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Sun HZ, Li Q, Shang W, Qiao B, Xu QM, Cheng JS. Combinatorial metabolic engineering of Bacillus subtilis for de novo production of polymyxin B. Metab Eng 2024; 83:123-136. [PMID: 38582143 DOI: 10.1016/j.ymben.2024.04.001] [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] [Received: 12/23/2023] [Revised: 03/07/2024] [Accepted: 04/01/2024] [Indexed: 04/08/2024]
Abstract
Polymyxin is a lipopeptide antibiotic that is effective against multidrug-resistant Gram-negative bacteria. However, its clinical development is limited due to low titer and the presence of homologs. To address this, the polymyxin gene cluster was integrated into Bacillus subtilis, and sfp from Paenibacillus polymyxa was expressed heterologously, enabling recombinant B. subtilis to synthesize polymyxin B. Regulating NRPS domain inhibited formation of polymyxin B2 and B3. The production of polymyxin B increased to 329.7 mg/L by replacing the native promoters of pmxA, pmxB, and pmxE with PfusA, C2up, and PfusA, respectively. Further enhancement in this production, up to 616.1 mg/L, was achieved by improving the synthesis ability of 6-methyloctanoic acid compared to the original strain expressing polymyxin heterologously. Additionally, incorporating an anikasin-derived domain into the hybrid nonribosomal peptide synthase of polymyxin increased the B1 ratio in polymyxin B from 57.5% to 62.2%. Through optimization of peptone supply in the fermentation medium and fermentation in a 5.0-L bioreactor, the final polymyxin B titer reached 962.1 mg/L, with a yield of 19.24 mg/g maltodextrin and a productivity of 10.02 mg/(L·h). This study demonstrates a successful approach for enhancing polymyxin B production and increasing the B1 ratio through combinatorial metabolic engineering.
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Affiliation(s)
- Hui-Zhong Sun
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Department of Pharmaceutical Engineering, School of Chemical Engineering and Technology, Tianjin University, Yaguan Road 135, Jinnan District, Tianjin, 300350, China
| | - Qing Li
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Department of Pharmaceutical Engineering, School of Chemical Engineering and Technology, Tianjin University, Yaguan Road 135, Jinnan District, Tianjin, 300350, China
| | - Wei Shang
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Department of Pharmaceutical Engineering, School of Chemical Engineering and Technology, Tianjin University, Yaguan Road 135, Jinnan District, Tianjin, 300350, China
| | - Bin Qiao
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Department of Pharmaceutical Engineering, School of Chemical Engineering and Technology, Tianjin University, Yaguan Road 135, Jinnan District, Tianjin, 300350, China
| | - Qiu-Man Xu
- Tianjin Key Laboratory of Animal and Plant Resistance, College of Life Science, Tianjin Normal University, Binshuixi Road 393, Xiqing District, Tianjin 300387, China.
| | - Jing-Sheng Cheng
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Department of Pharmaceutical Engineering, School of Chemical Engineering and Technology, Tianjin University, Yaguan Road 135, Jinnan District, Tianjin, 300350, China.
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Liu J, Mandlaa, Wang J, Sun Z, Chen Z. A strategy to enhance and modify fatty acid synthesis in Corynebacterium glutamicum and Escherichia coli: overexpression of acyl-CoA thioesterases. Microb Cell Fact 2023; 22:191. [PMID: 37735384 PMCID: PMC10512533 DOI: 10.1186/s12934-023-02189-w] [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] [Received: 06/29/2023] [Accepted: 08/30/2023] [Indexed: 09/23/2023] Open
Abstract
BACKGROUND Fatty acid (FA) is an important platform compound for the further synthesis of high-value biofuels and oleochemicals, but chemical synthesis of FA has many limitations. One way to meet the future demand for FA could be to use microbial cell factories for FA biosynthesis. RESULTS Thioesterase (TE; TesA, TesB, and TE9) of Corynebacterium glutamicum (CG) can potentially improve FA biosynthesis, and tesA, tesB, and te9 were overexpressed in C. glutamicum and Escherichia coli (EC), respectively, in this study. The results showed that the total fatty acid (TFA) production of CGtesB and ECtesB significantly increased to 180.52 mg/g dry cell weight (DCW) and 123.52 mg/g DCW, respectively (P < 0.05). Overexpression strains CG and EC could increase the production of C16:0, C18:1(t), C18:2, C20:1, C16:1, C18:0, and C18:1(c) (P < 0.05), respectively, and the changes of long-chain FA resulted in the enhancement of TFA production. The enzymatic properties of TesA, TesB, and TE9 in vitro were determined: they were specific for long-, broad and short-chain substrates, respectively; the optimal temperature was 30.0 °C and the optimal acid-base (pH) were 8.0, 8.0, and 9.0, respectively; they were inhibited by Fe2+, Cu2+, Zn2+, Mg2+, and K+. CONCLUSION Overexpression TE enhances and modifies FA biosynthesis with multiple productive applications, and the enzyme properties provided useful clues for optimizing FA synthesis.
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Affiliation(s)
- Jin Liu
- Food Science and Engineering College, Inner Mongolia Agricultural University, 306 Zhaowood Road, Saihan District, Hohhot, 010018, Inner Mongolia, China
| | - Mandlaa
- Food Science and Engineering College, Inner Mongolia Agricultural University, 306 Zhaowood Road, Saihan District, Hohhot, 010018, Inner Mongolia, China
| | - Jia Wang
- Food Science and Engineering College, Inner Mongolia Agricultural University, 306 Zhaowood Road, Saihan District, Hohhot, 010018, Inner Mongolia, China
| | - Ziyu Sun
- Food Science and Engineering College, Inner Mongolia Agricultural University, 306 Zhaowood Road, Saihan District, Hohhot, 010018, Inner Mongolia, China.
| | - Zhongjun Chen
- Food Science and Engineering College, Inner Mongolia Agricultural University, 306 Zhaowood Road, Saihan District, Hohhot, 010018, Inner Mongolia, China.
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3
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Strategies to Enhance the Biosynthesis of Monounsaturated Fatty Acids in Escherichia coli. BIOTECHNOL BIOPROC E 2023. [DOI: 10.1007/s12257-022-0295-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2023]
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4
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Muratovska N, Silva P, Pozdniakova T, Pereira H, Grey C, Johansson B, Carlquist M. Towards engineered yeast as production platform for capsaicinoids. Biotechnol Adv 2022; 59:107989. [PMID: 35623491 DOI: 10.1016/j.biotechadv.2022.107989] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 05/17/2022] [Accepted: 05/18/2022] [Indexed: 12/23/2022]
Abstract
Capsaicinoids are bioactive alkaloids produced by the chili pepper fruit and are known to be the most potent agonists of the human pain receptor TRPV1 (Transient Receptor Potential Cation Channel Subfamily V Member 1). They are currently produced by extraction from chili pepper fruit or by chemical synthesis. Transfer of the biosynthetic route to a microbial host could enable more efficient capsaicinoid production by fermentation and may also enable the use of synthetic biology to create a diversity of new compounds with potentially improved properties. This review summarises the current state of the art on the biosynthesis of capsaicinoid precursors in baker's yeast, Saccharomyces cerevisiae, and discusses bioengineering strategies for achieving total synthesis from sugar.
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Affiliation(s)
- Nina Muratovska
- Division of Applied Microbiology, Lund University, Box 124, 221 00 Lund, Sweden
| | - Paulo Silva
- CBMA - Center of Molecular and Environmental Biology Engineering, University of Minho, Campus de Gualtar, Braga 4710-057, Portugal
| | - Tatiana Pozdniakova
- CBMA - Center of Molecular and Environmental Biology Engineering, University of Minho, Campus de Gualtar, Braga 4710-057, Portugal
| | - Humberto Pereira
- CBMA - Center of Molecular and Environmental Biology Engineering, University of Minho, Campus de Gualtar, Braga 4710-057, Portugal
| | - Carl Grey
- Division of Biotechnology, Lund University, Box 118, SE-221 00 Lund, Sweden
| | - Björn Johansson
- CBMA - Center of Molecular and Environmental Biology Engineering, University of Minho, Campus de Gualtar, Braga 4710-057, Portugal.
| | - Magnus Carlquist
- Division of Applied Microbiology, Lund University, Box 124, 221 00 Lund, Sweden.
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5
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Fang L, Feng X, Liu D, Han Z, Liu M, Hao X, Cao Y. 大肠杆菌合成中链脂肪酸研究进展. CHINESE SCIENCE BULLETIN-CHINESE 2022. [DOI: 10.1360/tb-2022-0290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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6
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Prem S, Helmer CPO, Dimos N, Himpich S, Brück T, Garbe D, Loll B. Towards an understanding of oleate hydratases and their application in industrial processes. Microb Cell Fact 2022; 21:58. [PMID: 35397585 PMCID: PMC8994360 DOI: 10.1186/s12934-022-01777-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 03/18/2022] [Indexed: 11/21/2022] Open
Abstract
Fatty acid hydratases are unique to microorganisms. Their native function is the oxidation of unsaturated C–C bonds to enable detoxification of environmental toxins. Within this enzyme family, the oleate hydratases (Ohys), which catalyze the hydroxylation of oleic acid to 10-(R)-hydroxy stearic acid (10-HSA) have recently gained particular industrial interest. 10-HSA is considered to be a replacement for 12-(R)-hydroxy stearic acid (12-HSA), which has a broad application in the chemical and pharmaceutical industry. As 12-HSA is obtained through an energy consuming synthesis process, the biotechnological route for sustainable 10-HSA production is of significant industrial interest. All Ohys identified to date have a non-redox active FAD bound in their active site. Ohys can be divided in several subfamilies, that differ in their oligomerization state and the decoration with amino acids in their active sites. The latter observation indicates a different reaction mechanism across those subfamilies. Despite intensive biotechnological, biochemical and structural investigations, surprising little is known about substrate binding and the reaction mechanism of this enzyme family. This review, summarizes our current understanding of Ohys with a focus on sustainable biotransformation.
