate a natural aromatics degrading pathway to a synthetic production route, allowing the upgradation of lignin derived molecules to value-added products. We developed a highly ferulate-tolerant strain and established the biosynthesis of an industrially relevant chemical, 1-undecene, solely from the lignin-derived model compound. This study reports the production of alkenes from lignin derived molecules for the first time and demonstrates the potential of lignin as a sustainable resource in the bio-based synthesis of valuable products.
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22
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Nusantara Putra FJ, Putri SP, Fukusaki E. Metabolomics-based profiling of three terminal alkene-producing Jeotgalicoccus spp. during different growth phase. J Biosci Bioeng 2019; 127:52-58. [DOI: 10.1016/j.jbiosc.2018.06.014] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Revised: 06/13/2018] [Accepted: 06/19/2018] [Indexed: 10/28/2022]
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23
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Li F, Yang K, Xu Y, Qiao Y, Yan Y, Yan J. A genetically-encoded synthetic self-assembled multienzyme complex of lipase and P450 fatty acid decarboxylase for efficient bioproduction of fatty alkenes. BIORESOURCE TECHNOLOGY 2019; 272:451-457. [PMID: 30390537 DOI: 10.1016/j.biortech.2018.10.067] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2018] [Revised: 10/24/2018] [Accepted: 10/25/2018] [Indexed: 05/21/2023]
Abstract
We develop an efficient and economic cascade multienzymes for fatty alkene bioproduction based on the lipase hydrolysis coupled to the P450 decarboxylation in the form of multiple enzyme complex. One step preparation of a multienzyme complex was based on a mixture of cell extracts including dockerin-enzyme fusions and one cohesin-cellulose binding module (CBM) fusion through high specific interaction of dockerin and cohesin. Simultaneously, the CBM was bound to cellulose carrier to form co-immobilized multienzyme. The key factors affecting overall efficiency of alkene bioproduction including substrate channeling of hydrolysis and decarboxylation, the ratio and position of two enzymes, stability were all addressed by genetically engineering of the synthetic CBM-cohesin fusions. The multienzymes exhibited more than 9.2 fold enhancement in initial reaction rate and much higher conversion yields (69%-72%) compared to mixture of free enzyme counterpart. The enzymatic cascade based multienzymes could efficiently convert renewable triglycerides to alkenes.
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Affiliation(s)
- Fei Li
- Key Lab of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, 1037 Luoyu Road, Wuhan 430074, China
| | - Kaixin Yang
- Key Lab of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, 1037 Luoyu Road, Wuhan 430074, China
| | - Yun Xu
- Key Lab of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, 1037 Luoyu Road, Wuhan 430074, China
| | - Yangge Qiao
- Key Lab of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, 1037 Luoyu Road, Wuhan 430074, China
| | - Yunjun Yan
- Key Lab of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, 1037 Luoyu Road, Wuhan 430074, China
| | - Jinyong Yan
- Key Lab of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, 1037 Luoyu Road, Wuhan 430074, China; Shenzhen Huazhong University of Science and Technology Research Institute, Shenzhen Production and Research Base Block B, No. 9 Avenue 3 Yuexing, Yuehai Street, Nanshan District, Shenzhen 518057, China.
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24
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Lee JW, Niraula NP, Trinh CT. Harnessing a P450 fatty acid decarboxylase from Macrococcus caseolyticus for microbial biosynthesis of odd chain terminal alkenes. Metab Eng Commun 2018; 7:e00076. [PMID: 30197865 PMCID: PMC6127365 DOI: 10.1016/j.mec.2018.e00076] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2018] [Revised: 07/23/2018] [Accepted: 07/23/2018] [Indexed: 12/21/2022] Open
Abstract
Alkenes are industrially important platform chemicals with broad applications. In this study, we report a direct microbial biosynthesis of terminal alkenes from fermentable sugars by harnessing a P450 fatty acid (FA) decarboxylase from Macrococcus caseolyticus (OleTMC). We first characterized OleTMC and demonstrated its in vitro H2O2-independent activities towards linear C10:0-C18:0 FAs, with higher activity for C16:0-C18:0 FAs. Next, we engineered a de novo alkene biosynthesis pathway, consisting of OleTMC and an engineered E. coli thioesterase (TesA) with compatible substrate specificities, and introduced this pathway into E. coli for terminal alkene biosynthesis from glucose. The recombinant E. coli EcNN101 produced a total of 17.78 ± 0.63 mg/L odd-chain terminal alkenes, comprising of 0.9% ± 0.5% C11 alkene, 12.7% ± 2.2% C13 alkene, 82.7% ± 1.7% C15 alkene, and 3.7% ± 0.8% C17 alkene, and a yield of 0.87 ± 0.03 (mg/g) on glucose. To improve alkene production, we identified and overcame the electron transfer limitation in OleTMC, by introducing a two-component redox system, consisting of a putidaredoxin reductase (CamA) and a putidaredoxin (CamB) from Pseudomonas putida, into EcNN101, and demonstrated the alkene production increased ~2.8 fold. Finally, to better understand the substrate specificities of OleTMC observed, we employed in silico protein modeling to illuminate the functional role of FA binding pocket.
