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Jing F, Chen K, Yandeau-Nelson MD, Nikolau BJ. Machine learning model of the catalytic efficiency and substrate specificity of acyl-ACP thioesterase variants generated from natural and in vitro directed evolution. Front Bioeng Biotechnol 2024; 12:1379121. [PMID: 38665811 PMCID: PMC11043601 DOI: 10.3389/fbioe.2024.1379121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Accepted: 03/28/2024] [Indexed: 04/28/2024] Open
Abstract
Modulating the catalytic activity of acyl-ACP thioesterase (TE) is an important biotechnological target for effectively increasing flux and diversifying products of the fatty acid biosynthesis pathway. In this study, a directed evolution approach was developed to improve the fatty acid titer and fatty acid diversity produced by E. coli strains expressing variant acyl-ACP TEs. A single round of in vitro directed evolution, coupled with a high-throughput colorimetric screen, identified 26 novel acyl-ACP TE variants that convey up to a 10-fold increase in fatty acid titer, and generate altered fatty acid profiles when expressed in a bacterial host strain. These in vitro-generated variant acyl-ACP TEs, in combination with 31 previously characterized natural variants isolated from diverse phylogenetic origins, were analyzed with a random forest classifier machine learning tool. The resulting quantitative model identified 22 amino acid residues, which define important structural features that determine the catalytic efficiency and substrate specificity of acyl-ACP TE.
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Affiliation(s)
- Fuyuan Jing
- Roy J. Carver Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, IA, United States
- Center for Metabolic Biology, Iowa State University, Ames, IA, United States
- Engineering Research Center for Biorenewable Chemicals, Iowa State University, Ames, IA, United States
| | - Keting Chen
- Roy J. Carver Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, IA, United States
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA, United States
| | - Marna D. Yandeau-Nelson
- Center for Metabolic Biology, Iowa State University, Ames, IA, United States
- Engineering Research Center for Biorenewable Chemicals, Iowa State University, Ames, IA, United States
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA, United States
| | - Basil J. Nikolau
- Roy J. Carver Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, IA, United States
- Center for Metabolic Biology, Iowa State University, Ames, IA, United States
- Engineering Research Center for Biorenewable Chemicals, Iowa State University, Ames, IA, United States
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2
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Nyunoya H, Ishibashi Y, Ito M, Okino N. Significance of mitochondrial fatty acid β-oxidation for the survivability of Aurantiochytrium limacinum ATCC MYA-1381 during sugar starvation. Biosci Biotechnol Biochem 2022; 86:1524-1535. [PMID: 35998312 DOI: 10.1093/bbb/zbac141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 08/10/2022] [Indexed: 11/12/2022]
Abstract
Thraustochytrids are marine protists that accumulate large amounts of palmitic acid and docosahexaenoic acid in lipid droplets. Random insertional mutagenesis was adopted for Aurantiochytrium limacinum ATCC MYA-1381 to search for genes that regulate lipid metabolism in thraustochytrids. A mutant strain, M17, was selected because of its significant decrease in myristic acid, palmitic acid, and triacylglycerol contents and cell growth defect. Genome analysis revealed that the gene encoding for mitochondrial electron-transfer flavoprotein ubiquinone oxidoreductase (ETFQO) was lacking in the M17 strain. This mutant strain exhibited a growth defect at the stationary phase, possibly due to stagnation of mitochondrial fatty acid β-oxidation and branched-chain amino acid degradation, both of which were caused by lack of ETFQO. This study shows the usability of random insertional mutagenesis to obtain mutants of lipid metabolism in A. limacinum and clarifies that ETFQO is integral for survival under sugar starvation in A. limacinum.
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Affiliation(s)
- Hayato Nyunoya
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Yohei Ishibashi
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Makoto Ito
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Nozomu Okino
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
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3
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Chaturvedi S, Bhattacharya A, Rout PK, Nain L, Khare SK. An Overview of Enzymes and Rate-Limiting Steps Responsible for Lipid Production in Oleaginous Yeast. Ind Biotechnol (New Rochelle N Y) 2022. [DOI: 10.1089/ind.2021.0003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Shivani Chaturvedi
- Enzyme and Microbial Biochemistry Laboratory, Department of Chemistry, Indian Institute of Technology, Delhi, India
| | - Amrik Bhattacharya
- Enzyme and Microbial Biochemistry Laboratory, Department of Chemistry, Indian Institute of Technology, Delhi, India
| | - Prasant K. Rout
- Phytochemistry Division, CSIR-Central Institute of Medicinal and Aromatic Plants, Lucknow, Uttar Pradesh, India
| | - Lata Nain
- Division of Microbiology, ICAR- Indian Agricultural Research Institute, New Delhi, India
| | - Sunil K. Khare
- Enzyme and Microbial Biochemistry Laboratory, Department of Chemistry, Indian Institute of Technology, Delhi, India
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Hu XM, Zhang J, Ding WY, Liang X, Wan R, Dobretsov S, Yang JL. Reduction of mussel metamorphosis by inactivation of the bacterial thioesterase gene via alteration of the fatty acid composition. BIOFOULING 2021; 37:911-921. [PMID: 34620016 DOI: 10.1080/08927014.2021.1981882] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 09/12/2021] [Accepted: 09/14/2021] [Indexed: 06/13/2023]
Abstract
The molecular mechanism underlying modulation of metamorphosis of the bivalve Mytilus coruscus by bacteria remains unclear. Here, the functional role of the thioesterase gene tesA of the bacterium Pseudoalteromonas marina in larval metamorphosis was examined. The aim was to determine whether inactivation of the tesA gene altered the biofilm-inducing capacity, bacterial cell motility, biopolymers, or the intracellular c-di-GMP levels. Complete inactivation of tesA increased the c-di-GMP content in P. marina, accompanied by a reduced fatty acid content, weaker motility, upregulation of bacterial aggregation, and biofilm formation. The metamorphosis rate of mussel larvae on ΔtesA biofilms was reduced by ∼ 80% compared with those settling on wild-type P. marina. Exogenous addition of a mixture of extracted fatty acids from P. marina into the ΔtesA biofilms promoted the biofilm-inducing capacity. This study suggests that the bacterial thioesterase gene tesA altered the fatty acid composition of ΔtesA P. marina biofilms (BF) through regulation of its c-di-GMP, subsequently impacting mussel metamorphosis.
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Affiliation(s)
- Xiao-Meng Hu
- International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University, Shanghai, PR China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, PR China
| | - Junbo Zhang
- College of Marine Sciences, Shanghai Ocean University, Shanghai, PR China
- National Engineering Research Center for Oceanic Fisheries, Shanghai, PR China
| | - Wen-Yang Ding
- International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University, Shanghai, PR China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, PR China
| | - Xiao Liang
- International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University, Shanghai, PR China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, PR China
| | - Rong Wan
- College of Marine Sciences, Shanghai Ocean University, Shanghai, PR China
- National Engineering Research Center for Oceanic Fisheries, Shanghai, PR China
- Zhoushan Branch of National Engineering Research Center for Oceanic Fisheries, Zhoushan, PR China
| | - Sergey Dobretsov
- Department of Marine Science and Fisheries, College of Agricultural and Marine Sciences, Sultan Qaboos University, Muscat, Oman
- Center of Excellence in Marine Biotechnology, Sultan Qaboos University, Muscat, Oman
| | - Jin-Long Yang
- International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University, Shanghai, PR China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, PR China
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5
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Machinandiarena F, Nakamatsu L, Schujman GE, de Mendoza D, Albanesi D. Revisiting the coupling of fatty acid to phospholipid synthesis in bacteria with FapR regulation. Mol Microbiol 2020; 114:653-663. [PMID: 32671874 DOI: 10.1111/mmi.14574] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 07/07/2020] [Accepted: 07/11/2020] [Indexed: 12/31/2022]
Abstract
A key aspect in membrane biogenesis is the coordination of fatty acid to phospholipid synthesis rates. In most bacteria, PlsX is the first enzyme of the phosphatidic acid synthesis pathway, the common precursor of all phospholipids. Previously, we proposed that PlsX is a key regulatory point that synchronizes the fatty acid synthase II with phospholipid synthesis in Bacillus subtilis. However, understanding the basis of such coordination mechanism remained a challenge in Gram-positive bacteria. Here, we show that the inhibition of fatty acid and phospholipid synthesis caused by PlsX depletion leads to the accumulation of long-chain acyl-ACPs, the end products of the fatty acid synthase II. Hydrolysis of the acyl-ACP pool by heterologous expression of a cytosolic thioesterase relieves the inhibition of fatty acid synthesis, indicating that acyl-ACPs are feedback inhibitors of this metabolic route. Unexpectedly, inactivation of PlsX triggers a large increase of malonyl-CoA leading to induction of the fap regulon. This finding discards the hypothesis, proposed for B. subtilis and extended to other Gram-positive bacteria, that acyl-ACPs are feedback inhibitors of the acetyl-CoA carboxylase. Finally, we propose that the continuous production of malonyl-CoA during phospholipid synthesis inhibition provides an additional mechanism for fine-tuning the coupling between phospholipid and fatty acid production in bacteria with FapR regulation.