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Paiva P, Medina FE, Viegas M, Ferreira P, Neves RPP, Sousa JPM, Ramos MJ, Fernandes PA. Animal Fatty Acid Synthase: A Chemical Nanofactory. Chem Rev 2021; 121:9502-9553. [PMID: 34156235 DOI: 10.1021/acs.chemrev.1c00147] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Fatty acids are crucial molecules for most living beings, very well spread and conserved across species. These molecules play a role in energy storage, cell membrane architecture, and cell signaling, the latter through their derivative metabolites. De novo synthesis of fatty acids is a complex chemical process that can be achieved either by a metabolic pathway built by a sequence of individual enzymes, such as in most bacteria, or by a single, large multi-enzyme, which incorporates all the chemical capabilities of the metabolic pathway, such as in animals and fungi, and in some bacteria. Here we focus on the multi-enzymes, specifically in the animal fatty acid synthase (FAS). We start by providing a historical overview of this vast field of research. We follow by describing the extraordinary architecture of animal FAS, a homodimeric multi-enzyme with seven different active sites per dimer, including a carrier protein that carries the intermediates from one active site to the next. We then delve into this multi-enzyme's detailed chemistry and critically discuss the current knowledge on the chemical mechanism of each of the steps necessary to synthesize a single fatty acid molecule with atomic detail. In line with this, we discuss the potential and achieved FAS applications in biotechnology, as biosynthetic machines, and compare them with their homologous polyketide synthases, which are also finding wide applications in the same field. Finally, we discuss some open questions on the architecture of FAS, such as their peculiar substrate-shuttling arm, and describe possible reasons for the emergence of large megasynthases during evolution, questions that have fascinated biochemists from long ago but are still far from answered and understood.
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Affiliation(s)
- Pedro Paiva
- LAQV, REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - Fabiola E Medina
- Departamento de Ciencias Químicas, Facultad de Ciencias Exactas, Universidad Andres Bello, Autopista Concepción-Talcahuano, 7100 Talcahuano, Chile
| | - Matilde Viegas
- LAQV, REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - Pedro Ferreira
- LAQV, REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - Rui P P Neves
- LAQV, REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - João P M Sousa
- LAQV, REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - Maria J Ramos
- LAQV, REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - Pedro A Fernandes
- LAQV, REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
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Suharti, Mahardika G, Raissa, Dewi L, Yohandini H, Widhiastuty MP, Sakti RAW, Wahyudi ST, Akhmaloka. Cloning, heterologous expression, and characterization of a novel thioesterase from natural sample. Heliyon 2021; 7:e06542. [PMID: 33851045 PMCID: PMC8024609 DOI: 10.1016/j.heliyon.2021.e06542] [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: 06/22/2020] [Revised: 11/24/2020] [Accepted: 03/15/2021] [Indexed: 11/30/2022] Open
Abstract
A novel thioesterse gene was successfully cloned and sequenced directly from natural sample of Domas Hot Spring, West Java, Indonesia. Homological analysis of the sequence showed that the gene appeared high homology to thioesterase genes with the highest to a putative thioesterase gene from uncultured Acidilobus sp. JCHS at 66% identity. However, phylogenetic analysis showed that the protein was separated from the branch with other known thioesterases. The size of the gene is around 500 base pairs, lied into 2 kb DNA fragment from a random PCR amplicon. The gene was overexpressed in Escherichia coli, a dominant band appeared at 17 kDa in SDS-PAGE with expression level at around 32% of total proteins. The activity of the purified protein using acetyl-CoA as substrate showed that the protein exhibited thioesterase activity. Furthermore, the enzyme also showed esterase activity on p-nitrophenyl ester as substrate. Detail characterization of esterolytic activity showed that the enzyme preferred p-nitrophenyl decanoate as substrate. The optimum activity of the enzyme was at 80 °C and pH 8. Activity of the enzyme was maintained after incubation at 80 °C up to 24 h. In addition, the enzyme was favorable on polar organic solvents. All the data obtained suggested that the enzyme is a novel alkaline thermostable thioesterase.
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Affiliation(s)
- Suharti
- Biochemistry Research Group, Faculty of Mathematics and Natural Sciences, Institut Teknologi Bandung, Jl. Ganesha 10, Bandung, Indonesia
- Department of Chemistry, Faculty of Science and Computer, Universitas Pertamina, Jl. Teuku Nyak Arief, Simprug Kebayoran, South Jakarta, Indonesia
| | - Gita Mahardika
- Biochemistry Research Group, Faculty of Mathematics and Natural Sciences, Institut Teknologi Bandung, Jl. Ganesha 10, Bandung, Indonesia
| | - Raissa
- Department of Chemistry, Faculty of Science and Computer, Universitas Pertamina, Jl. Teuku Nyak Arief, Simprug Kebayoran, South Jakarta, Indonesia
| | - Laksmi Dewi
- Department of Chemical Engineering, Faculty of Industrial Engineering, Universitas Pertamina, Jl. Teuku Nyak Arief, Simprug Kebayoran, South Jakarta, Indonesia
| | - Heni Yohandini
- Biochemistry Research Group, Faculty of Mathematics and Natural Sciences, Institut Teknologi Bandung, Jl. Ganesha 10, Bandung, Indonesia
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, Universitas Sriwijaya, Jl. Raya Palembang Prabumulih KM 32, Indralaya-Ogan Ilir, Indonesia
| | - Made Puspasari Widhiastuty
- Biochemistry Research Group, Faculty of Mathematics and Natural Sciences, Institut Teknologi Bandung, Jl. Ganesha 10, Bandung, Indonesia
| | - Raden Aditya Wibawa Sakti
- Department of Chemistry, Faculty of Science and Computer, Universitas Pertamina, Jl. Teuku Nyak Arief, Simprug Kebayoran, South Jakarta, Indonesia
| | - Setyanto Tri Wahyudi
- Biochemistry Research Group, Faculty of Mathematics and Natural Sciences, Institut Teknologi Bandung, Jl. Ganesha 10, Bandung, Indonesia
- Department of Physics, IPB University, Bogor, 16680, Indonesia
| | - Akhmaloka
- Biochemistry Research Group, Faculty of Mathematics and Natural Sciences, Institut Teknologi Bandung, Jl. Ganesha 10, Bandung, Indonesia
- Department of Chemistry, Faculty of Science and Computer, Universitas Pertamina, Jl. Teuku Nyak Arief, Simprug Kebayoran, South Jakarta, Indonesia
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9
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Li H, Zhang D, Luo J, Jones KC, Martin FL. Applying Raman Microspectroscopy to Evaluate the Effects of Nutrient Cations on Alkane Bioavailability to Acinetobacter baylyi ADP1. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2020; 54:15800-15810. [PMID: 33274919 DOI: 10.1021/acs.est.0c04944] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Contamination with petroleum hydrocarbons causes extensive damage to ecological systems. On oil-contaminated sites, alkanes are major components; many indigenous bacteria can access and/or degrade alkanes. However, their ability to do so is affected by external properties of the soil, including nutrient cations. This study used Raman microspectroscopy to study how nutrient cations affect alkanes' bioavailability to Acinetobacter baylyi ADP1 (a known degrader). Treated with Na, K, Mg, and Ca at 10 mM, A. baylyi was exposed to seven n-alkanes (decane, dodecane, tetradecane, hexadecane, nonadecane, eicosane, and tetracosane) and one alkane mixture (mineral oil). Raman spectral analysis indicated that bioavailability of alkanes varied with carbon chain lengths, and additional cations altered the bacterial response to n-alkanes. Sodium significantly increased the bacterial affinity toward decane and dodecane, and K and Mg enhanced the bioavailability of tetradecane and hexadecane. In contrast, the bacterial response was inhibited by Ca for all alkanes. Similar results were observed in mineral oil exposure. Our study employed Raman spectral assay to offer a deep insight into how nutrient cations affect the bioavailability of alkanes, suggesting that nutrient cations can play a key role in influencing the harmful effects of hydrocarbons and could be optimized to enhance the bioremediation strategy.