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Affiliation(s)
- Jong-Won Lee
- Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee, Knoxville, TN, USA
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Narayan P. Niraula
- Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, TN, USA
| | - Cong T. Trinh
- Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee, Knoxville, TN, USA
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, USA
- Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, TN, USA
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25
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Wise CE, Hsieh CH, Poplin NL, Makris TM. Dioxygen Activation by the Biofuel-Generating Cytochrome P450 OleT. ACS Catal 2018. [DOI: 10.1021/acscatal.8b02631] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Courtney E. Wise
- University of South Carolina, Department of Chemistry and Biochemistry, 631 Sumter Street, Columbia, South Carolina 29208, United States
| | - Chun H. Hsieh
- University of South Carolina, Department of Chemistry and Biochemistry, 631 Sumter Street, Columbia, South Carolina 29208, United States
| | - Nathan L. Poplin
- University of South Carolina, Department of Chemistry and Biochemistry, 631 Sumter Street, Columbia, South Carolina 29208, United States
| | - Thomas M. Makris
- University of South Carolina, Department of Chemistry and Biochemistry, 631 Sumter Street, Columbia, South Carolina 29208, United States
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26
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Young EM, Zhao Z, Gielesen BE, Wu L, Benjamin Gordon D, Roubos JA, Voigt CA. Iterative algorithm-guided design of massive strain libraries, applied to itaconic acid production in yeast. Metab Eng 2018; 48:33-43. [DOI: 10.1016/j.ymben.2018.05.002] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Revised: 05/04/2018] [Accepted: 05/04/2018] [Indexed: 11/25/2022]
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27
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Zhang Y, Nielsen J, Liu Z. Metabolic engineering ofSaccharomyces cerevisiaefor production of fatty acid–derived hydrocarbons. Biotechnol Bioeng 2018; 115:2139-2147. [DOI: 10.1002/bit.26738] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Revised: 05/23/2018] [Accepted: 05/31/2018] [Indexed: 01/13/2023]
Affiliation(s)
- Yiming Zhang
- Beijing Innovation Center for Soft Matter Science and EngineeringBeijing University of Chemical Technology Beijing China
| | - Jens Nielsen
- Beijing Innovation Center for Soft Matter Science and EngineeringBeijing University of Chemical Technology Beijing China
- Department of Biology and Biological EngineeringChalmers University of TechnologyGothenburg Sweden
- Novo Nordisk Foundation Center for BiosustainabilityTechnical University of Denmark Hørsholm Denmark
| | - Zihe Liu
- Beijing Innovation Center for Soft Matter Science and EngineeringBeijing University of Chemical Technology Beijing China
- College of Life Science and Technology, Beijing University of Chemical TechnologyBeijing China
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28
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Wang J, Zhu K. Microbial production of alka(e)ne biofuels. Curr Opin Biotechnol 2018; 50:11-18. [DOI: 10.1016/j.copbio.2017.08.009] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Revised: 08/14/2017] [Accepted: 08/14/2017] [Indexed: 10/18/2022]
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29
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Zhou YJ, Hu Y, Zhu Z, Siewers V, Nielsen J. Engineering 1-Alkene Biosynthesis and Secretion by Dynamic Regulation in Yeast. ACS Synth Biol 2018; 7:584-590. [PMID: 29284088 DOI: 10.1021/acssynbio.7b00338] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Microbial production of fatty acid-derived hydrocarbons offers a great opportunity to sustainably supply biofuels and oleochemicals. One challenge is to achieve a high production rate. Besides, low efficiency in secretion will cause high separation costs, and it is therefore desirable to have product secretion. Here, we engineered the budding yeast Saccharomyces cerevisiae to produce and secrete 1-alkenes by manipulation of the fatty acid metabolism, enzyme selection, engineering the electron transfer system and expressing a transporter. Furthermore, we implemented a dynamic regulation strategy to control the expression of membrane enzyme and transporter, which improved 1-alkene production and cell growth by relieving the possible toxicity of overexpressed membrane proteins. With these efforts, the engineered yeast cell factory produced 35.3 mg/L 1-alkenes with more than 80% being secreted. This represents a 10-fold improvement compared with earlier reported hydrocarbon production by S. cerevisiae.