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Affiliation(s)
- Federico Machinandiarena
- Instituto de Biología Molecular y Celular de Rosario (IBR), CONICET, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Leandro Nakamatsu
- División de Biología Sintética, Ingeniería Metabólica SA (INMET), Rosario, Argentina
| | - Gustavo E Schujman
- División de Biología Sintética, Ingeniería Metabólica SA (INMET), Rosario, Argentina.,CONICET, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Diego de Mendoza
- Instituto de Biología Molecular y Celular de Rosario (IBR), CONICET, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Daniela Albanesi
- Instituto de Biología Molecular y Celular de Rosario (IBR), CONICET, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
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6
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Increased Accumulation of Medium-Chain Fatty Acids by Dynamic Degradation of Long-Chain Fatty Acids in Mucor circinelloides. Genes (Basel) 2020; 11:genes11080890. [PMID: 32764225 PMCID: PMC7464202 DOI: 10.3390/genes11080890] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 07/22/2020] [Accepted: 07/27/2020] [Indexed: 12/12/2022] Open
Abstract
Concerns about global warming, fossil-fuel depletion, food security, and human health have promoted metabolic engineers to develop tools/strategies to overproduce microbial functional oils directly from renewable resources. Medium-chain fatty acids (MCFAs, C8–C12) have been shown to be important sources due to their diverse biotechnological importance, providing benefits ranging from functional lipids to uses in bio-fuel production. However, oleaginous microbes do not carry native pathways for the production of MCFAs, and therefore, diverse approaches have been adapted to compensate for the requirements of industrial demand. Mucor circinelloides is a promising organism for lipid production (15–36% cell dry weight; CDW) and the investigation of mechanisms of lipid accumulation; however, it mostly produces long-chain fatty acids (LCFAs). To address this challenge, we genetically modified strain M. circinelloides MU758, first by integrating heterologous acyl-ACP thioesterase (TE) into fatty acid synthase (FAS) complex and subsequently by modifying the β-oxidation pathway by disrupting the acyl-CoA oxidase (ACOX) and/or acyl-CoA thioesterase (ACOT) genes with a preference for medium-chain acyl-CoAs, to elevate the yield of MCFAs. The resultant mutant strains (M-1, M-2, and M-3, respectively) showed a significant increase in lipid production in comparison to the wild-type strain (WT). MCFAs in M-1 (47.45%) was sharply increased compared to the wild type strain (2.25%), and it was further increased in M-2 (60.09%) suggesting a negative role of ACOX in MCFAs production. However, MCFAs in M-3 were much decreased compared to M-1,suggesting a positive role of ACOT in MCFAs production. The M-2 strain showed maximum lipid productivity (~1800 milligram per liter per day or mg/L.d) and MCFAs productivity (~1100 mg/L.d). Taken together, this study elaborates on how the combination of two multidimensional approaches, TE gene over-expression and modification of the β-oxidation pathway via substantial knockout of specific ACOX gene, significantly increased the production of MCFAs. This synergistic approach ultimately offers a novel opportunity for synthetic/industrial biologists to increase the content of MCFAs.
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7
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Lim JW, Shin KS, Ryu YS, Lee Y, Lee SK, Kim T. High-Throughput Screening of Acyl-CoA Thioesterase I Mutants Using a Fluid Array Platform. ACS OMEGA 2019; 4:21848-21854. [PMID: 31891062 PMCID: PMC6933594 DOI: 10.1021/acsomega.9b02826] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/01/2019] [Accepted: 11/26/2019] [Indexed: 06/10/2023]
Abstract
Screening target microorganisms from a mutated recombinant library plays a crucial role in advancing synthetic biology and metabolic engineering. However, conventional screening tools have several limitations regarding throughput, cost, and labor. Here, we used the fluid array platform to conduct high-throughput screening (HTS) that identified Escherichia coli 'TesA thioesterase mutants producing elevated yields of free fatty acids (FFAs) from a large (106) mutant library. A growth-based screening method using a TetA-RFP fusion sensing mechanism and a reporter-based screening method using high-level FFA producing mutants were employed to identify these mutants via HTS. The platform was able to cover >95% of the mutation library, and it screened target cells from many arrays of the fluid array platform so that a post-analysis could be conducted by gas chromatography. The 'TesA mutation of each isolated mutant showing improved FFA production in E. coli was characterized, and its enhanced FFA production capability was confirmed.
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Affiliation(s)
- Ji Won Lim
- Department
of Biomedical Engineering, Department of Mechanical Engineering, and Department of
Chemical Engineering, Ulsan National Institute
of Science and Technology, 50 UNIST-gil, Eonyang-eup, Ulsan 44919, Republic
of Korea
| | - Kwang Soo Shin
- Department
of Biomedical Engineering, Department of Mechanical Engineering, and Department of
Chemical Engineering, Ulsan National Institute
of Science and Technology, 50 UNIST-gil, Eonyang-eup, Ulsan 44919, Republic
of Korea
| | - Young Shin Ryu
- Department
of Biomedical Engineering, Department of Mechanical Engineering, and Department of
Chemical Engineering, Ulsan National Institute
of Science and Technology, 50 UNIST-gil, Eonyang-eup, Ulsan 44919, Republic
of Korea
| | - Yongjoo Lee
- Department
of Biomedical Engineering, Department of Mechanical Engineering, and Department of
Chemical Engineering, Ulsan National Institute
of Science and Technology, 50 UNIST-gil, Eonyang-eup, Ulsan 44919, Republic
of Korea
| | - Sung Kuk Lee
- Department
of Biomedical Engineering, Department of Mechanical Engineering, and Department of
Chemical Engineering, Ulsan National Institute
of Science and Technology, 50 UNIST-gil, Eonyang-eup, Ulsan 44919, Republic
of Korea
| | - Taesung Kim
- Department
of Biomedical Engineering, Department of Mechanical Engineering, and Department of
Chemical Engineering, Ulsan National Institute
of Science and Technology, 50 UNIST-gil, Eonyang-eup, Ulsan 44919, Republic
of Korea
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8
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Zuo G, Chen ZP, Jiang YL, Zhu Z, Ding C, Zhang Z, Chen Y, Zhou CZ, Li Q. Structural insights into repression of the Pneumococcal fatty acid synthesis pathway by repressor FabT and co-repressor acyl-ACP. FEBS Lett 2019; 593:2730-2741. [PMID: 31291684 DOI: 10.1002/1873-3468.13534] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2019] [Revised: 06/23/2019] [Accepted: 07/01/2019] [Indexed: 12/26/2022]
Abstract
The Streptococcus pneumoniae fatty acid synthesis (FAS) pathway is globally controlled at the transcriptional level by the repressor FabT and its co-repressor acyl carrier protein (acyl-ACP), the intermediate of phospholipid synthesis. Here, we report the crystal structure of FabT complexed with a 23-bp dsDNA, which indicates that FabT is a weak repressor with low DNA-binding affinity in the absence of acyl-ACP. Modification of ACP with a long-chain fatty acid is necessary for the formation of a stable complex with FabT, mimicked in vitro by cross-linking, which significantly elevates the DNA-binding affinity of FabT. Altogether, we propose a putative working model of gene repression under the double control of FabT and acyl-ACP, elucidating a distinct repression network for Pneumococcus to precisely coordinate FAS.