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Affiliation(s)
- Hanbing Li
- Lancaster Environment Centre, Lancaster University, Lancaster LA1 4YQ, U.K
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, China
| | - Dayi Zhang
- Lancaster Environment Centre, Lancaster University, Lancaster LA1 4YQ, U.K
- School of Environment, Tsinghua University, Beijing 100086, China
| | - Jun Luo
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, China
| | - Kevin C Jones
- Lancaster Environment Centre, Lancaster University, Lancaster LA1 4YQ, U.K
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, China
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Enhanced Production of Fatty Acid Ethyl Ester with Engineered fabHDG Operon in Escherichia coli. Microorganisms 2019; 7:microorganisms7110552. [PMID: 31717929 PMCID: PMC6920873 DOI: 10.3390/microorganisms7110552] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Revised: 10/23/2019] [Accepted: 11/05/2019] [Indexed: 12/16/2022] Open
Abstract
Biodiesel, or fatty acid ethyl ester (FAEE), is an environmentally safe, next-generation biofuel. Conventionally, FAEE is produced by the conversion of oil/fats, obtained from plants, animals, and microorganisms, by transesterification. Recently, metabolic engineering of bacteria for ready-to-use biodiesel was developed. In Escherichia coli, it is produced by fatty acyl-carrier proteins and ethanol, with the help of thioesterase (TesB) and wax synthase (WS) enzymes. One of the foremost barriers in microbial FAEE production is the feedback inhibition of the fatty acid (FA) operon (fabHDG). Here, we studied the effect of biodiesel biosynthesis in E. coli with an engineered fabHDG operon. With a basic FAEE producing BD1 strain harboring tes and ws genes, biodiesel of 32 mg/L were produced. Optimal FAEE biosynthesis was achieved in the BD2 strain that carries an overexpressed operon (fabH, fabD, and fabG genes) and achieved up to 1291 mg/L of biodiesel, a 40-fold rise compared to the BD1 strain. The composition of FAEE obtained from the BD2 strain was 65% (C10:C2, decanoic acid ethyl ester) and 35% (C12:C2, dodecanoic acid ethyl ester). Our findings indicate that overexpression of the native FA operon, along with FAEE biosynthesis enzymes, improved biodiesel biosynthesis in E. coli.
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Chacón MG, Kendrick EG, Leak DJ. Engineering Escherichia coli for the production of butyl octanoate from endogenous octanoyl-CoA. PeerJ 2019; 7:e6971. [PMID: 31304053 PMCID: PMC6610577 DOI: 10.7717/peerj.6971] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Accepted: 04/18/2019] [Indexed: 11/20/2022] Open
Abstract
Medium chain esters produced from fruits and flowering plants have a number of commercial applications including use as flavour and fragrance ingredients, biofuels, and in pharmaceutical formulations. These esters are typically made via the activity of an alcohol acyl transferase (AAT) enzyme which catalyses the condensation of an alcohol and an acyl-CoA. Developing a microbial platform for medium chain ester production using AAT activity presents several obstacles, including the low product specificity of these enzymes for the desired ester and/or low endogenous substrate availability. In this study, we engineered Escherichia coli for the production of butyl octanoate from endogenously produced octanoyl-CoA. This was achieved through rational protein engineering of an AAT enzyme from Actinidia chinensis for improved octanoyl-CoA substrate specificity and metabolic engineering of E. coli fatty acid metabolism for increased endogenous octanoyl-CoA availability. This resulted in accumulation of 3.3 + 0.1 mg/L butyl octanoate as the sole product from E. coli after 48 h. This study represents a preliminary examination of the feasibility of developing E. coli platforms for the synthesis single medium chain esters from endogenous fatty acids.
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Affiliation(s)
- Micaela G Chacón
- Department of Biology and Biochemistry, University of Bath, Bath, England
| | | | - David J Leak
- Department of Biology and Biochemistry, University of Bath, Bath, England
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12
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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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Microbial Production of Fatty Acid via Metabolic Engineering and Synthetic Biology. BIOTECHNOL BIOPROC E 2019. [DOI: 10.1007/s12257-018-0374-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Afrin S, Khan MRI, Zhang W, Wang Y, Zhang W, He L, Ma G. Membrane-Located Expression of Thioesterase From Acinetobacter baylyi Enhances Free Fatty Acid Production With Decreased Toxicity in Synechocystis sp. PCC6803. Front Microbiol 2018; 9:2842. [PMID: 30538684 PMCID: PMC6277518 DOI: 10.3389/fmicb.2018.02842] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Accepted: 11/05/2018] [Indexed: 12/18/2022] Open
Abstract
It has been previously reported that photosynthetic production of extracellular free fatty acids (FFAs) in cyanobacteria was realized by thioesterases (TesA) mediated hydrolysis of fatty acyl-ACP in cytosol and excretion of the FFA outside of the cell. However, two major issues related to the genetically modified strains need to be addressed before the scale-up commercial application becomes possible: namely, the toxicity of FFAs, and the diversity of carbon lengths of fatty acids that could mimic the fossil fuel. To address those issues, we hypothesized that generating FFAs near membrane could facilitate rapid excretion of the FFA outside of the cell and thus decrease toxicity caused by intracellular FFAs in the cytosolic expression of thioesterase. To realize this, we localized a leaderless thioesterase (AcTesA) from Acinetobacter baylyi on the cytosolic side of the inner membrane of Synechocystis sp. PCC6803 using a membrane scaffolding system. The engineered strain with AcTesA on its membrane (mAcT) produced extracellular FFAs up to 171.9 ± 13.22 mg⋅L-1 compared with 40.24 ± 10.94 and 1.904 ± 0.158 mg⋅L-1 in the cytosol-expressed AcTesA (AcT) and wild-type (WT) strains, respectively. Moreover, the mAcT strain generated around 1.5 and 1.9 times less reactive oxygen species than AcT and WT, respectively. Approximately 78% of total FFAs were secreted with an average rate of 1 mg⋅L-1⋅h-1, which was higher than 0.44 mg⋅L-1⋅h-1 reported previously. In the case of mAcT strain, 60% of total secreted FFAs was monounsaturated (C18:1) which is the preferable biodiesel component. Therefore, the engineered mAcT strain shows enhanced FFAs production with less toxicity which is highly desirable for biodiesel production.
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Affiliation(s)
- Shajia Afrin
- Bio-X-Renji Hospital Research Center, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai, China
| | - Md Rezaul Islam Khan
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai, China
| | - Weiyi Zhang
- Shanghai Animal Disease Control Center, Shanghai, China
| | - Yushu Wang
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai, China
| | - Weiwen Zhang
- Laboratory of Synthetic Microbiology, School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
| | - Lin He
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai, China
| | - Gang Ma
- Bio-X-Renji Hospital Research Center, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai, China
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15
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Sarria S, Bartholow TG, Verga A, Burkart MD, Peralta-Yahya P. Matching Protein Interfaces for Improved Medium-Chain Fatty Acid Production. ACS Synth Biol 2018; 7:1179-1187. [PMID: 29722970 DOI: 10.1021/acssynbio.7b00334] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Medium-chain fatty acids (MCFAs) are key intermediates in the synthesis of medium-chain chemicals including α-olefins and dicarboxylic acids. In bacteria, microbial production of MCFAs is limited by the activity and product profile of fatty acyl-ACP thioesterases. Here, we engineer a heterologous bacterial medium-chain fatty acyl-ACP thioesterase for improved MCFA production in Escherichia coli. Electrostatically matching the interface between the heterologous medium-chain Acinetobacter baylyi fatty acyl-ACP thioesterase (AbTE) and the endogenous E. coli fatty acid ACP ( E. coli AcpP) by replacing small nonpolar amino acids on the AbTE surface for positively charged ones increased secreted MCFA titers more than 3-fold. Nuclear magnetic resonance titration of E. coli 15N-octanoyl-AcpP with a single AbTE point mutant and the best double mutant showed a progressive and significant increase in the number of interactions when compared to AbTE wildtype. The best AbTE mutant produced 131 mg/L of MCFAs, with MCFAs being 80% of all secreted fatty acid chain lengths after 72 h. To enable the future screening of larger numbers of AbTE variants to further improve MCFA titers, we show that a previously developed G-protein coupled receptor (GPCR)-based MCFA sensor differentially detects MCFAs secreted by E. coli expressing different AbTE variants. This work demonstrates that engineering the interface of heterologous enzymes to better couple with endogenous host proteins is a useful strategy to increase the titers of microbially produced chemicals. Further, this work shows that GPCR-based sensors are producer microbe agnostic and can detect chemicals directly in the producer microbe supernatant, setting the stage for the sensor-guided engineering of MCFA producing microbes.
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Affiliation(s)
- Stephen Sarria
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Thomas G. Bartholow
- Department of Chemistry and Biochemistry, University of California, San Diego, California 92093, United States
| | - Adam Verga
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Michael D. Burkart
- Department of Chemistry and Biochemistry, University of California, San Diego, California 92093, United States
| | - Pamela Peralta-Yahya
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
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16
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Rullán‐Lind C, Pietri RB, Vázquez‐Cintrón M, Baerga‐Ortiz A. Fused dimerization increases expression, solubility, and activity of bacterial dehydratase enzymes. Protein Sci 2018; 27:969-975. [PMID: 29520922 PMCID: PMC5916124 DOI: 10.1002/pro.3404] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2017] [Revised: 03/05/2018] [Accepted: 03/07/2018] [Indexed: 01/12/2023]
Abstract
FabA and FabZ are the two dehydratase enzymes in Escherichia coli that catalyze the dehydration of acyl intermediates in the biosynthesis of fatty acids. Both enzymes form obligate dimers in which the active site contains key amino acids from both subunits. While FabA is a soluble protein that has been relatively straightforward to express and to purify from cultured E. coli, FabZ has shown to be mostly insoluble and only partially active. In an effort to increase the solubility and activity of both dehydratases, we made constructs consisting of two identical subunits of FabA or FabZ fused with a naturally occurring peptide linker, so as to force their dimerization. The fused dimer of FabZ (FabZ-FabZ) was expressed as a soluble enzyme with an ninefold higher activity in vitro than the unfused FabZ. This construct exemplifies a strategy for the improvement of enzymes from the fatty acid biosynthesis pathways, many of which function as dimers, catalyzing critical steps for the production of fatty acids.