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Affiliation(s)
- Yongjin J. Zhou
- Division
of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, PR China
- Department
of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, SE-41296 Gothenburg, Sweden
| | - Yating Hu
- Department
of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, SE-41296 Gothenburg, Sweden
- Novo
Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, SE-41296 Gothenburg, Sweden
| | - Zhiwei Zhu
- Department
of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, SE-41296 Gothenburg, Sweden
- Novo
Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, SE-41296 Gothenburg, Sweden
| | - Verena Siewers
- Department
of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, SE-41296 Gothenburg, Sweden
- Novo
Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, SE-41296 Gothenburg, Sweden
| | - Jens Nielsen
- Department
of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, SE-41296 Gothenburg, Sweden
- Novo
Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, SE-41296 Gothenburg, Sweden
- Novo
Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
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30
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Microbial synthesis of medium-chain chemicals from renewables. Nat Biotechnol 2017; 35:1158-1166. [PMID: 29220020 DOI: 10.1038/nbt.4022] [Citation(s) in RCA: 83] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Accepted: 10/31/2017] [Indexed: 12/28/2022]
Abstract
Linear, medium-chain (C8-C12) hydrocarbons are important components of fuels as well as commodity and specialty chemicals. As industrial microbes do not contain pathways to produce medium-chain chemicals, approaches such as overexpression of endogenous enzymes or deletion of competing pathways are not available to the metabolic engineer; instead, fatty acid synthesis and reversed β-oxidation are manipulated to synthesize medium-chain chemical precursors. Even so, chain lengths remain difficult to control, which means that purification must be used to obtain the desired products, titers of which are typically low and rarely exceed milligrams per liter. By engineering the substrate specificity and activity of the pathway enzymes that generate the fatty acyl intermediates and chain-tailoring enzymes, researchers can boost the type and yield of medium-chain chemicals. Development of technologies to both manipulate chain-tailoring enzymes and to assay for products promises to enable the generation of g/L yields of medium-chain chemicals.
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31
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Wang M, Chen B, Fang Y, Tan T. Cofactor engineering for more efficient production of chemicals and biofuels. Biotechnol Adv 2017; 35:1032-1039. [DOI: 10.1016/j.biotechadv.2017.09.008] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Revised: 09/14/2017] [Accepted: 09/15/2017] [Indexed: 01/04/2023]
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32
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Engineering microbial fatty acid metabolism for biofuels and biochemicals. Curr Opin Biotechnol 2017; 50:39-46. [PMID: 29101852 DOI: 10.1016/j.copbio.2017.10.002] [Citation(s) in RCA: 86] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Revised: 10/06/2017] [Accepted: 10/09/2017] [Indexed: 11/22/2022]
Abstract
Traditional oleochemical industry chemically processes animal fats and plant oils to produce detergents, lubricants, biodiesel, plastics, coatings, and other products. Biotechnology offers an alternative process, where the same oleochemicals can be produced from abundant biomass feedstocks using microbial catalysis. This review summarizes the recent advances in the engineering of microbial metabolism for production of fatty acid-derived products. We highlight the efforts in engineering the central carbon metabolism, redox metabolism, controlling the chain length of the products, and obtaining metabolites with different functionalities. The prospects of commercializing microbial oleochemicals are also discussed.
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33
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Jin E, Wong L, Jiao Y, Engel J, Holdridge B, Xu P. Rapid evolution of regulatory element libraries for tunable transcriptional and translational control of gene expression. Synth Syst Biotechnol 2017; 2:295-301. [PMID: 29552654 PMCID: PMC5851936 DOI: 10.1016/j.synbio.2017.10.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2017] [Revised: 10/12/2017] [Accepted: 10/12/2017] [Indexed: 12/16/2022] Open
Abstract
Engineering cell factories for producing biofuels and pharmaceuticals has spurred great interests to develop rapid and efficient synthetic biology tools customized for modular pathway engineering. Along the way, combinatorial gene expression control through modification of regulatory element offered tremendous opportunity for fine-tuning gene expression and generating digital-like genetic circuits. In this report, we present an efficient evolutionary approach to build a range of regulatory control elements. The reported method allows for rapid construction of promoter, 5'UTR, terminator and trans-activating RNA libraries. Synthetic overlapping oligos with high portion of degenerate nucleotides flanking the regulatory element could be efficiently assembled to a vector expressing fluorescence reporter. This approach combines high mutation rate of the synthetic DNA with the high assembly efficiency of Gibson Mix. Our constructed library demonstrates broad range of transcriptional or translational gene expression dynamics. Specifically, both the promoter library and 5'UTR library exhibits gene expression dynamics spanning across three order of magnitude. The terminator library and trans-activating RNA library displays relatively narrowed gene expression pattern. The reported study provides a versatile toolbox for rapidly constructing a large family of prokaryotic regulatory elements. These libraries also facilitate the implementation of combinatorial pathway engineering principles and the engineering of more efficient microbial cell factory for various biomanufacturing applications.