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Affiliation(s)
- Gang Zuo
- Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, China
| | - Zhi-Peng Chen
- Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, China
| | - Yong-Liang Jiang
- Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, China
| | - Zhongliang Zhu
- Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, China
| | - Chengtao Ding
- Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, China
| | - Zhiyong Zhang
- Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, China
| | - Yuxing Chen
- Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, China
| | - Cong-Zhao Zhou
- Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, China
| | - Qiong Li
- Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, China
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9
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Heil CS, Wehrheim SS, Paithankar KS, Grininger M. Fatty Acid Biosynthesis: Chain‐Length Regulation and Control. Chembiochem 2019; 20:2298-2321. [DOI: 10.1002/cbic.201800809] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Revised: 03/20/2019] [Indexed: 12/18/2022]
Affiliation(s)
- Christina S. Heil
- Institute of Organic Chemistry and Chemical BiologyBuchmann Institute for Molecular Life ScienceGoethe University Frankfurt Max-von-Laue-Strasse 15 60438 Frankfurt am Main Germany
| | - S. Sophia Wehrheim
- Institute of Organic Chemistry and Chemical BiologyBuchmann Institute for Molecular Life ScienceGoethe University Frankfurt Max-von-Laue-Strasse 15 60438 Frankfurt am Main Germany
| | - Karthik S. Paithankar
- Institute of Organic Chemistry and Chemical BiologyBuchmann Institute for Molecular Life ScienceGoethe University Frankfurt Max-von-Laue-Strasse 15 60438 Frankfurt am Main Germany
| | - Martin Grininger
- Institute of Organic Chemistry and Chemical BiologyBuchmann Institute for Molecular Life ScienceGoethe University Frankfurt Max-von-Laue-Strasse 15 60438 Frankfurt am Main Germany
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Yan Q, Pfleger BF. Revisiting metabolic engineering strategies for microbial synthesis of oleochemicals. Metab Eng 2019; 58:35-46. [PMID: 31022535 DOI: 10.1016/j.ymben.2019.04.009] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Revised: 04/20/2019] [Accepted: 04/21/2019] [Indexed: 02/06/2023]
Abstract
Microbial production of oleochemicals from renewable feedstocks remains an attractive route to produce high-energy density, liquid transportation fuels and high-value chemical products. Metabolic engineering strategies have been applied to demonstrate production of a wide range of oleochemicals, including free fatty acids, fatty alcohols, esters, olefins, alkanes, ketones, and polyesters in both bacteria and yeast. The majority of these demonstrations synthesized products containing long-chain fatty acids. These successes motivated additional effort to produce analogous molecules comprised of medium-chain fatty acids, molecules that are less common in natural oils and therefore of higher commercial value. Substantial progress has been made towards producing a subset of these chemicals, but significant work remains for most. The other primary challenge to producing oleochemicals in microbes is improving the performance, in terms of yield, rate, and titer, of biocatalysts such that economic large-scale processes are feasible. Common metabolic engineering strategies include blocking pathways that compete with synthesis of oleochemical building blocks and/or consume products, pulling flux through pathways by removing regulatory signals, pushing flux into biosynthesis by overexpressing rate-limiting enzymes, and engineering cells to tolerate the presence of oleochemical products. In this review, we describe the basic fundamentals of oleochemical synthesis and summarize advances since 2013 towards improving performance of heterotrophic microbial cell factories.
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Affiliation(s)
- Qiang Yan
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI 53706, United States; DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Wisconsin-Madison, Madison, WI 53706, United States
| | - Brian F Pfleger
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI 53706, United States; DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Wisconsin-Madison, Madison, WI 53706, United States; Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, WI 53706, United States.
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11
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Engineering of Fatty Acid Synthases (FASs) to Boost the Production of Medium-Chain Fatty Acids (MCFAs) in Mucor circinelloides. Int J Mol Sci 2019; 20:ijms20030786. [PMID: 30759801 PMCID: PMC6387429 DOI: 10.3390/ijms20030786] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Revised: 02/06/2019] [Accepted: 02/09/2019] [Indexed: 02/06/2023] Open
Abstract
Increasing energy demands and health-related concerns worldwide have motivated researchers to adopt diverse strategies to improve medium-chain fatty acid (MCFA) biosynthesis for use in the functional food and aviation industries. The abundance of naturally produced MCFAs from botanical sources (i.e., coconut fruit/seeds and palm tree) has been observed to be insufficient compared with the various microorganisms used to cope with industrial demands. Mucor circinelloides is one of many promising microorganisms; it exhibits diverse biotechnological importance ranging from the production of functional lipids to applications in the manufacture of bio-fuel. Thus, research was conducted to acquire the desired elevated amounts of MCFAs (i.e., C8–C12) from metabolically engineered strains of M. circinelloides M65. To achieve this goal, four different acyl-acyl carrier protein (ACP) thioesterase (TE)-encoding genes exhibiting a substrate preference for medium-chain acyl-ACP molecules were expressed in M. circinelloides M65, resulting in the generation of C8–C12 fatty acids. Among all the engineered strains, M65-TE-03 and M65-TE-04 demonstrated the highest production of non-native C8–C10 and C12 fatty acids, respectively, in comparison to the control. These recombinant strains biosynthesized MCFAs de novo within the range from 28 to 46% (i.e., 1.14 to 2.77 g/L) of total cell lipids. Moreover, the reduction in chain length eventually resulted in a 1.5–1.75-fold increase in total lipid productivity in the engineered strains. The MCFAs were also found to be integrated into all lipid classes. This work illustrates how the integration of heterologous enzymes in M. circinelloides can offer a novel opportunity to edit the fatty acid synthases (FAS) complex, resulting in increased production of microbial MFCAs.
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12
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LipG a bifunctional phospholipase/thioesterase involved in mycobacterial envelope remodeling. Biosci Rep 2018; 38:BSR20181953. [PMID: 30487163 PMCID: PMC6435540 DOI: 10.1042/bsr20181953] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Revised: 11/27/2018] [Accepted: 11/27/2018] [Indexed: 12/28/2022] Open
Abstract
Tuberculosis caused by Mycobacterium tuberculosis is currently one of the leading causes of death from an infectious agent. The main difficulties encountered in eradicating this bacteria are mainly related to (i) a very complex lipid composition of the bacillus cell wall, (ii) its ability to hide from the immune system inside the granulomas, and (iii) the increasing number of resistant strains. In this context, we were interested in the Rv0646c (lipGMTB ) gene located upstream to the mmaA cluster which is described as being crucial for the production of cell wall components and required for the bacilli adaptation and survival in mouse macrophages. Using biochemical experiments combined with the construction of deletion and overexpression mutant strains in Mycobacterium smegmatis, we found that LipGMTB is a cytoplasmic membrane-associated enzyme that displays both phospholipase and thioesterase activities. Overproduction of LipGMTB decreases the glycopeptidolipids (GPL) level concomitantly to an increase in phosphatidylinositol (PI) which is the precursor of the PI mannoside (PIM), an essential lipid component of the bacterial cell wall. Conversely, deletion of the lipGMS gene in M. smegmatis leads to an overproduction of GPL, and subsequently decreases the strain susceptibility to various antibiotics. All these findings demonstrate that LipG is involved in cell envelope biosynthesis/remodeling, and consequently this enzyme may thus play an important role in mycobacterial physiology.