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Affiliation(s)
- Carlos Rullán‐Lind
- Department of BiochemistryUniversity of Puerto Rico, Medical Sciences CampusSan Juan00936‐5067Puerto Rico
- Molecular Sciences Research Center, University of Puerto RicoSan JuanPuerto Rico
| | - Ruth B. Pietri
- Department of ChemistryUniversity of Puerto Rico, Cayey CampusCayeyPuerto Rico
| | - Melvin Vázquez‐Cintrón
- Department of BiochemistryUniversity of Puerto Rico, Medical Sciences CampusSan Juan00936‐5067Puerto Rico
- Molecular Sciences Research Center, University of Puerto RicoSan JuanPuerto Rico
| | - Abel Baerga‐Ortiz
- Department of BiochemistryUniversity of Puerto Rico, Medical Sciences CampusSan Juan00936‐5067Puerto Rico
- Molecular Sciences Research Center, University of Puerto RicoSan JuanPuerto Rico
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17
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Kim J, Yoo HW, Kim M, Kim EJ, Sung C, Lee PG, Park BG, Kim BG. Rewiring FadR regulon for the selective production of ω-hydroxy palmitic acid from glucose in Escherichia coli. Metab Eng 2018; 47:414-422. [PMID: 29719215 DOI: 10.1016/j.ymben.2018.04.021] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Revised: 04/19/2018] [Accepted: 04/28/2018] [Indexed: 12/28/2022]
Abstract
ω-Hydroxy palmitic acid (ω-HPA) is a valuable compound for an ingredient of artificially synthesized ceramides and an additive for lubricants and adhesives. Production of such a fatty acid derivative is limited by chemical catalysis, but plausible by biocatalysis. However, its low productivity issue, including formations of unsaturated fatty acid (UFA) byproducts in host cells, remains as a hurdle toward industrial biological processes. In this study, to achieve selective and high-level production of ω-HPA from glucose in Escherichia coli, FadR, a native transcriptional regulator of fatty acid metabolism, and its regulon were engineered. First, FadR was co-expressed with a thioesterase with a specificity toward palmitic acid production to enhance palmitic acid production yield, but a considerable quantity of UFAs was also produced. In order to avoid the UFA production caused by fadR overexpression, FadR regulon was rewired by i) mutating FadR consensus binding sites of fabA or fabB, ii) integrating fabZ into fabI operon, and iii) enhancing the strength of fabI promoter. This approach led to dramatic increases in both proportion (48.3-83.0%) and titer (377.8 mg/L to 675.8 mg/L) of palmitic acid, mainly due to the decrease in UFA synthesis. Introducing a fatty acid ω-hydroxylase, CYP153A35, into the engineered strain resulted in a highly selective production of ω-HPA (83.5 mg/L) accounting for 87.5% of total ω-hydroxy fatty acids. Furthermore, strategies, such as i) enhancement in CYP153A35 activity, ii) expression of a fatty acid transporter, iii) supplementation of triton X-100, and iv) separation of the ω-HPA synthetic pathway into two strains for a co-culture system, were applied and resulted in 401.0 mg/L of ω-HPA production. For such selective productions of palmitic acid and ω-HPA, the rewiring of FadR regulation in E. coli is a promising strategy to develop an industrial process with economical downstream processing.
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Affiliation(s)
- Joonwon Kim
- School of Chemical and Biological Engineering, Seoul National University, 1, Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea; Institute of Molecular Biology and Genetics, Seoul National University, Seoul 08826, Republic of Korea
| | - Hee-Wang Yoo
- Institute of Molecular Biology and Genetics, Seoul National University, Seoul 08826, Republic of Korea; Interdisciplinary Program of Bioengineering, Seoul National University, Seoul 08826, Republic of Korea
| | - Minsuk Kim
- Institute of Engineering Research, Seoul National University, Seoul 08826, Republic of Korea
| | - Eun-Jung Kim
- Institute of Molecular Biology and Genetics, Seoul National University, Seoul 08826, Republic of Korea; Bio-MAX Institute, Seoul National University, Seoul 08826, Republic of Korea
| | - Changmin Sung
- Doping Control Center, Korea Institute of Science and Technology, Seoul 02792, Republic of Korea
| | - Pyung-Gang Lee
- School of Chemical and Biological Engineering, Seoul National University, 1, Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea; Institute of Molecular Biology and Genetics, Seoul National University, Seoul 08826, Republic of Korea
| | - Beom Gi Park
- School of Chemical and Biological Engineering, Seoul National University, 1, Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea; Institute of Molecular Biology and Genetics, Seoul National University, Seoul 08826, Republic of Korea
| | - Byung-Gee Kim
- School of Chemical and Biological Engineering, Seoul National University, 1, Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea; Institute of Molecular Biology and Genetics, Seoul National University, Seoul 08826, Republic of Korea; Interdisciplinary Program of Bioengineering, Seoul National University, Seoul 08826, Republic of Korea; Institute of Engineering Research, Seoul National University, Seoul 08826, Republic of Korea.
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18
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Tan Z, Yoon JM, Chowdhury A, Burdick K, Jarboe LR, Maranas CD, Shanks JV. Engineering of E. coli inherent fatty acid biosynthesis capacity to increase octanoic acid production. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:87. [PMID: 29619083 PMCID: PMC5879999 DOI: 10.1186/s13068-018-1078-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Accepted: 03/13/2018] [Indexed: 05/26/2023]
Abstract
BACKGROUND As a versatile platform chemical, construction of microbial catalysts for free octanoic acid production from biorenewable feedstocks is a promising alternative to existing petroleum-based methods. However, the bio-production strategy has been restricted by the low capacity of E. coli inherent fatty acid biosynthesis. In this study, a combination of integrated computational and experimental approach was performed to manipulate the E. coli existing metabolic network, with the objective of improving bio-octanoic acid production. RESULTS First, a customized OptForce methodology was run to predict a set of four genetic interventions required for production of octanoic acid at 90% of the theoretical yield. Subsequently, all the ten candidate proteins associated with the predicted interventions were regulated individually, as well as in contrast to the combination of interventions as suggested by the OptForce strategy. Among these enzymes, increased production of 3-hydroxy-acyl-ACP dehydratase (FabZ) resulted in the highest increase (+ 45%) in octanoic acid titer. But importantly, the combinatorial application of FabZ with the other interventions as suggested by OptForce further improved octanoic acid production, resulting in a high octanoic acid-producing E. coli strain +fabZ ΔfadE ΔfumAC ΔackA (TE10) (+ 61%). Optimization of TE10 expression, medium pH, and C:N ratio resulted in the identified strain producing 500 mg/L of C8 and 805 mg/L of total FAs, an 82 and 155% increase relative to wild-type MG1655 (TE10) in shake flasks. The best engineered strain produced with high selectivity (> 70%) and extracellularly (> 90%) up to 1 g/L free octanoic acid in minimal medium fed-batch culture. CONCLUSIONS This work demonstrates the effectiveness of integration of computational strain design and experimental characterization as a starting point in rewiring metabolism for octanoic acid production. This result in conjunction with the results of other studies using OptForce in strain design demonstrates that this strategy may be also applicable to engineering E. coli for other customized bioproducts.
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Affiliation(s)
- Zaigao Tan
- Department of Chemical and Biological Engineering, Iowa State University, 3031 Sweeney, Ames, IA 50011 USA
| | - Jong Moon Yoon
- Department of Chemical and Biological Engineering, Iowa State University, 3031 Sweeney, Ames, IA 50011 USA
| | - Anupam Chowdhury
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA 16802 USA
| | - Kaitlin Burdick
- Department of Chemical and Biological Engineering, Iowa State University, 3031 Sweeney, Ames, IA 50011 USA
| | - Laura R. Jarboe
- Department of Chemical and Biological Engineering, Iowa State University, 3031 Sweeney, Ames, IA 50011 USA
| | - Costas D. Maranas
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA 16802 USA
| | - Jacqueline V. Shanks
- Department of Chemical and Biological Engineering, Iowa State University, 3031 Sweeney, Ames, IA 50011 USA
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19
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Grisewood MJ, Hernández-Lozada NJ, Thoden JB, Gifford NP, Mendez-Perez D, Schoenberger HA, Allan MF, Floy ME, Lai RY, Holden HM, Pfleger BF, Maranas CD. Computational Redesign of Acyl-ACP Thioesterase with Improved Selectivity toward Medium-Chain-Length Fatty Acids. ACS Catal 2017; 7:3837-3849. [PMID: 29375928 DOI: 10.1021/acscatal.7b00408] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Enzyme and metabolic engineering offer the potential to develop biocatalysts for converting natural resources into a wide range of chemicals. To broaden the scope of potential products beyond natural metabolites, methods of engineering enzymes to accept alternative substrates and/or perform novel chemistries must be developed. DNA synthesis can create large libraries of enzyme-coding sequences, but most biochemistries lack a simple assay to screen for promising enzyme variants. Our solution to this challenge is structure-guided mutagenesis in which optimization algorithms select the best sequences from libraries based on specified criteria (i.e. binding selectivity). Here, we demonstrate this approach by identifying medium-chain (C6-C12) acyl-ACP thioesterases through structure-guided mutagenesis. Medium-chain fatty acids, products of thioesterase-catalyzed hydrolysis, are limited in natural abundance compared to long-chain fatty acids; the limited supply leads to high costs of C6-C10 oleochemicals such as fatty alcohols, amines, and esters. Here, we applied computational tools to tune substrate binding to the highly-active 'TesA thioesterase in Escherichia coli. We used the IPRO algorithm to design thioesterase variants with enhanced C12- or C8-specificity while maintaining high activity. After four rounds of structure-guided mutagenesis, we identified three thioesterases with enhanced production of dodecanoic acid (C12) and twenty-seven thioesterases with enhanced production of octanoic acid (C8). The top variants reached up to 49% C12 and 50% C8 while exceeding native levels of total free fatty acids. A comparably sized library created by random mutagenesis failed to identify promising mutants. The chain length-preference of 'TesA and the best mutant were confirmed in vitro using acyl-CoA substrates. Molecular dynamics simulations, confirmed by resolved crystal structures, of 'TesA variants suggest that hydrophobic forces govern 'TesA substrate specificity. We expect that the design rules we uncovered and the thioesterase variants identified will be useful to metabolic engineering projects aimed at sustainable production of medium-chain oleochemicals.