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Affiliation(s)
- Erqing Jin
- Department of Chemical, Biochemical and Environmental Engineering, University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, MD 21250, United States.,Department of Food Science and Engineering, Jinan University, 601 West Huangpu Road, Guangzhou 510632, China
| | - Lynn Wong
- Department of Chemical, Biochemical and Environmental Engineering, University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, MD 21250, United States
| | - Yun Jiao
- Department of Chemical, Biochemical and Environmental Engineering, University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, MD 21250, United States
| | - Jake Engel
- Department of Chemical, Biochemical and Environmental Engineering, University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, MD 21250, United States
| | - Benjamin Holdridge
- Department of Chemical, Biochemical and Environmental Engineering, University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, MD 21250, United States
| | - Peng Xu
- Department of Chemical, Biochemical and Environmental Engineering, University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, MD 21250, United States
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Zhu Z, Zhou YJ, Kang MK, Krivoruchko A, Buijs NA, Nielsen J. Enabling the synthesis of medium chain alkanes and 1-alkenes in yeast. Metab Eng 2017; 44:81-88. [PMID: 28939277 DOI: 10.1016/j.ymben.2017.09.007] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Revised: 09/11/2017] [Accepted: 09/13/2017] [Indexed: 01/15/2023]
Abstract
Microbial synthesis of medium chain aliphatic hydrocarbons, attractive drop-in molecules to gasoline and jet fuels, is a promising way to reduce our reliance on petroleum-based fuels. In this study, we enabled the synthesis of straight chain hydrocarbons (C7-C13) by yeast Saccharomyces cerevisiae through engineering fatty acid synthases to control the chain length of fatty acids and introducing heterologous pathways for alkane or 1-alkene synthesis. We carried out enzyme engineering/screening of the fatty aldehyde deformylating oxygenase (ADO), and compartmentalization of the alkane biosynthesis pathway into peroxisomes to improve alkane production. The two-step synthesis of alkanes was found to be inefficient due to the formation of alcohols derived from aldehyde intermediates. Alternatively, the drain of aldehyde intermediates could be circumvented by introducing a one-step decarboxylation of fatty acids to 1-alkenes, which could be synthesized at a level of 3mg/L, 25-fold higher than that of alkanes produced via aldehydes.
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Affiliation(s)
- Zhiwei Zhu
- Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, SE-41296 Gothenburg, Sweden; Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, SE-41296 Gothenburg, Sweden
| | - Yongjin J Zhou
- Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, SE-41296 Gothenburg, Sweden; Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, SE-41296 Gothenburg, Sweden
| | - Min-Kyoung Kang
- Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, SE-41296 Gothenburg, Sweden; Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, SE-41296 Gothenburg, Sweden
| | - Anastasia Krivoruchko
- Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, SE-41296 Gothenburg, Sweden; Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, SE-41296 Gothenburg, Sweden
| | - Nicolaas A Buijs
- Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, SE-41296 Gothenburg, Sweden; Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, SE-41296 Gothenburg, Sweden
| | - Jens Nielsen
- Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, SE-41296 Gothenburg, Sweden; Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, SE-41296 Gothenburg, Sweden; Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2970 Hørsholm, Denmark; Science for Life Laboratory, Royal Institute of Technology, SE-17121 Stockholm, Sweden.
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35
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Fernandez-Moya R, Da Silva NA. Engineering Saccharomyces cerevisiae for high-level synthesis of fatty acids and derived products. FEMS Yeast Res 2017; 17:4111148. [DOI: 10.1093/femsyr/fox071] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Accepted: 09/10/2017] [Indexed: 01/16/2023] Open
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36
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Metabolic engineering of Saccharomyces cerevisiae for production of very long chain fatty acid-derived chemicals. Nat Commun 2017; 8:15587. [PMID: 28548095 PMCID: PMC5458556 DOI: 10.1038/ncomms15587] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2016] [Accepted: 04/04/2017] [Indexed: 12/27/2022] Open
Abstract
Production of chemicals and biofuels through microbial fermentation is an economical and sustainable alternative for traditional chemical synthesis. Here we present the construction of a Saccharomyces cerevisiae platform strain for high-level production of very-long-chain fatty acid (VLCFA)-derived chemicals. Through rewiring the native fatty acid elongation system and implementing a heterologous Mycobacteria FAS I system, we establish an increased biosynthesis of VLCFAs in S. cerevisiae. VLCFAs can be selectively modified towards the fatty alcohol docosanol (C22H46O) by expressing a specific fatty acid reductase. Expression of this enzyme is shown to impair cell growth due to consumption of VLCFA-CoAs. We therefore implement a dynamic control strategy for separating cell growth from docosanol production. We successfully establish high-level and selective docosanol production of
83.5 mg l−1 in yeast. This approach will provide a universal strategy towards the production of similar high value chemicals in a more scalable, stable and sustainable manner. Production of chemicals by microbial fermentation is an economical alternative to chemical synthesis. Here the authors re-engineer the yeast S. cerevisiae to produce the very long chain fatty alcohol docosanol by expressing a heterologous Mycobacteria fatty acid synthase and a specific fatty acid reductase.