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13
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van Mastrigt O, Gallegos Tejeda D, Kristensen MN, Abee T, Smid EJ. Aroma formation during cheese ripening is best resembled by Lactococcus lactis retentostat cultures. Microb Cell Fact 2018; 17:104. [PMID: 29973201 PMCID: PMC6030761 DOI: 10.1186/s12934-018-0950-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Accepted: 06/26/2018] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND Cheese ripening is a complex, time consuming and expensive process, which involves the generation of precursors from carbohydrates, proteins and fats and their subsequent conversion into a wide range of compounds responsible for the flavour and texture of the cheese. This study aims to investigate production of cheese aroma compounds outside the cheese matrix that could be applied for instance as food supplements in dairy or non-dairy products. RESULTS In this study, aroma formation by a dairy Lactococcus lactis was analysed as a function of the growth medium [milk, hydrolysed micellar casein isolate (MCI) and chemically defined medium (CDM)] and the cultivation conditions (batch culture, retentostat culture and a milli-cheese model system). In the retentostat cultures, the nutrient supply was severely restricted resulting in low growth rates (~ 0.001 h-1), thereby mimicking cheese ripening conditions in which nutrients are scarce and bacteria hardly grow. In total 82 volatile organic compounds were produced by the bacteria. Despite the use of a chemically defined medium, retentostat cultures had the biggest qualitative overlap in aroma production with the milli-cheese model system (36 out of 54 compounds). In the retentostat cultures, 52 known cheese compounds were produced and several important cheese aroma compounds and/or compounds with a buttery or cheese-like aroma increased in retentostat cultures compared to batch cultures and milli-cheeses, such as esters, methyl ketones, diketones and unsaturated ketones. In cultures on CDM and MCI, free fatty acids and their corresponding degradation products were underrepresented compared to what was found in the milli-cheeses. Addition of a mixture of free fatty acids to CDM and MCI could help to enhance flavour formation in these media, thereby even better resembling flavour formation in cheese. CONCLUSIONS This study demonstrates that retentostat cultivation is the preferred method to produce cheese flavours outside the cheese matrix by mimicking the slow growth of bacteria during cheese ripening.
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Affiliation(s)
- Oscar van Mastrigt
- Food Microbiology, Wageningen University & Research, P.O. Box 17, 6700AA Wageningen, The Netherlands
| | - Diego Gallegos Tejeda
- Food Microbiology, Wageningen University & Research, P.O. Box 17, 6700AA Wageningen, The Netherlands
| | - Mette N. Kristensen
- Arla Innovation Centre, Arla Foods Amba, Agro Food Park 19, 8200 Aarhus N, Denmark
| | - Tjakko Abee
- Food Microbiology, Wageningen University & Research, P.O. Box 17, 6700AA Wageningen, The Netherlands
| | - Eddy J. Smid
- Food Microbiology, Wageningen University & Research, P.O. Box 17, 6700AA Wageningen, The Netherlands
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14
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Evans A, Ribble W, Schexnaydre E, Waldrop GL. Acetyl-CoA carboxylase from Escherichia coli exhibits a pronounced hysteresis when inhibited by palmitoyl-acyl carrier protein. Arch Biochem Biophys 2017; 636:100-109. [DOI: 10.1016/j.abb.2017.10.016] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Revised: 10/24/2017] [Accepted: 10/25/2017] [Indexed: 01/05/2023]
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15
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Ng I, Tan S, Kao P, Chang Y, Chang J. Recent Developments on Genetic Engineering of Microalgae for Biofuels and Bio‐Based Chemicals. Biotechnol J 2017; 12. [DOI: 10.1002/biot.201600644] [Citation(s) in RCA: 121] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Revised: 07/24/2017] [Indexed: 12/15/2022]
Affiliation(s)
- I‐Son Ng
- Department of Chemical EngineeringNational Cheng Kung UniversityTainan70101Taiwan
- Research Center for Energy Technology and StrategyNational Cheng Kung UniversityTainan70101Taiwan
| | - Shih‐I Tan
- Department of Chemical EngineeringNational Cheng Kung UniversityTainan70101Taiwan
| | - Pei‐Hsun Kao
- Department of Chemical EngineeringNational Cheng Kung UniversityTainan70101Taiwan
| | - Yu‐Kaung Chang
- Graduate School of Biochemical EngineeringMing Chi University of TechnologyNew Taipei City24301Taiwan
| | - Jo‐Shu Chang
- Department of Chemical EngineeringNational Cheng Kung UniversityTainan70101Taiwan
- Research Center for Energy Technology and StrategyNational Cheng Kung UniversityTainan70101Taiwan
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16
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Efficient production of free fatty acids from ionic liquid-based acid- or enzyme-catalyzed bamboo hydrolysate. ACTA ACUST UNITED AC 2017; 44:419-430. [DOI: 10.1007/s10295-016-1888-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2016] [Accepted: 12/14/2016] [Indexed: 10/20/2022]
Abstract
Abstract
Two engineered Escherichia coli strains, DQ101 (MG1655 fadD−)/pDQTES and DQ101 (MG1655 fadD−)/pDQTESZ were constructed to investigate the free fatty acid production using ionic liquid-based acid- or enzyme-catalyzed bamboo hydrolysate as carbon source in this study. The plasmid, pDQTES, carrying an acyl-ACP thioesterase ‘TesA of E. coli in pTrc99A was constructed firstly, and then (3R)-hydroxyacyl-ACP dehydratase was ligated after the TesA to give the plasmid pDQTESZ. These two strains exhibited efficient fatty acid production when glucose was used as the sole carbon source, with a final concentration of 2.45 and 3.32 g/L, respectively. The free fatty acid production of the two strains on xylose is not as efficient as that on glucose, which was 2.32 and 2.96 g/L, respectively. For mixed sugars, DQ101 (MG1655 fadD−)-based strains utilized glucose and pentose sequentially under the carbon catabolite repression (CCR) regulation. The highest total FFAs concentration from the mixed sugar culture reached 2.81 g/L by DQ101 (MG1655 fadD−)/pDQTESZ. Furthermore, when ionic liquid-based enzyme-catalyzed bamboo hydrolysate was used as the carbon source, the strain DQ101 (MG1655 fadD−)/pDQTESZ could produce 1.23 g/L FFAs with a yield of 0.13 g/g, and while it just produced 0.65 g/L free fatty acid with the ionic liquid-based acid-catalyzed bamboo hydrolysate as the feedstock. The results suggested that enzymatic catalyzed bamboo hydrolysate with ionic liquid pretreatment could serve as an efficient feedstock for free fatty acid production.
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17
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Qin D, Hu Y, Cheng J, Wang N, Li S, Wang D. An auto-inducible Escherichia coli strain obtained by adaptive laboratory evolution for fatty acid synthesis from ionic liquid-treated bamboo hydrolysate. BIORESOURCE TECHNOLOGY 2016; 221:375-384. [PMID: 27658174 DOI: 10.1016/j.biortech.2016.09.024] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2016] [Revised: 09/03/2016] [Accepted: 09/06/2016] [Indexed: 06/06/2023]
Abstract
Adaptive laboratory evolution (ALE) is a useful metabolic engineering strategy, which allows the selection of the microorganisms with beneficial phenotype through accumulative beneficial mutations among genetic variations occurrencely. Following ALE strategy, a rational constructed Escherichia coli strain DQ101 for fatty acids synthesis was adaptively evolved for 90days with increasing [C4mim]Cl concentration from 1% to 7% (w/v). The evolved strain DQ102 reached a final OD600 of 4.93 at the end of the 24h culture with 7% (w/v) ionic liquid. DQ102/pDQTES with a thioesterase 'TesA overexpression could produce 1.12g/L fatty acid with a productivity of 0.023g/L-h from ionic liquid-treated bamboo hydrolysate. With another β-hydroxyacyl-ACP dehydratases (fabZ) overexpression, DQ102/pDQTESZ could reach a higher concentration of 2.29g/L with a productivity of 0.048g/L-h. These results indicated that ALE could be implemented as a useful tool for metabolic engineering and production of bio-fuels, as well as commodity and specialty chemicals.
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Affiliation(s)
- Dandan Qin
- School of Chemistry and Chemical Engineering, Chongqing University, Chongqing 400044, PR China; State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing University of Technology, Nanjing 210009, PR China
| | - Yuanliang Hu
- Hubei Key Laboratory of Edible Wild Plants Conservation and Utilization, 11 Cihu Road, Huangshi 435002, PR China
| | - Jie Cheng
- School of Chemistry and Chemical Engineering, Chongqing University, Chongqing 400044, PR China
| | - Nan Wang
- School of Chemistry and Chemical Engineering, Chongqing University, Chongqing 400044, PR China
| | - Sha Li
- State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing University of Technology, Nanjing 210009, PR China
| | - Dan Wang
- School of Chemistry and Chemical Engineering, Chongqing University, Chongqing 400044, PR China; State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing University of Technology, Nanjing 210009, PR China.