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Affiliation(s)
- Matthew J. Grisewood
- Department
of Chemical Engineering, Pennsylvania State University, 158 Fenske Laboratory, University Park, Pennsylvania 16802, United States
| | - Néstor J. Hernández-Lozada
- Department
of Chemical and Biological Engineering, University of Wisconsin−Madison, 1415 Engineering Drive, Madison, Wisconsin 53706, United States
| | - James B. Thoden
- Department
of Biochemistry, University of Wisconsin−Madison, 440 Henry Mall, Madison, Wisconsin 53706, United States
| | - Nathanael P. Gifford
- Department
of Chemical Engineering, Pennsylvania State University, 158 Fenske Laboratory, University Park, Pennsylvania 16802, United States
| | - Daniel Mendez-Perez
- Department
of Chemical and Biological Engineering, University of Wisconsin−Madison, 1415 Engineering Drive, Madison, Wisconsin 53706, United States
| | - Haley A. Schoenberger
- Department
of Chemical and Biological Engineering, University of Wisconsin−Madison, 1415 Engineering Drive, Madison, Wisconsin 53706, United States
| | - Matthew F. Allan
- Department
of Chemical Engineering, Pennsylvania State University, 158 Fenske Laboratory, University Park, Pennsylvania 16802, United States
| | - Martha E. Floy
- Department
of Chemical and Biological Engineering, University of Wisconsin−Madison, 1415 Engineering Drive, Madison, Wisconsin 53706, United States
| | - Rung-Yi Lai
- Department
of Chemical and Biological Engineering, University of Wisconsin−Madison, 1415 Engineering Drive, Madison, Wisconsin 53706, United States
| | - Hazel M. Holden
- Department
of Biochemistry, University of Wisconsin−Madison, 440 Henry Mall, Madison, Wisconsin 53706, United States
| | - Brian F. Pfleger
- Department
of Chemical and Biological Engineering, University of Wisconsin−Madison, 1415 Engineering Drive, Madison, Wisconsin 53706, United States
| | - Costas D. Maranas
- Department
of Chemical Engineering, Pennsylvania State University, 158 Fenske Laboratory, University Park, Pennsylvania 16802, United States
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20
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Ukey R, Holmes WE, Bajpai R, Chistoserdov AY. Evaluation of thioesterases from Acinetobacter baylyi for production of free fatty acids. Can J Microbiol 2017; 63:321-329. [PMID: 28335611 DOI: 10.1139/cjm-2016-0458] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Acinetobacter baylyi is one of few Gram-negative bacteria capable of accumulating storage lipids in the form of triacylglycerides and wax esters, which makes it an attractive candidate for production of lipophilic products, including biofuel precursors. Thioesterases play a significant dual role in the triacylglyceride and wax ester biosynthesis by either providing or removing acyl-CoA from this pathway. Therefore, 4 different thioesterase genes were cloned from Acinetobacter baylyi ADP1 and expressed in Escherichia coli to investigate their contribution to free fatty acids (FFAs) accumulation. Overexpression of the genes tesA' (a leaderless form of the gene tesA) and tesC resulted in increased accumulation of FFAs when compared with the host E. coli strain. Overexpression of tesA' showed a 1.87-fold increase in production of long-chain fatty acids (C16 to C18) over the host strain. Unlike TesC and the other investigated thioesterases, the TesA' thioesterase also produced shorter chain FFAs (e.g., myristic acid) and unsaturated FFAs (e.g., cis-vaccenic acid (18:1Δ11)). A comparison of the remaining 3 A. baylyi ADP1 thioesterases (encoded by the tesB, tesC, and tesD genes) revealed that only the strain containing the tesC gene produced statistically higher levels of FFAs over the control, suggesting that it possesses the acyl-ACP thioesterase activity. Both E. coli strains containing the tesB and tesD genes produced levels of FFAs similar to those of the plasmid-free control E. coli strain, which indicates that TesB and TesD lack the acyl-ACP thioesterase activity.
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Affiliation(s)
- Rahul Ukey
- a Department of Biology, University of Louisiana at Lafayette, Lafayette, LA 70504, USA
| | - William E Holmes
- b Energy Institute, University of Louisiana at Lafayette, Lafayette, LA 70504, USA
| | - Rakesh Bajpai
- c Department of Chemical Engineering, University of Louisiana at Lafayette, Lafayette, LA 70504, USA
| | - Andrei Y Chistoserdov
- a Department of Biology, University of Louisiana at Lafayette, Lafayette, LA 70504, USA
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21
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High-efficiency extracellular release of free fatty acids from Aspergillus oryzae using non-ionic surfactants. J Biotechnol 2017; 248:9-14. [PMID: 28300661 DOI: 10.1016/j.jbiotec.2017.03.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Revised: 02/13/2017] [Accepted: 03/04/2017] [Indexed: 11/21/2022]
Abstract
Free fatty acids (FFAs) are useful for generating biofuel compounds and functional lipids. Microbes are increasingly exploited to produce FFAs via metabolic engineering. However, in many microorganisms, FFAs accumulate in the cytosol, and disrupting cells to extract them is energy intensive. Thus, a simple cost-effective extraction technique must be developed to remove this drawback. We found that FFAs were released from cells of the filamentous fungus Aspergillus oryzae with high efficiency when they were cultured or incubated with non-ionic surfactants such as Triton X-100. The surfactants did not reduce hyphal growth, even at 5% (w/v). When the faaA disruptant was cultured with 1% Triton X-100, more than 80% of the FFAs synthesized de novo were released. When the disruptant cells grown without surfactants were incubated for 1h in 1% Triton X-100 solution, more than 50% of the FFAs synthesized de novo were also released. Other non-ionic surfactants in the same ether series, such as Brij 58, IGEPAL CA-630, and Tergitol NP-40, elicited a similar FFA release. The dry cell weight of total hyphae decreased when grown with 1% Triton X-100. The decrement was 4.9-fold greater than the weight of the released FFAs, implying release of other intracellular compounds. Analysis of the culture supernatant showed that intracellular lactate dehydrogenase was also released, suggesting that FFAs are not released by a specific transporter. Therefore, ether-type non-ionic surfactants probably cause non-specific release of FFAs and other intracellular compounds by increasing cell membrane permeability.
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22
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Zhu Z, Zhou YJ, Krivoruchko A, Grininger M, Zhao ZK, Nielsen J. Expanding the product portfolio of fungal type I fatty acid synthases. Nat Chem Biol 2017; 13:360-362. [DOI: 10.1038/nchembio.2301] [Citation(s) in RCA: 81] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Accepted: 11/14/2016] [Indexed: 12/29/2022]
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Tamano K, Miura A. Further increased production of free fatty acids by overexpressing a predicted transketolase gene of the pentose phosphate pathway in Aspergillus oryzae faaA disruptant. Biosci Biotechnol Biochem 2016; 80:1829-35. [DOI: 10.1080/09168451.2016.1162086] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Abstract
Free fatty acids are useful as source materials for the production of biodiesel fuel and various chemicals such as pharmaceuticals and dietary supplements. Previously, we attained a 9.2-fold increase in free fatty acid productivity by disrupting a predicted acyl-CoA synthetase gene (faaA, AO090011000642) in Aspergillus oryzae. In this study, we achieved further increase in the productivity by overexpressing a predicted transketolase gene of the pentose phosphate pathway in the faaA disruptant. The A. oryzae genome is predicted to have three transketolase genes and overexpression of AO090023000345, one of the three genes, resulted in phenotypic change and further increase (corresponding to an increased production of 0.38 mmol/g dry cell weight) in free fatty acids at 1.4-fold compared to the faaA disruptant. Additionally, the biomass of hyphae increased at 1.2-fold by the overexpression. As a result, free fatty acid production yield per liter of liquid culture increased at 1.7-fold by the overexpression.