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37
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Mutagenesis and redox partners analysis of the P450 fatty acid decarboxylase OleT JE. Sci Rep 2017; 7:44258. [PMID: 28276499 PMCID: PMC5343568 DOI: 10.1038/srep44258] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2017] [Accepted: 02/06/2017] [Indexed: 02/04/2023] Open
Abstract
The cytochrome P450 enzyme OleTJE from Jeotgalicoccus sp. ATCC 8456 is capable of converting free long-chain fatty acids into α-alkenes via one-step oxidative decarboxylation in presence of H2O2 as cofactor or using redox partner systems. This enzyme has attracted much attention due to its intriguing but unclear catalytic mechanism and potential application in biofuel production. Here, we investigated the functionality of a select group of residues (Arg245, Cys365, His85, and Ile170) in the active site of OleTJE through extensive mutagenesis analysis. The key roles of these residues for catalytic activity and reaction type selectivity were identified. In addition, a range of heterologous redox partners were found to be able to efficiently support the decarboxylation activity of OleTJE. The best combination turned out to be SeFdx-6 (ferredoxin) from Synechococcus elongatus PCC 7942 and CgFdR-2 (ferredoxin reductase) from Corynebacterium glutamicum ATCC 13032, which gave the highest myristic acid conversion rate of 94.4%. Moreover, Michaelis-Menton kinetic parameters of OleTJE towards myristic acid were determined.
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38
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Xu P, Rizzoni EA, Sul SY, Stephanopoulos G. Improving Metabolic Pathway Efficiency by Statistical Model-Based Multivariate Regulatory Metabolic Engineering. ACS Synth Biol 2017; 6:148-158. [PMID: 27490704 DOI: 10.1021/acssynbio.6b00187] [Citation(s) in RCA: 83] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Metabolic engineering entails target modification of cell metabolism to maximize the production of a specific compound. For empowering combinatorial optimization in strain engineering, tools and algorithms are needed to efficiently sample the multidimensional gene expression space and locate the desirable overproduction phenotype. We addressed this challenge by employing design of experiment (DoE) models to quantitatively correlate gene expression with strain performance. By fractionally sampling the gene expression landscape, we statistically screened the dominant enzyme targets that determine metabolic pathway efficiency. An empirical quadratic regression model was subsequently used to identify the optimal gene expression patterns of the investigated pathway. As a proof of concept, our approach yielded the natural product violacein at 525.4 mg/L in shake flasks, a 3.2-fold increase from the baseline strain. Violacein production was further increased to 1.31 g/L in a controlled benchtop bioreactor. We found that formulating discretized gene expression levels into logarithmic variables (Linlog transformation) was essential for implementing this DoE-based optimization procedure. The reported methodology can aid multivariate combinatorial pathway engineering and may be generalized as a standard procedure for accelerating strain engineering and improving metabolic pathway efficiency.