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18
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Hauf W, Schmid K, Gerhardt ECM, Huergo LF, Forchhammer K. Interaction of the Nitrogen Regulatory Protein GlnB (P II) with Biotin Carboxyl Carrier Protein (BCCP) Controls Acetyl-CoA Levels in the Cyanobacterium Synechocystis sp. PCC 6803. Front Microbiol 2016; 7:1700. [PMID: 27833596 PMCID: PMC5080355 DOI: 10.3389/fmicb.2016.01700] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Accepted: 10/12/2016] [Indexed: 11/13/2022] Open
Abstract
The family of PII signal transduction proteins (members GlnB, GlnK, NifI) plays key roles in various cellular processes related to nitrogen metabolism at different functional levels. Recent studies implied that PII proteins may also be involved in the regulation of fatty acid metabolism, since GlnB proteins from Proteobacteria and from Arabidopsis thaliana were shown to interact with biotin carboxyl carrier protein (BCCP) of acetyl-CoA carboxylase (ACC). In case of Escherichia coli ACCase, this interaction reduces the kcat of acetyl-CoA carboxylation, which should have a marked impact on the acetyl-CoA metabolism. In this study we show that the PII protein of a unicellular cyanobacterium inhibits the biosynthetic activity of E. coli ACC and also interacts with cyanobacterial BCCP in an ATP and 2-oxoglutarate dependent manner. In a PII mutant strain of Synechocystis strain PCC 6803, the lacking control leads to reduced acetyl-CoA levels, slightly increased levels of fatty acids and formation of lipid bodies as well as an altered fatty acid composition.
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Affiliation(s)
- Waldemar Hauf
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen, Eberhard-Karls-Universität Tübingen Tübingen, Germany
| | - Katharina Schmid
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen, Eberhard-Karls-Universität Tübingen Tübingen, Germany
| | - Edileusa C M Gerhardt
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Paraná Curitiba, Brazil
| | - Luciano F Huergo
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal do ParanáCuritiba, Brazil; Setor Litoral, Universidade Federal do ParanáMatinhos, Brazil
| | - Karl Forchhammer
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen, Eberhard-Karls-Universität Tübingen Tübingen, Germany
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Shin KS, Kim S, Lee SK. Improvement of free fatty acid production using a mutant acyl-CoA thioesterase I with high specific activity in Escherichia coli. BIOTECHNOLOGY FOR BIOFUELS 2016; 9:208. [PMID: 27761152 PMCID: PMC5053343 DOI: 10.1186/s13068-016-0622-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Accepted: 09/24/2016] [Indexed: 06/06/2023]
Abstract
BACKGROUND Microbial production of oleochemicals has been actively studied in the last decade. Free fatty acids (FFAs) could be converted into a variety of molecules such as industrial products, consumer products, and fuels. FFAs have been produced in metabolically engineered Escherichia coli cells expressing a signal sequence-deficient acyl-CoA thioesterase I ('TesA). Nonetheless, increasing the expression level of 'TesA seems not to be an appropriate approach to scale up FFA production because a certain ratio of each component including fatty acid synthase and 'TesA is required for optimal production of FFAs. Thus, the catalytic activity of 'TesA should be rationally engineered instead of merely increasing the enzyme expression level to enhance the production of FFAs. RESULTS In this study, we constructed a sensing system with a fusion protein of tetracycline resistance protein and red fluorescent protein (RFP) under the control of a FadR-responsive promoter to select the desired mutants. Fatty acid-dependent growth and RFP expression allowed for selection of FFA-overproducing cells. A 'TesA mutant that produces a twofold greater amount of FFAs was isolated from an error-prone PCR mutant library of E. coli 'TesA. Its kinetic analysis revealed that substitution of Arg64 with Cys64 in the enzyme causes an approximately twofold increase in catalytic activity. CONCLUSIONS Because the expression of 'TesA in E. coli for the production of oleochemicals is almost an indispensable process, the proposed engineering approach has a potential to enhance the production of oleochemicals. The use of the catalytically active mutant 'TesAR64C should accelerate the manufacture of FFA-derived chemicals and fuels.
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Affiliation(s)
- Kwang Soo Shin
- School of Life Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919 Republic of Korea
| | - Sangwoo Kim
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919 Republic of Korea
| | - Sung Kuk Lee
- School of Life Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919 Republic of Korea
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919 Republic of Korea
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20
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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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21
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Garg S, Rizhsky L, Jin H, Yu X, Jing F, Yandeau-Nelson MD, Nikolau BJ. Microbial production of bi-functional molecules by diversification of the fatty acid pathway. Metab Eng 2016; 35:9-20. [DOI: 10.1016/j.ymben.2016.01.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2015] [Accepted: 01/07/2016] [Indexed: 10/22/2022]
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22
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Liao JC, Mi L, Pontrelli S, Luo S. Fuelling the future: microbial engineering for the production of sustainable biofuels. Nat Rev Microbiol 2016; 14:288-304. [DOI: 10.1038/nrmicro.2016.32] [Citation(s) in RCA: 386] [Impact Index Per Article: 48.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
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23
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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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Cross B, Garcia A, Faustoferri R, Quivey RG. PlsX deletion impacts fatty acid synthesis and acid adaptation in Streptococcus mutans. MICROBIOLOGY-SGM 2016; 162:662-671. [PMID: 26850107 DOI: 10.1099/mic.0.000252] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Streptococcus mutans, one of the primary causative agents of dental caries in humans, ferments dietary sugars in the mouth to produce organic acids. These acids lower local pH values, resulting in demineralization of the tooth enamel, leading to caries. To survive acidic environments, Strep. mutans employs several adaptive mechanisms, including a shift from saturated to unsaturated fatty acids in membrane phospholipids. PlsX is an acyl-ACP : phosphate transacylase that links the fatty acid synthase II (FASII) pathway to the phospholipid synthesis pathway, and is therefore central to the movement of unsaturated fatty acids into the membrane. Recently, we discovered that plsX is not essential in Strep. mutans. A plsX deletion mutant was not a fatty acid or phospholipid auxotroph. Gas chromatography of fatty acid methyl esters indicated that membrane fatty acid chain length in the plsX deletion strain differed from those detected in the parent strain, UA159. The deletion strain displayed a fatty acid shift similar to WT, but had a higher percentage of unsaturated fatty acids at low pH. The deletion strain survived significantly longer than the parent strain when cultures were subjected to an acid challenge of pH 2.5.The ΔplsX strain also exhibited elevated F-ATPase activity at pH 5.2, compared with the parent. These results indicate that the loss of plsX affects both the fatty acid synthesis pathway and the acid-adaptive response of Strep. mutans.
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Affiliation(s)
- Benjamin Cross
- Department of Microbiology and Immunology, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642, USA
| | - Ariana Garcia
- Center for Oral Biology in the Eastman Institute for Oral Health, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642, USA
| | - Roberta Faustoferri
- Center for Oral Biology in the Eastman Institute for Oral Health, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642, USA
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Metabolic engineering Corynebacterium glutamicum to produce triacylglycerols. Metab Eng 2015; 33:86-97. [PMID: 26645801 DOI: 10.1016/j.ymben.2015.11.002] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2015] [Revised: 10/04/2015] [Accepted: 11/17/2015] [Indexed: 01/09/2023]
Abstract
In this study, we metabolically engineered Corynebacterium glutamicum to produce triacylglycerols (TAGs) by completing and constraining a de novo TAG biosynthesis pathway. First, the plasmid pZ8_TAG4 was constructed which allows the heterologous expression of four genes: three (atf1 and atf2, encoding the diacylglycerol acyltransferase; pgpB, encoding the phosphatidic acid phosphatase) to complete the TAG biosynthesis pathway, and one gene (tadA) for lipid body assembly. Second, we applied four metabolic strategies to increase TAGs accumulation: (i) boosting precursor supply by heterologous expression of tesA (encoding thioesterase to form free fatty acid to reduce the feedback inhibition by acyl-ACP) and fadD (encoding acyl-CoA synthetase to enhance acyl-CoA supply), (ii) reduction of TAG degradation and precursor consumption by deleting four cellular lipases (cg0109, cg0110, cg1676 and cg1320) and the diacylglycerol kinase (cg2849), (iii) enhancement of fatty acid biosynthesis by deletion of fasR (cg2737, TetR-type transcriptional regulator of genes for the fatty acid biosynthesis), and (iv) elimination of the observed by-product formation of organic acids by blocking the acetic acid (pqo) and lactic acid production (ldh) pathways. The final strain (CgTesRtcEfasEbp/pZ8_TAG4) achieved a 7.5% yield of total fatty acids (2.38 ± 0.05 g/L intracellular fatty acids and 0.64 ± 0.09 g/L extracellular fatty acids) from 4% glucose in shake flasks after process optimization. This corresponds to maximum intracellular fatty acids content of 17.8 ± 0.5% of the dry cell.