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Affiliation(s)
- Koichi Tamano
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Sapporo, Japan
| | - Ai Miura
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Sapporo, Japan
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24
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Rahman Z, Rashid N, Nawab J, Ilyas M, Sung BH, Kim SC. Escherichia coli as a fatty acid and biodiesel factory: current challenges and future directions. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2016; 23:12007-12018. [PMID: 26961532 DOI: 10.1007/s11356-016-6367-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2015] [Accepted: 02/29/2016] [Indexed: 06/05/2023]
Abstract
Biodiesel has received widespread attention as a sustainable, environment-friendly, and alternative source of energy. It can be derived from plant, animal, and microbial organisms in the form of vegetable oil, fats, and lipids, respectively. However, biodiesel production from such sources is not economically feasible due to extensive downstream processes, such as trans-esterification and purification. To obtain cost-effective biodiesel, these bottlenecks need to be overcome. Escherichia coli, a model microorganism, has the potential to produce biodiesel directly from ligno-cellulosic sugars, bypassing trans-esterification. In this process, E. coli is engineered to produce biodiesel using metabolic engineering technology. The entire process of biodiesel production is carried out in a single microbial cell, bypassing the expensive downstream processing steps. This review focuses mainly on production of fatty acid and biodiesel in E. coli using metabolic engineering approaches. In the first part, we describe fatty acid biosynthesis in E. coli. In the second half, we discuss bottlenecks and strategies to enhance the production yield. A complete understanding of current developments in E. coli-based biodiesel production and pathway optimization strategies would reduce production costs for biofuels and plant-derived chemicals.
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Affiliation(s)
- Ziaur Rahman
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea.
- Department of Environmental and Conservation Sciences, University of Swat, Swat, 19130, Pakistan.
- Center for Biotechnology and Microbiology, University of Swat, Swat, Pakistan.
- Department of Microbiology, AWKUM, Mardan, Pakistan.
| | - Naim Rashid
- Department of Chemical Engineering, COMSATS, Lahore, Pakistan
| | - Javed Nawab
- Department of Environmental and Conservation Sciences, University of Swat, Swat, 19130, Pakistan
| | | | - Bong Hyun Sung
- Bioenergy and Biochemical Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 34141, Republic of Korea
| | - Sun Chang Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea.
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Production of FAME biodiesel in E. coli by direct methylation with an insect enzyme. Sci Rep 2016; 6:24239. [PMID: 27053100 PMCID: PMC4823748 DOI: 10.1038/srep24239] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Accepted: 03/23/2016] [Indexed: 12/13/2022] Open
Abstract
Most biodiesel currently in use consists of fatty acid methyl esters (FAMEs) produced by transesterification of plant oils with methanol. To reduce competition with food supplies, it would be desirable to directly produce biodiesel in microorganisms. To date, the most effective pathway for the production of biodiesel in bacteria yields fatty acid ethyl esters (FAEEs) at up to ~1.5 g/L. A much simpler route to biodiesel produces FAMEs by direct S-adenosyl-L-methionine (SAM) dependent methylation of free fatty acids, but FAME production by this route has been limited to only ~16 mg/L. Here we employ an alternative, broad spectrum methyltransferase, Drosophila melanogaster Juvenile Hormone Acid O-Methyltransferase (DmJHAMT). By introducing DmJHAMT in E. coli engineered to produce medium chain fatty acids and overproduce SAM, we obtain medium chain FAMEs at titers of 0.56 g/L, a 35-fold increase over titers previously achieved. Although considerable improvements will be needed for viable bacterial production of FAMEs and FAEEs for biofuels, it may be easier to optimize and transport the FAME production pathway to other microorganisms because it involves fewer enzymes.
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Huang L, Zhao L, Zan X, Song Y, Ratledge C. Boosting fatty acid synthesis in Rhodococcus opacus PD630 by overexpression of autologous thioesterases. Biotechnol Lett 2016; 38:999-1008. [PMID: 26956236 DOI: 10.1007/s10529-016-2072-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2015] [Accepted: 03/01/2016] [Indexed: 02/05/2023]
Abstract
OBJECTIVES To explore the role of thioesterases in Rhodococcus opacus PD630 by endogenously overexpression in this bacteria for increased lipid production. RESULTS Overexpression of four thioesterases from R. opacus PD630 in E. coli led to a 2- to 8-fold increase in C16:1 and C18:1 fatty acids while, when overexpressed in R. opacus PD630, only two recombinants had significant effect on the quantities and compositions of total fatty acid. The contents of total fatty acids (FAs) in two recombinants, pJTE2 (OPAG_00508 thioesterase) and pJTE4 (WP_012687673.1 thioesterase), were 400-460 mg/g (CDW) which is 1.5 times of wild-type strain PD630 (300-350 mg/g CDW), and 20-30 % (w/w) more than that of the control strain PDpJAM2 (330-370 mg/g CDW). The contents of 17:1 and 18:1 fatty acids increased by about 27 and 35 %, respectively, in pJTE2 and by 35 and 20 %, respectively, in pJTE4 compared with the control strain. CONCLUSIONS The engineered strains showed improved production of lipid (as total fatty acids), and could also tailor the composition of the fatty acid profile when cultured in mineral salts medium using glucose as sole carbon source.
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Affiliation(s)
- Luxuan Huang
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, Jiangsu, People's Republic of China
| | - Lina Zhao
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, Jiangsu, People's Republic of China
| | - Xinyi Zan
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, Jiangsu, People's Republic of China
| | - Yuanda Song
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, Jiangsu, People's Republic of China. .,Colin Ratledge Center for Microbial Lipids, School of Agricultural Engineering and Food Science, Shandong University of Technology, Zibo, 255049, Shandong, People's Republic of China.
| | - Colin Ratledge
- School of Biological Sciences, University of Hull, Hull, HU6 7RX, UK
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Tao H, Guo D, Zhang Y, Deng Z, Liu T. Metabolic engineering of microbes for branched-chain biodiesel production with low-temperature property. BIOTECHNOLOGY FOR BIOFUELS 2015; 8:92. [PMID: 26120362 PMCID: PMC4483204 DOI: 10.1186/s13068-015-0270-7] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Accepted: 06/05/2015] [Indexed: 05/08/2023]
Abstract
BACKGROUND The steadily increasing demand for diesel fuels calls for renewable energy sources. This has attracted a growing amount of research to develop advanced, alternative biodiesel worldwide. Several major disadvantages of current biodiesels are the undesirable physical properties such as high viscosity and poor low-temperature operability. Therefore, there is an urgent need to develop novel and advanced biodiesels. RESULTS Inspired by the proven capability of wax ester synthase/acyl-coenzyme A, diacylglycerol acyltransferase (WS/DGAT) to generate fatty acid esters, de novo biosynthesis of fatty acid branched-chain esters (FABCEs) and branched fatty acid branched-chain esters (BFABCEs) was performed in engineered Escherichia coli through combination of the (branched) fatty acid biosynthetic pathway and the branched-chain amino acid biosynthetic pathway. Furthermore, by modifying the fatty acid pathway, we improved FABCE production to 273 mg/L and achieved a high proportion of FABCEs at 99.3 % of total fatty acid esters. In order to investigate the universality of this strategy, Pichia pastoris yeast was engineered and produced desirable levels of FABCEs for the first time with a good starting point of 169 mg/L. CONCLUSIONS We propose new pathways of fatty acid ester biosynthesis and establish proof of concept through metabolic engineering of E. coli and P. pastoris yeast. We were able to produce advanced biodiesels with high proportions FABCEs and BFABCEs. Furthermore, this new strategy promises to achieve advanced biodiesels with beneficial low-temperature properties.