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Affiliation(s)
- Peng Xu
- Department
of Chemical Engineering, Massachusetts Institute of Technology, 77 Massachusetts
Avenue, Cambridge, Massachusetts 02139, United States
| | - Elizabeth Anne Rizzoni
- Department
of Chemistry, Wellesley College, 106 Central Street, Wellesley, Massachusetts 02481, United States
| | - Se-Yeong Sul
- Department
of Chemical Engineering, Massachusetts Institute of Technology, 77 Massachusetts
Avenue, Cambridge, Massachusetts 02139, United States
| | - Gregory Stephanopoulos
- Department
of Chemical Engineering, Massachusetts Institute of Technology, 77 Massachusetts
Avenue, Cambridge, Massachusetts 02139, United States
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39
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Xu H, Ning L, Yang W, Fang B, Wang C, Wang Y, Xu J, Collin S, Laeuffer F, Fourage L, Li S. In vitro oxidative decarboxylation of free fatty acids to terminal alkenes by two new P450 peroxygenases. BIOTECHNOLOGY FOR BIOFUELS 2017; 10:208. [PMID: 28912830 PMCID: PMC5588734 DOI: 10.1186/s13068-017-0894-x] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Accepted: 08/28/2017] [Indexed: 05/21/2023]
Abstract
BACKGROUND P450 fatty acid decarboxylases represented by the unusual CYP152 peroxygenase family member OleTJE have been receiving great attention recently since these P450 enzymes are able to catalyze the simple and direct production of 1-alkenes for potential applications in biofuels and biomaterials. To gain more mechanistic insights, broader substrate spectra, and improved decarboxylative activities, it is demanded to discover and investigate more P450 fatty acid decarboxylases. RESULTS Here, we describe for the first time the expression, purification, and in vitro biochemical characterization of two new CYP152 peroxygenases, CYP-Aa162 and CYP-Sm46Δ29, that are capable of decarboxylating straight-chain saturated fatty acids. Both enzymes were found to catalyze the decarboxylation and hydroxylation of a broad range of free fatty acids (C10-C20) with overlapping substrate specificity, yet distinct chemoselectivity. CYP-Sm46Δ29 works primarily as a fatty (lauric) acid decarboxylase (66.1 ± 3.9% 1-undecene production) while CYP-Aa162 more as a fatty (lauric) acid hydroxylase (72.2 ± 0.9% hydroxy lauric acid production). Notably, the optical spectroscopic analysis of functional CYP-Sm46Δ29 revealed no characteristic P450 band, suggesting a unique heme coordination environment. Active-site mutagenesis analysis showed that substitution with the proposed key decarboxylation-modulating residues, His85 and Ile170, enhanced the decarboxylation activity of CYP-Aa162 and P450BSβ, emphasizing the importance of these residues in directing the decarboxylation pathway. Furthermore, the steady-state kinetic analysis of CYP-Aa162 and CYP-Sm46Δ29 revealed both cooperative and substrate inhibition behaviors which are substrate carbon chain length dependent. CONCLUSIONS Our data identify CYP-Sm46Δ29 as an efficient OleTJE-like fatty acid decarboxylase. Oxidative decarboxylation chemoselectivity of the CYP152 decarboxylases is largely dependent upon the carbon chain length of fatty acid substrates and their precise positioning in the enzyme active site. Finally, the kinetic mode analysis of the enzymes could provide important guidance for future process design.
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Affiliation(s)
- Huifang Xu
- Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Qingdao, 266101 Shandong China
- CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Qingdao, 266101 Shandong China
| | - Linlin Ning
- Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Qingdao, 266101 Shandong China
- CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Qingdao, 266101 Shandong China
- University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Wenxia Yang
- Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Qingdao, 266101 Shandong China
- CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Qingdao, 266101 Shandong China
| | - Bo Fang
- Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Qingdao, 266101 Shandong China
- CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Qingdao, 266101 Shandong China
| | - Cong Wang
- Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Qingdao, 266101 Shandong China
- CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Qingdao, 266101 Shandong China
| | - Yun Wang
- CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Qingdao, 266101 Shandong China
- Single-Cell Center, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Qingdao, 266101 Shandong China
| | - Jian Xu
- CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Qingdao, 266101 Shandong China
- Single-Cell Center, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Qingdao, 266101 Shandong China
| | - Severine Collin
- Total Refinery and Chemistry, SDR/Biofuels, Tour Coupole, 2, PI. Jean Millier, 92400 Courbevoie, France
| | - Frederic Laeuffer
- Total Refinery and Chemistry, SDR/Biofuels, Tour Coupole, 2, PI. Jean Millier, 92400 Courbevoie, France
| | - Laurent Fourage
- Total Refinery and Chemistry, SDR/Biofuels, Tour Coupole, 2, PI. Jean Millier, 92400 Courbevoie, France
| | - Shengying Li
- Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Qingdao, 266101 Shandong China
- CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Qingdao, 266101 Shandong China
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40
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Zhou YJ, Buijs NA, Zhu Z, Gómez DO, Boonsombuti A, Siewers V, Nielsen J. Harnessing Yeast Peroxisomes for Biosynthesis of Fatty-Acid-Derived Biofuels and Chemicals with Relieved Side-Pathway Competition. J Am Chem Soc 2016; 138:15368-15377. [DOI: 10.1021/jacs.6b07394] [Citation(s) in RCA: 125] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
| | | | | | | | | | | | - Jens Nielsen
- Novo
Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2800 Kgs, Lyngby, Denmark
- Science
for Life Laboratory, Royal Institute of Technology, SE-17121 Stockholm, Sweden
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41
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Biobased production of alkanes and alkenes through metabolic engineering of microorganisms. J Ind Microbiol Biotechnol 2016; 44:613-622. [PMID: 27565672 PMCID: PMC5408033 DOI: 10.1007/s10295-016-1814-y] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Accepted: 07/30/2016] [Indexed: 12/02/2022]
Abstract
Advancement in metabolic engineering of microorganisms has enabled bio-based production of a range of chemicals, and such engineered microorganism can be used for sustainable production leading to reduced carbon dioxide emission there. One area that has attained much interest is microbial hydrocarbon biosynthesis, and in particular, alkanes and alkenes are important high-value chemicals as they can be utilized for a broad range of industrial purposes as well as ‘drop-in’ biofuels. Some microorganisms have the ability to biosynthesize alkanes and alkenes naturally, but their production level is extremely low. Therefore, there have been various attempts to recruit other microbial cell factories for production of alkanes and alkenes by applying metabolic engineering strategies. Here we review different pathways and involved enzymes for alkane and alkene production and discuss bottlenecks and possible solutions to accomplish industrial level production of these chemicals by microbial fermentation.