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Wang D, Thakker C, Liu P, Bennett GN, San KY. Efficient production of free fatty acids from soybean meal carbohydrates. Biotechnol Bioeng 2015; 112:2324-33. [PMID: 25943383 DOI: 10.1002/bit.25633] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2015] [Revised: 04/05/2015] [Accepted: 04/29/2015] [Indexed: 11/09/2022]
Abstract
Conversion of biomass feedstock to chemicals and fuels has attracted increasing attention recently. Soybean meal, containing significant quantities of carbohydrates, is an inexpensive renewable feedstock. Glucose, galactose, and fructose can be obtained by enzymatic hydrolysis of soluble carbohydrates of soybean meal. Free fatty acids (FFAs) are valuable molecules that can be used as precursors for the production of fuels and other value-added chemicals. In this study, free fatty acids were produced by mutant Escherichia coli strains with plasmid pXZ18Z (carrying acyl-ACP thioesterase (TE) and (3R)-hydroxyacyl-ACP dehydratase) using individual sugars, sugar mixtures, and enzymatic hydrolyzed soybean meal extract. For individual sugar fermentations, strain ML211 (MG1655 fadD(-) fabR(-) )/pXZ18Z showed the best performance, which produced 4.22, 3.79, 3.49 g/L free fatty acids on glucose, fructose, and galactose, respectively. While the strain ML211/pXZ18Z performed the best with individual sugars, however, for sugar mixture fermentation, the triple mutant strain XZK211 (MG1655 fadD(-) fabR(-) ptsG(-) )/pXZ18Z with an additional deletion of ptsG encoding the glucose-specific transporter, functioned the best due to relieved catabolite repression. This strain produced approximately 3.18 g/L of fatty acids with a yield of 0.22 g fatty acids/g total sugar. Maximum free fatty acids production of 2.78 g/L with a high yield of 0.21 g/g was achieved using soybean meal extract hydrolysate. The results suggested that soybean meal carbohydrates after enzymatic treatment could serve as an inexpensive feedstock for the efficient production of free fatty acids.
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Affiliation(s)
- Dan Wang
- Department of Bioengineering, Rice University, 6100 Main Street, MS-362, Houston, Texas, 77005-1892
- College of Chemistry and Chemical Engineering, Chongqing University, Chongqing, P. R. China
| | | | - Ping Liu
- Department of Bioengineering, Rice University, 6100 Main Street, MS-362, Houston, Texas, 77005-1892
| | | | - Ka-Yiu San
- Department of Bioengineering, Rice University, 6100 Main Street, MS-362, Houston, Texas, 77005-1892.
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, Texas.
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Abstract
The pathways in Escherichia coli and (largely by analogy) S. enterica remain the paradigm of bacterial lipid synthetic pathways, although recently considerable diversity among bacteria in the specific areas of lipid synthesis has been demonstrated. The structural biology of the fatty acid synthetic proteins is essentially complete. However, the membrane-bound enzymes of phospholipid synthesis remain recalcitrant to structural analyses. Recent advances in genetic technology have allowed the essentialgenes of lipid synthesis to be tested with rigor, and as expected most genes are essential under standard growth conditions. Conditionally lethal mutants are available in numerous genes, which facilitates physiological analyses. The array of genetic constructs facilitates analysis of the functions of genes from other organisms. Advances in mass spectroscopy have allowed very accurate and detailed analyses of lipid compositions as well as detection of the interactions of lipid biosynthetic proteins with one another and with proteins outside the lipid pathway. The combination of these advances has resulted in use of E. coli and S. enterica for discovery of new antimicrobials targeted to lipid synthesis and in deciphering the molecular actions of known antimicrobials. Finally,roles for bacterial fatty acids other than as membrane lipid structural components have been uncovered. For example, fatty acid synthesis plays major roles in the synthesis of the essential enzyme cofactors, biotin and lipoic acid. Although other roles for bacterial fatty acids, such as synthesis of acyl-homoserine quorum-sensing molecules, are not native to E. coli introduction of the relevant gene(s) synthesis of these foreign molecules readily proceeds and the sophisticated tools available can used to decipher the mechanisms of synthesis of these molecules.
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Coursolle D, Lian J, Shanklin J, Zhao H. Production of long chain alcohols and alkanes upon coexpression of an acyl-ACP reductase and aldehyde-deformylating oxygenase with a bacterial type-I fatty acid synthase in E. coli. MOLECULAR BIOSYSTEMS 2015; 11:2464-72. [PMID: 26135500 DOI: 10.1039/c5mb00268k] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Microbial long chain alcohols and alkanes are renewable biofuels that could one day replace petroleum-derived fuels. Here we report a novel pathway for high efficiency production of these products in Escherichia coli strain BL21(DE3). We first identified the acyl-ACP reductase/aldehyde deformylase combinations with the highest activity in this strain. Next, we used catalase coexpression to remove toxic byproducts and increase the overall titer. Finally, by introducing the type-I fatty acid synthase from Corynebacterium ammoniagenes, we were able to bypass host regulatory mechanisms of fatty acid synthesis that have thus far hampered efforts to optimize the yield of acyl-ACP-derived products in BL21(DE3). When all these engineering strategies were combined with subsequent optimization of fermentation conditions, we were able to achieve a final titer around 100 mg L(-1) long chain alcohol/alkane products including a 57 mg L(-1) titer of pentadecane, the highest titer reported in E. coli BL21(DE3) to date. The expression of prokaryotic type-I fatty acid synthases offer a unique strategy to produce fatty acid-derived products in E. coli that does not rely exclusively on the endogenous type-II fatty acid synthase system.
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Affiliation(s)
- Dan Coursolle
- Department of Chemical and Biomolecular Engineering, Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
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Haushalter RW, Groff D, Deutsch S, The L, Chavkin TA, Brunner SF, Katz L, Keasling JD. Development of an orthogonal fatty acid biosynthesis system in E. coli for oleochemical production. Metab Eng 2015; 30:1-6. [DOI: 10.1016/j.ymben.2015.04.003] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2014] [Revised: 04/03/2015] [Accepted: 04/06/2015] [Indexed: 01/02/2023]
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Rutter CD, Zhang S, Rao CV. Engineering Yarrowia lipolytica for production of medium-chain fatty acids. Appl Microbiol Biotechnol 2015; 99:7359-68. [PMID: 26129951 DOI: 10.1007/s00253-015-6764-1] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Revised: 06/04/2015] [Accepted: 06/08/2015] [Indexed: 12/30/2022]
Abstract
Lipids are naturally derived products that offer an attractive, renewable alternative to petroleum-based hydrocarbons. While naturally produced long-chain fatty acids can replace some petroleum analogs, medium-chain fatty acid would more closely match the desired physical and chemical properties of currently employed petroleum products. In this study, we engineered Yarrowia lipolytica, an oleaginous yeast that naturally produces lipids at high titers, to produce medium-chain fatty acids. Five different acyl-acyl carrier protein (ACP) thioesterases with specificity for medium-chain acyl-ACP molecules were expressed in Y. lipolytica, resulting in formation of either decanoic or octanoic acid. These novel fatty acid products were found to comprise up to 40 % of the total cell lipids. Furthermore, the reduction in chain length resulted in a twofold increase in specific lipid productivity in these engineered strains. The medium-chain fatty acids were found to be incorporated into all lipid classes.