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Affiliation(s)
- Hui Tao
- />Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education and Wuhan University School of Pharmaceutical Sciences, Wuhan, 430071 China
- />Hubei Engineering Laboratory for Synthetic Microbiology, Wuhan Institute of Biotechnology, Wuhan, 430075 China
| | - Daoyi Guo
- />Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education and Wuhan University School of Pharmaceutical Sciences, Wuhan, 430071 China
| | - Yuchen Zhang
- />Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education and Wuhan University School of Pharmaceutical Sciences, Wuhan, 430071 China
- />Hubei Engineering Laboratory for Synthetic Microbiology, Wuhan Institute of Biotechnology, Wuhan, 430075 China
| | - Zixin Deng
- />Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education and Wuhan University School of Pharmaceutical Sciences, Wuhan, 430071 China
- />Hubei Engineering Laboratory for Synthetic Microbiology, Wuhan Institute of Biotechnology, Wuhan, 430075 China
- />State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240 China
| | - Tiangang Liu
- />Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education and Wuhan University School of Pharmaceutical Sciences, Wuhan, 430071 China
- />Hubei Engineering Laboratory for Synthetic Microbiology, Wuhan Institute of Biotechnology, Wuhan, 430075 China
- />Hubei Provincial Cooperative Innovation Center of Industrial Fermentation, Wuhan, 430068 China
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Liu X, Yu H, Jiang X, Ai G, Yu B, Zhu K. Biosynthesis of butenoic acid through fatty acid biosynthesis pathway in Escherichia coli. Appl Microbiol Biotechnol 2014; 99:1795-804. [DOI: 10.1007/s00253-014-6233-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2014] [Revised: 11/05/2014] [Accepted: 11/13/2014] [Indexed: 11/29/2022]
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Rahman Z, Sung BH, Yi JY, Bui LM, Lee JH, Kim SC. Enhanced production of n-alkanes in Escherichia coli by spatial organization of biosynthetic pathway enzymes. J Biotechnol 2014; 192 Pt A:187-91. [DOI: 10.1016/j.jbiotec.2014.10.014] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2014] [Revised: 10/10/2014] [Accepted: 10/13/2014] [Indexed: 11/28/2022]
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Sherkhanov S, Korman TP, Bowie JU. Improving the tolerance of Escherichia coli to medium-chain fatty acid production. Metab Eng 2014; 25:1-7. [DOI: 10.1016/j.ymben.2014.06.003] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2014] [Revised: 05/22/2014] [Accepted: 06/04/2014] [Indexed: 12/17/2022]
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Tee TW, Chowdhury A, Maranas CD, Shanks JV. Systems metabolic engineering design: fatty acid production as an emerging case study. Biotechnol Bioeng 2014; 111:849-57. [PMID: 24481660 PMCID: PMC4241050 DOI: 10.1002/bit.25205] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2013] [Revised: 01/21/2014] [Accepted: 01/28/2014] [Indexed: 12/20/2022]
Abstract
Increasing demand for petroleum has stimulated industry to develop sustainable production of chemicals and biofuels using microbial cell factories. Fatty acids of chain lengths from C6 to C16 are propitious intermediates for the catalytic synthesis of industrial chemicals and diesel-like biofuels. The abundance of genetic information available for Escherichia coli and specifically, fatty acid metabolism in E. coli, supports this bacterium as a promising host for engineering a biocatalyst for the microbial production of fatty acids. Recent successes rooted in different features of systems metabolic engineering in the strain design of high-yielding medium chain fatty acid producing E. coli strains provide an emerging case study of design methods for effective strain design. Classical metabolic engineering and synthetic biology approaches enabled different and distinct design paths towards a high-yielding strain. Here we highlight a rational strain design process in systems biology, an integrated computational and experimental approach for carboxylic acid production, as an alternative method. Additional challenges inherent in achieving an optimal strain for commercialization of medium chain-length fatty acids will likely require a collection of strategies from systems metabolic engineering. Not only will the continued advancement in systems metabolic engineering result in these highly productive strains more quickly, this knowledge will extend more rapidly the carboxylic acid platform to the microbial production of carboxylic acids with alternate chain-lengths and functionalities.
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Affiliation(s)
- Ting Wei Tee
- Department of Chemical and Biological Engineering, Iowa State University, Ames, Iowa
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Janßen HJ, Steinbüchel A. Fatty acid synthesis in Escherichia coli and its applications towards the production of fatty acid based biofuels. BIOTECHNOLOGY FOR BIOFUELS 2014; 7:7. [PMID: 24405789 PMCID: PMC3896788 DOI: 10.1186/1754-6834-7-7] [Citation(s) in RCA: 180] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2013] [Accepted: 12/24/2013] [Indexed: 05/04/2023]
Abstract
The idea of renewable and regenerative resources has inspired research for more than a hundred years. Ideally, the only spent energy will replenish itself, like plant material, sunlight, thermal energy or wind. Biodiesel or ethanol are examples, since their production relies mainly on plant material. However, it has become apparent that crop derived biofuels will not be sufficient to satisfy future energy demands. Thus, especially in the last decade a lot of research has focused on the production of next generation biofuels. A major subject of these investigations has been the microbial fatty acid biosynthesis with the aim to produce fatty acids or derivatives for substitution of diesel. As an industrially important organism and with the best studied microbial fatty acid biosynthesis, Escherichia coli has been chosen as producer in many of these studies and several reviews have been published in the fields of E. coli fatty acid biosynthesis or biofuels. However, most reviews discuss only one of these topics in detail, despite the fact, that a profound understanding of the involved enzymes and their regulation is necessary for efficient genetic engineering of the entire pathway. The first part of this review aims at summarizing the knowledge about fatty acid biosynthesis of E. coli and its regulation, and it provides the connection towards the production of fatty acids and related biofuels. The second part gives an overview about the achievements by genetic engineering of the fatty acid biosynthesis towards the production of next generation biofuels. Finally, the actual importance and potential of fatty acid-based biofuels will be discussed.
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Affiliation(s)
- Helge Jans Janßen
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität Münster, Corrensstrasse 3, D-48149, Münster, Germany
| | - Alexander Steinbüchel
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität Münster, Corrensstrasse 3, D-48149, Münster, Germany
- Environmental Sciences Department, King Abdulaziz University, Jeddah, Saudi Arabia
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Janßen HJ, Steinbüchel A. Production of triacylglycerols in Escherichia coli by deletion of the diacylglycerol kinase gene and heterologous overexpression of atfA from Acinetobacter baylyi ADP1. Appl Microbiol Biotechnol 2014; 98:1913-24. [PMID: 24389701 DOI: 10.1007/s00253-013-5460-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2013] [Revised: 12/03/2013] [Accepted: 12/05/2013] [Indexed: 12/20/2022]
Abstract
This study investigated the production of triacylglycerols in cells of the wild type of Escherichia coli and of a strain with a deleted diacylglycerol kinase gene (dgkA). By overexpression of atfA from Acinetobacter baylyi ADP1 and fadD from E. coli in the dgkA deletion mutant, cellular contents of up to 4.9% (w/w) triacylglycerols could be achieved in batch cultivation. Furthermore, heterologous expression of atfA relieves the negative effects of dgkA deletion on growth. Process optimization and fed-batch fermentation resulted in the production of 530 mg l (-1) triacylglycerols and a maximal content of 8.5% (w/w) triacylglycerols of the cell dry mass. This clearly exceeded all previous results concerning triacylglycerol production in E. coli. Furthermore, the production of extracellular free fatty acids and fatty acid ethyl esters was investigated. Like triacylglycerols, both products are potential biofuels, and we show their continuous production in a repeated batch process, with recovery of the production cells.
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Affiliation(s)
- Helge Jans Janßen
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität Münster, Corrensstrasse 3, 48149, Münster, Germany,
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Cao Y, Liu W, Xu X, Zhang H, Wang J, Xian M. Production of free monounsaturated fatty acids by metabolically engineered Escherichia coli. BIOTECHNOLOGY FOR BIOFUELS 2014; 7:59. [PMID: 24716602 PMCID: PMC4021618 DOI: 10.1186/1754-6834-7-59] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2013] [Accepted: 03/17/2014] [Indexed: 05/22/2023]
Abstract
BACKGROUND Monounsaturated fatty acids (MUFAs) are the best components for biodiesel when considering the low temperature fluidity and oxidative stability. However, biodiesel derived from vegetable oils or microbial lipids always consists of significant amounts of polyunsaturated and saturated fatty acids (SFAs) alkyl esters, which hampers its practical applications. Therefore, the fatty acid composition should be modified to increase MUFA contents as well as enhancing oil and lipid production. RESULTS The model microorganism Escherichia coli was engineered to produce free MUFAs. The fatty acyl-ACP thioesterase (AtFatA) and fatty acid desaturase (SSI2) from Arabidopsis thaliana were heterologously expressed in E. coli BL21 star(DE3) to specifically release free unsaturated fatty acids (UFAs) and convert SFAs to UFAs. In addition, the endogenous fadD gene (encoding acyl-CoA synthetase) was disrupted to block fatty acid catabolism while the native acetyl-CoA carboxylase (ACCase) was overexpressed to increase the malonyl coenzyme A (malonyl-CoA) pool and boost fatty acid biosynthesis. The finally engineered strain BL21ΔfadD/pE-AtFatAssi2&pA-acc produced 82.6 mg/L free fatty acids (FFAs) under shake-flask conditions and FFAs yield on glucose reached about 3.3% of the theoretical yield. Two types of MUFAs, palmitoleate (16:1Δ9) and cis-vaccenate (18:1Δ11) made up more than 75% of the FFA profiles. Fed-batch fermentation of this strain further enhanced FFAs production to a titer of 1.27 g/L without affecting fatty acid compositions. CONCLUSIONS This study demonstrated the possibility to regulate fatty acid composition by using metabolic engineering approaches. FFAs produced by the recombinant E. coli strain consisted of high-level MUFAs and biodiesel manufactured from these fatty acids would be more suitable for current diesel engines.