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42
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Production of 1-decanol by metabolically engineered Yarrowia lipolytica. Metab Eng 2016; 38:139-147. [PMID: 27471068 DOI: 10.1016/j.ymben.2016.07.011] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Revised: 05/24/2016] [Accepted: 07/25/2016] [Indexed: 12/14/2022]
Abstract
Medium-chain alcohols are used to produce solvents, surfactants, lubricants, waxes, creams, and cosmetics. In this study, we engineered the oleaginous yeast Yarrowia lipolytica to produce 1-decanol from glucose. Expression of a fatty acyl-CoA reductase from Arabidopsis thaliana in strains of Y. lipolytica previously engineered to produce medium-chain fatty acids resulted in the production of 1-decanol. However, the resulting titers were very low (<10mg/mL), most likely due to product catabolism. In addition, these strains produced small quantities of 1-hexadecanol and 1-octadecanol. Deleting the major peroxisome assembly factor Pex10 was found to significantly increase 1-decanol production, resulting in titers exceeding 500mg/L. It also increased 1-hexadecanoland and 1-octadecanol titers, though the resulting increases were less than those for 1-decanol. These results demonstrate that Y. lipolytica can potentially be used for the industrial production of 1-decanol and other fatty alcohols from simple sugars.
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43
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Dennig A, Kurakin S, Kuhn M, Dordic A, Hall M, Faber K. Enzymatic Oxidative Tandem Decarboxylation of Dioic Acids to Terminal Dienes. European J Org Chem 2016. [DOI: 10.1002/ejoc.201600358] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Alexander Dennig
- Austrian Centre of Industrial Biotechnology (ACIB); c/o Department of Chemistry; Organic & Bioorganic Chemistry; University of Graz; Heinrichstrasse 28 8010 Graz Austria
| | - Sara Kurakin
- Department of Chemistry; Organic & Bioorganic Chemistry; University of Graz; Heinrichstrasse 28 8010 Graz Austria
| | - Miriam Kuhn
- Department of Chemistry; Organic & Bioorganic Chemistry; University of Graz; Heinrichstrasse 28 8010 Graz Austria
| | - Andela Dordic
- Austrian Centre of Industrial Biotechnology (ACIB); c/o Department of Chemistry; Organic & Bioorganic Chemistry; University of Graz; Heinrichstrasse 28 8010 Graz Austria
| | - Mélanie Hall
- Department of Chemistry; Organic & Bioorganic Chemistry; University of Graz; Heinrichstrasse 28 8010 Graz Austria
| | - Kurt Faber
- Department of Chemistry; Organic & Bioorganic Chemistry; University of Graz; Heinrichstrasse 28 8010 Graz Austria
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44
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Luo X, Zhao S, Huan T, Sun D, Friis RMN, Schultz MC, Li L. High-Performance Chemical Isotope Labeling Liquid Chromatography-Mass Spectrometry for Profiling the Metabolomic Reprogramming Elicited by Ammonium Limitation in Yeast. J Proteome Res 2016; 15:1602-12. [PMID: 26947805 DOI: 10.1021/acs.jproteome.6b00070] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Information about how yeast metabolism is rewired in response to internal and external cues can inform the development of metabolic engineering strategies for food, fuel, and chemical production in this organism. We report a new metabolomics workflow for the characterization of such metabolic rewiring. The workflow combines efficient cell lysis without using chemicals that may interfere with downstream sample analysis and differential chemical isotope labeling liquid chromatography mass spectrometry (CIL LC-MS) for in-depth yeast metabolome profiling. Using (12)C- and (13)C-dansylation (Dns) labeling to analyze the amine/phenol submetabolome, we detected and quantified a total of 5719 peak pairs or metabolites. Among them, 120 metabolites were positively identified using a library of 275 Dns-metabolite standards, and 2980 metabolites were putatively identified based on accurate mass matches to metabolome databases. We also applied (12)C- and (13)C-dimethylaminophenacyl (DmPA) labeling to profile the carboxylic acid submetabolome and detected over 2286 peak pairs, from which 33 metabolites were positively identified using a library of 188 DmPA-metabolite standards, and 1595 metabolites were putatively identified. Using this workflow for metabolomic profiling of cells challenged by ammonium limitation revealed unexpected links between ammonium assimilation and pantothenate accumulation that might be amenable to engineering for better acetyl-CoA production in yeast. We anticipate that efforts to improve other schemes of metabolic engineering will benefit from application of this workflow to multiple cell types.