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Affiliation(s)
- Charles D Rutter
- Department of Chemical and Biomolecular Engineering, University of Illinois-Urbana Champaign, 600 S. Mathews Ave, Urbana, IL, 61801, USA
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Beld J, Lee DJ, Burkart MD. Fatty acid biosynthesis revisited: structure elucidation and metabolic engineering. MOLECULAR BIOSYSTEMS 2015; 11:38-59. [PMID: 25360565 PMCID: PMC4276719 DOI: 10.1039/c4mb00443d] [Citation(s) in RCA: 121] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Fatty acids are primary metabolites synthesized by complex, elegant, and essential biosynthetic machinery. Fatty acid synthases resemble an iterative assembly line, with an acyl carrier protein conveying the growing fatty acid to necessary enzymatic domains for modification. Each catalytic domain is a unique enzyme spanning a wide range of folds and structures. Although they harbor the same enzymatic activities, two different types of fatty acid synthase architectures are observed in nature. During recent years, strained petroleum supplies have driven interest in engineering organisms to either produce more fatty acids or specific high value products. Such efforts require a fundamental understanding of the enzymatic activities and regulation of fatty acid synthases. Despite more than one hundred years of research, we continue to learn new lessons about fatty acid synthases' many intricate structural and regulatory elements. In this review, we summarize each enzymatic domain and discuss efforts to engineer fatty acid synthases, providing some clues to important challenges and opportunities in the field.
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Affiliation(s)
- Joris Beld
- Department of Chemistry and Biochemistry, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0358, USA.
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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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Wu H, San KY. Efficient odd straight medium chain free fatty acid production by metabolically engineered Escherichia coli. Biotechnol Bioeng 2014; 111:2209-19. [PMID: 24889416 DOI: 10.1002/bit.25296] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2014] [Revised: 04/24/2014] [Accepted: 05/25/2014] [Indexed: 11/11/2022]
Abstract
Free fatty acids (FFAs) can be used as precursors for the production of biofuels or chemicals. Different composition of FFAs will be useful for further modification of the biofuel/biochemical quality. Microbial biosynthesis of even chain FFAs can be achieved by introducing an acyl-acyl carrier protein thioesterase gene into E. coli. In this study, odd straight medium chain FFAs production was investigated by using metabolic engineered E. coli carrying acyl-ACP thioesterase (TE, Ricinus communis), propionyl-CoA synthase (Salmonella enterica), and β-ketoacyl-acyl carrier protein synthase III (four different sources) with supplement of extracellular propionate. By using these metabolically engineered E. coli, significant quantity of C13 and C15 odd straight-chain FFAs could be produced from glucose and propionate. The highest concentration of total odd straight chain FFAs attained was 1205 mg/L by the strain HWK201 (pXZ18, pBHE2), and 85% of the odd straight chain FFAs was C15. However, the highest percentage of odd straight chain FFAs was achieved by the strain HWK201 (pXZ18, pBHE3) of 83.2% at 48 h. This strategy was also applied successfully in strains carrying different TE, such as the medium length acyl-ACP thioesterase gene from Umbellularia californica. C11 and C13 became the major odd straight-chain FFAs.
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Affiliation(s)
- Hui Wu
- Department of Bioengineering, Rice University, Houston, Texas
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Enhancement of free fatty acid production in Saccharomyces cerevisiae by control of fatty acyl-CoA metabolism. Appl Microbiol Biotechnol 2014; 98:6739-50. [PMID: 24769906 DOI: 10.1007/s00253-014-5758-8] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2014] [Revised: 04/04/2014] [Accepted: 04/05/2014] [Indexed: 01/05/2023]
Abstract
Production of biofuels derived from microbial fatty acids has attracted great attention in recent years owing to their potential to replace petroleum-derived fuels. To be cost competitive with current petroleum fuel, flux toward the direct precursor fatty acids needs to be enhanced to approach high yields. Herein, fatty acyl-CoA metabolism in Saccharomyces cerevisiae was engineered to accumulate more free fatty acids (FFA). For this purpose, firstly, haploid S. cerevisiae double deletion strain △faa1△faa4 was constructed, in which the genes FAA1 and FAA4 encoding two acyl-CoA synthetases were deleted. Then the truncated version of acyl-CoA thioesterase ACOT5 (Acot5s) encoding Mus musculus peroxisomal acyl-CoA thioesterase 5 was expressed in the cytoplasm of the strain △faa1△faa4. The resulting strain △faa1△faa4 [Acot5s] accumulated more extracellular FFA with higher unsaturated fatty acid (UFA) ratio as compared to the wild-type strain and double deletion strain △faa1△faa4. The extracellular total fatty acids (TFA) in the strain △faa1△faa4 [Acot5s] increased to 6.43-fold as compared to the wild-type strain during the stationary phase. UFA accounted for 42 % of TFA in the strain △faa1△faa4 [Acot5s], while no UFA was detected in the wild-type strain. In addition, the expression of Acot5s in △faa1△faa4 restored the growth, which indicates that FFA may not be the reason for growth inhibition in the strain △faa1△faa4. RT-PCR results demonstrated that the de-repression of fatty acid synthesis genes led to the increase of extracellular fatty acids. The study presented here showed that through control of the acyl-CoA metabolism by deleting acyl-CoA synthetase and expressing thioesterase, more FFA could be produced in S. cerevisiae, demonstrating great potential for exploitation in the platform of microbial fatty acid-derived biofuels.
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Liu H, Cheng T, Xian M, Cao Y, Fang F, Zou H. Fatty acid from the renewable sources: A promising feedstock for the production of biofuels and biobased chemicals. Biotechnol Adv 2014; 32:382-9. [DOI: 10.1016/j.biotechadv.2013.12.003] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2013] [Revised: 12/11/2013] [Accepted: 12/13/2013] [Indexed: 12/18/2022]
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Korkhovoy VI, Blume YB. Biodiesel from microalgae: Ways for increasing the effectiveness of lipid accumulation by genetic engineering methods. CYTOL GENET+ 2013. [DOI: 10.3103/s0095452713060030] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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37
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Biotechnological applications of halophilic lipases and thioesterases. Appl Microbiol Biotechnol 2013; 98:1011-21. [DOI: 10.1007/s00253-013-5417-5] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2013] [Revised: 11/14/2013] [Accepted: 11/16/2013] [Indexed: 12/13/2022]
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38
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An oleaginous bacterium that intrinsically accumulates long-chain free Fatty acids in its cytoplasm. Appl Environ Microbiol 2013; 80:1126-31. [PMID: 24296497 DOI: 10.1128/aem.03056-13] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Medium- and long-chain fatty acids are present in organisms in esterified forms that serve as cell membrane constituents and storage compounds. A large number of organisms are known to accumulate lipophilic materials as a source of energy and carbon. We found a bacterium, designated GK12, that intrinsically accumulates free fatty acids (FFAs) as intracellular droplets without exhibiting cytotoxicity. GK12 is an obligatory anaerobic, mesophilic lactic acid bacterium that was isolated from a methanogenic reactor. Phylogenetic analysis based on 16S rRNA gene sequences showed that GK12 is affiliated with the family Erysipelotrichaceae in the phylum Firmicutes but is distantly related to type species in this family (less than 92% similarity in 16S rRNA gene sequence). Saturated fatty acids with carbon chain lengths of 14, 16, 18, and 20 were produced from glucose under stress conditions, including higher-than-optimum temperatures and the presence of organic solvents that affect cell membrane integrity. FFAs were produced at levels corresponding to up to 25% (wt/wt) of the dry cell mass. Our data suggest that FFA accumulation is a result of an imbalance between excess membrane fatty acid biosynthesis due to homeoviscous adaptation and limited β-oxidation activity due to anaerobic growth involving lactic acid fermentation. FFA droplets were not further utilized as an energy and carbon source, even under conditions of starvation. A naturally occurring bacterium that accumulates significant amounts of long-chain FFAs with noncytotoxicity would provide useful strategies for microbial biodiesel production.