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Affiliation(s)
- Yujin Cao
- CAS Key Laboratory of Bio-based Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
| | - Wei Liu
- CAS Key Laboratory of Bio-based Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
| | - Xin Xu
- CAS Key Laboratory of Bio-based Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
| | - Haibo Zhang
- CAS Key Laboratory of Bio-based Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
| | - Jiming Wang
- CAS Key Laboratory of Bio-based Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
| | - Mo Xian
- CAS Key Laboratory of Bio-based Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
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Expression of dehydratase domains from a polyunsaturated fatty acid synthase increases the production of fatty acids in Escherichia coli. Enzyme Microb Technol 2013; 55:133-9. [PMID: 24411456 DOI: 10.1016/j.enzmictec.2013.10.010] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2013] [Revised: 10/24/2013] [Accepted: 10/25/2013] [Indexed: 12/26/2022]
Abstract
Increasing the production of fatty acids by microbial fermentation remains an important step toward the generation of biodiesel and other portable liquid fuels. In this work, we report an Escherichia coli strain engineered to overexpress a fragment consisting of four dehydratase domains from the polyunsaturated fatty acid (PUFA) synthase enzyme complex from the deep-sea bacterium, Photobacterium profundum. The DH1-DH2-UMA enzyme fragment was excised from its natural context within a multi-enzyme PKS and expressed as a stand-alone protein. Fatty acids were extracted from the cell pellet, esterified with methanol and quantified by GC-MS analysis. Results show that the E. coli strain expressing the DH tetradomain fragment was capable of producing up to a 5-fold increase (80.31 mg total FA/L culture) in total fatty acids over the negative control strain lacking the recombinant enzyme. The enhancement in production was observed across the board for all the fatty acids that are typically made by E. coli. The overexpression of the DH tetradomain did not affect E. coli cell growth, thus showing that the observed enhancement in fatty acid production was not a result of effects associated with cell density. The observed enhancement was more pronounced at lower temperatures (3.8-fold at 16 °C, 3.5-fold at 22 °C and 1.5-fold at 30 °C) and supplementation of the media with 0.4% glycerol did not result in an increase in fatty acid production. All these results taken together suggest that either the dehydration of fatty acid intermediates are a limiting step in the E. coli fatty acid biosynthesis machinery, or that the recombinant dehydratase domains used in this study are also capable of catalyzing thioester hydrolysis of the final products. The enzyme in this report is a new tool which could be incorporated into other existing strategies aimed at improving fatty acid production in bacterial fermentations toward accessible biodiesel precursors.
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Microbial production of short-chain alkanes. Nature 2013; 502:571-4. [DOI: 10.1038/nature12536] [Citation(s) in RCA: 356] [Impact Index Per Article: 32.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2013] [Accepted: 08/08/2013] [Indexed: 12/19/2022]
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37
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Youngquist JT, Rose JP, Pfleger BF. Free fatty acid production in Escherichia coli under phosphate-limited conditions. Appl Microbiol Biotechnol 2013; 97:5149-59. [PMID: 23619909 DOI: 10.1007/s00253-013-4911-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2013] [Revised: 03/27/2013] [Accepted: 04/07/2013] [Indexed: 01/30/2023]
Abstract
Microbially synthesized fatty acids are an attractive platform for producing renewable alternatives to petrochemically derived transportation fuels and oleochemicals. Free fatty acids (FFA) are a direct precursor to many high-value compounds that can be made via biochemical and ex vivo catalytic pathways. To be competitive with current petrochemicals, flux through these pathways must be optimized to approach theoretical yields. Using a plasmid-free, FFA-producing strain of Escherichia coli, a set of chemostat experiments were conducted to gather data for FFA production under phosphate limitation. A prior study focused on carbon-limited conditions strongly implicated non-carbon limitations as a preferred media formulation for maximizing FFA yield. Here, additional data were collected to expand an established kinetic model of FFA production and identify targets for further metabolic engineering. The updated model was able to successfully predict the strain's behavior and FFA production in a batch culture. The highest yield observed under phosphate-limiting conditions (0.1 g FFA/g glucose) was obtained at a dilution rate of 0.1 h(-1), and the highest biomass-specific productivity (0.068 g FFA/gDCW/h) was observed at a dilution rate of 0.25 h(-1). Phosphate limitation increased yield (∼45 %) and biomass-specific productivity (∼300 %) relative to carbon-limited cultivations using the same strain. FFA production under phosphate limitation also led to a cellular maintenance energy ∼400 % higher (0.28 g/gDCW/h) than that seen under carbon limitation.
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Affiliation(s)
- J Tyler Youngquist
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, 3629 Engineering Hall, 1415 Engineering Dr, Madison, WI 53706, USA
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Rodríguez-Guilbe M, Oyola-Robles D, Schreiter ER, Baerga-Ortiz A. Structure, activity, and substrate selectivity of the Orf6 thioesterase from Photobacterium profundum. J Biol Chem 2013; 288:10841-8. [PMID: 23430744 DOI: 10.1074/jbc.m112.446765] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Thioesterase activity is typically required for the release of products from polyketide synthase enzymes, but no such enzyme has been characterized in deep-sea bacteria associated with the production of polyunsaturated fatty acids. In this work, we have expressed and purified the Orf6 thioesterase from Photobacterium profundum. Enzyme assays revealed that Orf6 has a higher specific activity toward long-chain fatty acyl-CoA substrates (palmitoyl-CoA and eicosapentaenoyl-CoA) than toward short-chain or aromatic acyl-CoA substrates. We determined a high resolution (1.05 Å) structure of Orf6 that reveals a hotdog hydrolase fold arranged as a dimer of dimers. The putative active site of this structure is occupied by additional electron density not accounted for by the protein sequence, consistent with the presence of an elongated compound. A second crystal structure (1.40 Å) was obtained from a crystal that was grown in the presence of Mg(2+), which reveals the presence of a binding site for divalent cations at a crystal contact. The Mg(2+)-bound structure shows localized conformational changes (root mean square deviation of 1.63 Å), and its active site is unoccupied, suggesting a mechanism to open the active site for substrate entry or product release. These findings reveal a new thioesterase enzyme with a preference for long-chain CoA substrates in a deep-sea bacterium whose potential range of applications includes bioremediation and the production of biofuels.
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Affiliation(s)
- María Rodríguez-Guilbe
- Department of Biochemistry, University of Puerto Rico School of Medicine, San Juan, Puerto Rico
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Zheng Y, Liu Q, Li L, Qin W, Yang J, Zhang H, Jiang X, Cheng T, Liu W, Xu X, Xian M. Metabolic engineering of Escherichia coli for high-specificity production of isoprenol and prenol as next generation of biofuels. BIOTECHNOLOGY FOR BIOFUELS 2013; 6:57. [PMID: 23618128 PMCID: PMC3654967 DOI: 10.1186/1754-6834-6-57] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2013] [Accepted: 04/12/2013] [Indexed: 05/06/2023]
Abstract
BACKGROUND The isopentenols, including isoprenol and prenol, are excellent alternative fuels. However, they are not compounds largely accumulated in natural organism. The need for the next generation of biofuels with better physical and chemical properties impels us to develop biosynthetic routes for the production of isoprenol and prenol from renewable sugar. In this study, we use the heterogenous mevalonate-dependent (MVA) isoprenoid pathway for the synthesis of isopentenyl pyrophosphate (IPP) and dimethylallyl pyrophosphate (DMAPP) intermediates, and then convert IPP and DMAPP to isoprenol and prenol, respectively. RESULTS A mevalonate titer of 1.7 g/L was obtained by constructing an efficient MVA upper pathway in engineered E. coli. Different phosphatases and pyrophosphatases were investigated for their abilities in hydrolyzing the IPP and DMAPP. Consequently, ADP-ribose pyrophosphatase was found to be an efficient IPP and DMAPP hydrolase. Moreover, ADP-ribose pyrophosphatase from Bacillus subtilis (BsNudF) exhibited a equivalent substrate specificity towards IPP and DMAPP, while ADP-ribose pyrophosphatase from E. coli (EcNudF) presented a high substrate preference for DMAPP. Without the expression of any phosphatases or pyrophosphatases, a background level of isopentenols was synthesized. When the endogenous pyrophosphatase genes (EcNudF and yggV) that were capable of enhancing the hydrolyzation of the IPP and DMAPP were knocked out, the background level of isopentenols was still obtained. Maybe the synthesized IPP and DMAPP were hydrolyzed by some unknown hydrolases of E. coli. Finally, 1.3 g/L single isoprenol was obtained by blocking the conversion of IPP to DMAPP and employing the BsNudF, and 0.2 g/L ~80% prenol was produced by employing the EcNudF. A maximal yield of 12% was achieved in both isoprenol and prenol producing strains. CONCLUSIONS To the best of our knowledge, this is the first successful report on high-specificity production of isoprenol and prenol by microbial fermentation. Over 1.3 g/L isoprenol achieved in shake-flask experiments represents a quite encouraging titer of higher alcohols. In addition, the substrate specificities of ADP-ribose pyrophosphatases were determined and successfully applied for the high-specificity synthesis of isoprenol and prenol. Altogether, this work presents a promising strategy for high-specificity production of two excellent biofuels, isoprenol and prenol.
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Affiliation(s)
- Yanning Zheng
- CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No.189 Songling Road, Laoshan District, Qingdao, 266101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Qiang Liu
- College of Food Science, Sichuan Agricultural University, Yaan, 625014, China
| | - Lingling Li
- College of Food Science, Sichuan Agricultural University, Yaan, 625014, China
| | - Wen Qin
- College of Food Science, Sichuan Agricultural University, Yaan, 625014, China
| | - Jianming Yang
- CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No.189 Songling Road, Laoshan District, Qingdao, 266101, China
| | - Haibo Zhang
- CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No.189 Songling Road, Laoshan District, Qingdao, 266101, China
| | - Xinglin Jiang
- CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No.189 Songling Road, Laoshan District, Qingdao, 266101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Tao Cheng
- CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No.189 Songling Road, Laoshan District, Qingdao, 266101, China
| | - Wei Liu
- CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No.189 Songling Road, Laoshan District, Qingdao, 266101, China
| | - Xin Xu
- CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No.189 Songling Road, Laoshan District, Qingdao, 266101, China
| | - Mo Xian
- CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No.189 Songling Road, Laoshan District, Qingdao, 266101, China
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