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Affiliation(s)
- Xian Luo
- Department of Chemistry and ‡Department of Biochemistry, University of Alberta , Edmonton, Alberta, T6G 2R3 Canada
| | - Shuang Zhao
- Department of Chemistry and ‡Department of Biochemistry, University of Alberta , Edmonton, Alberta, T6G 2R3 Canada
| | - Tao Huan
- Department of Chemistry and ‡Department of Biochemistry, University of Alberta , Edmonton, Alberta, T6G 2R3 Canada
| | - Difei Sun
- Department of Chemistry and ‡Department of Biochemistry, University of Alberta , Edmonton, Alberta, T6G 2R3 Canada
| | - R Magnus N Friis
- Department of Chemistry and ‡Department of Biochemistry, University of Alberta , Edmonton, Alberta, T6G 2R3 Canada
| | - Michael C Schultz
- Department of Chemistry and ‡Department of Biochemistry, University of Alberta , Edmonton, Alberta, T6G 2R3 Canada
| | - Liang Li
- Department of Chemistry and ‡Department of Biochemistry, University of Alberta , Edmonton, Alberta, T6G 2R3 Canada
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45
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Yu AQ, Pratomo Juwono NK, Foo JL, Leong SSJ, Chang MW. Metabolic engineering of Saccharomyces cerevisiae for the overproduction of short branched-chain fatty acids. Metab Eng 2016; 34:36-43. [DOI: 10.1016/j.ymben.2015.12.005] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Revised: 11/14/2015] [Accepted: 12/14/2015] [Indexed: 10/22/2022]
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46
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Foo JL, Susanto AV, Keasling JD, Leong SSJ, Chang MW. Whole-cell biocatalytic and de novo production of alkanes from free fatty acids in Saccharomyces cerevisiae. Biotechnol Bioeng 2016; 114:232-237. [PMID: 26717118 PMCID: PMC5132040 DOI: 10.1002/bit.25920] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Revised: 12/15/2015] [Accepted: 12/29/2015] [Indexed: 12/17/2022]
Abstract
Rapid global industrialization in the past decades has led to extensive utilization of fossil fuels, which resulted in pressing environmental problems due to excessive carbon emission. This prompted increasing interest in developing advanced biofuels with higher energy density to substitute fossil fuels and bio‐alkane has gained attention as an ideal drop‐in fuel candidate. Production of alkanes in bacteria has been widely studied but studies on the utilization of the robust yeast host, Saccharomyces cerevisiae, for alkane biosynthesis have been lacking. In this proof‐of‐principle study, we present the unprecedented engineering of S. cerevisiae for conversion of free fatty acids to alkanes. A fatty acid α‐dioxygenase from Oryza sativa (rice) was expressed in S. cerevisiae to transform C12–18 free fatty acids to C11–17 aldehydes. Co‐expression of a cyanobacterial aldehyde deformylating oxygenase converted the aldehydes to the desired alkanes. We demonstrated the versatility of the pathway by performing whole‐cell biocatalytic conversion of exogenous free fatty acid feedstocks into alkanes as well as introducing the pathway into a free fatty acid overproducer for de novo production of alkanes from simple sugar. The results from this work are anticipated to advance the development of yeast hosts for alkane production. Biotechnol. Bioeng. 2017;114: 232–237. © 2016 The Authors. Biotechnology and Bioengineering Published by Wiley Periodicals, Inc.
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Affiliation(s)
- Jee Loon Foo
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore.,NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), Life Sciences Institute, National University of Singapore, Singapore
| | - Adelia Vicanatalita Susanto
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore.,NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), Life Sciences Institute, National University of Singapore, Singapore
| | - Jay D Keasling
- Joint BioEnergy Institute, Emeryville, California.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California.,Department of Chemical and Biomolecular Engineering and Department of Bioengineering, University of California, Berkeley, California
| | - Susanna Su Jan Leong
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore.,NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), Life Sciences Institute, National University of Singapore, Singapore.,Singapore Institute of Technology, Singapore
| | - Matthew Wook Chang
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore.,NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), Life Sciences Institute, National University of Singapore, Singapore
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Chen L, Lee J, Ning Chen W. The use of metabolic engineering to produce fatty acid-derived biofuel and chemicals in Saccharomyces cerevisiae: a review. AIMS BIOENGINEERING 2016. [DOI: 10.3934/bioeng.2016.4.468] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
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