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Parsons JB, Yao J, Jackson P, Frank M, Rock CO. Phosphatidylglycerol homeostasis in glycerol-phosphate auxotrophs of Staphylococcus aureus. BMC Microbiol 2013; 13:260. [PMID: 24238430 PMCID: PMC3840577 DOI: 10.1186/1471-2180-13-260] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2013] [Accepted: 11/04/2013] [Indexed: 12/27/2022] Open
Abstract
Background The balanced synthesis of membrane phospholipids, fatty acids and cell wall constituents is a vital facet of bacterial physiology, but there is little known about the biochemical control points that coordinate these activities in Gram-positive bacteria. In Escherichia coli, the glycerol-phosphate acyltransferase (PlsB) plays a key role in coordinating fatty acid and phospholipid synthesis, but pathogens like Staphylococcus aureus have a different acyltransferase (PlsY), and the headgroup of the major membrane phospholipid, phosphatidylglycerol (PtdGro), is used as a precursor for lipoteichoic acid synthesis. Results The PlsY acyltransferase in S. aureus was switched off by depriving strain PDJ28 (ΔgpsA) of the required glycerol supplement. Removal of glycerol from the growth medium led to the rapid cessation of phospholipid synthesis. However, the continued utilization of the headgroup caused a reduction in PtdGro coupled with the accumulation of CDP-diacylglycerol and phosphatidic acid. PtdGro was further decreased by its stimulated conversion to cardiolipin. Although acyl-acyl carrier protein (ACP) and malonyl-CoA accumulated, fatty acid synthesis continued at a reduced level leading to the intracellular accumulation of unusually long-chain free fatty acids. Conclusions The cessation of new phospholipid synthesis led to an imbalance in membrane compositional homeostasis. PtdGro biosynthesis was not coupled to headgroup turnover leading to the accumulation of pathway intermediates. The synthesis of cardiolipin significantly increased revealing a stress response to liberate glycerol-phosphate for PtdGro synthesis. Acyl-ACP accumulation correlated with a decrease in fatty acid synthesis; however, the coupling was not tight leading to the accumulation of intracellular fatty acids.
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Affiliation(s)
- Joshua B Parsons
- Department of Infectious Diseases, St, Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis TN 38105, USA.
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40
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Lin F, Chen Y, Levine R, Lee K, Yuan Y, Lin XN. Improving fatty acid availability for bio-hydrocarbon production in Escherichia coli by metabolic engineering. PLoS One 2013; 8:e78595. [PMID: 24147139 PMCID: PMC3798384 DOI: 10.1371/journal.pone.0078595] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2013] [Accepted: 09/22/2013] [Indexed: 02/03/2023] Open
Abstract
Previous studies have demonstrated the feasibility of producing fatty-acid-derived hydrocarbons in Escherichia coli. However, product titers and yields remain low. In this work, we demonstrate new methods for improving fatty acid production by modifying central carbon metabolism and storing fatty acids in triacylglycerol. Based on suggestions from a computational model, we deleted seven genes involved in aerobic respiration, mixed-acid fermentation, and glyoxylate bypass (in the order of cyoA, nuoA, ndh, adhE, dld, pta, and iclR) to modify the central carbon metabolic/regulatory networks. These gene deletions led to increased total fatty acids, which were the highest in the mutants containing five or six gene knockouts. Additionally, when two key enzymes in the fatty acid biosynthesis pathway were over-expressed, we observed further increase in strain △cyoA△adhE△nuoA△ndh△pta△dld, leading to 202 mg/g dry cell weight of total fatty acids, ~250% of that in the wild-type strain. Meanwhile, we successfully introduced a triacylglycerol biosynthesis pathway into E. coli through heterologous expression of wax ester synthase/acyl-coenzyme:diacylglycerol acyltransferase (WS/DGAT) enzymes. The added pathway improved both the amount and fuel quality of the fatty acids. These new metabolic engineering strategies are providing promising directions for future investigation.
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Affiliation(s)
- Fengming Lin
- Department of Chemical Engineering, University of Michigan, Ann Arbor, Michigan, United States of America
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, P.R. China
| | - Yu Chen
- Department of Chemical Engineering, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Robert Levine
- Department of Chemical Engineering, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Kilho Lee
- Department of Chemical Engineering, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Yingjin Yuan
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, P.R. China
| | - Xiaoxia Nina Lin
- Department of Chemical Engineering, University of Michigan, Ann Arbor, Michigan, United States of America
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, Michigan, United States of America
- Center for Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, United States of America
- * E-mail:
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41
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Liang MH, Jiang JG. Advancing oleaginous microorganisms to produce lipid via metabolic engineering technology. Prog Lipid Res 2013; 52:395-408. [DOI: 10.1016/j.plipres.2013.05.002] [Citation(s) in RCA: 231] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2013] [Revised: 05/03/2013] [Accepted: 05/06/2013] [Indexed: 02/04/2023]
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Fan L, Liu J, Nie K, Liu L, Wang F, Tan T, Deng L. Synthesis of medium chain length fatty acid ethyl esters in engineered Escherichia coli using endogenously produced medium chain fatty acids. Enzyme Microb Technol 2013; 53:128-33. [DOI: 10.1016/j.enzmictec.2013.03.012] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2012] [Revised: 03/07/2013] [Accepted: 03/12/2013] [Indexed: 01/15/2023]
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Parsons JB, Rock CO. Bacterial lipids: metabolism and membrane homeostasis. Prog Lipid Res 2013; 52:249-76. [PMID: 23500459 PMCID: PMC3665635 DOI: 10.1016/j.plipres.2013.02.002] [Citation(s) in RCA: 298] [Impact Index Per Article: 27.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2013] [Revised: 02/27/2013] [Accepted: 02/28/2013] [Indexed: 11/29/2022]
Abstract
Membrane lipid homeostasis is a vital facet of bacterial cell physiology. For decades, research in bacterial lipid synthesis was largely confined to the Escherichia coli model system. This basic research provided a blueprint for the biochemistry of lipid metabolism that has largely defined the individual steps in bacterial fatty acid and phospholipids synthesis. The advent of genomic sequencing has revealed a surprising amount of diversity in the genes, enzymes and genetic organization of the components responsible for bacterial lipid synthesis. Although the chemical steps in fatty acid synthesis are largely conserved in bacteria, there are surprising differences in the structure and cofactor requirements for the enzymes that perform these reactions in Gram-positive and Gram-negative bacteria. This review summarizes how the explosion of new information on the diversity of biochemical and genetic regulatory mechanisms has impacted our understanding of bacterial lipid homeostasis. The potential and problems of developing therapeutics that block pathogen phospholipid synthesis are explored and evaluated. The study of bacterial lipid metabolism continues to be a rich source for new biochemistry that underlies the variety and adaptability of bacterial life styles.
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Affiliation(s)
- Joshua B Parsons
- Department of Infectious Diseases, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
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44
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Tailored fatty acid synthesis via dynamic control of fatty acid elongation. Proc Natl Acad Sci U S A 2013; 110:11290-5. [PMID: 23798438 DOI: 10.1073/pnas.1307129110] [Citation(s) in RCA: 135] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Medium-chain fatty acids (MCFAs, 4-12 carbons) are valuable as precursors to industrial chemicals and biofuels, but are not canonical products of microbial fatty acid synthesis. We engineered microbial production of the full range of even- and odd-chain-length MCFAs and found that MCFA production is limited by rapid, irreversible elongation of their acyl-ACP precursors. To address this limitation, we programmed an essential ketoacyl synthase to degrade in response to a chemical inducer, thereby slowing acyl-ACP elongation and redirecting flux from phospholipid synthesis to MCFA production. Our results show that induced protein degradation can be used to dynamically alter metabolic flux, and thereby increase the yield of a desired compound. The strategy reported herein should be widely useful in a range of metabolic engineering applications in which essential enzymes divert flux away from a desired product, as well as in the production of polyketides, bioplastics, and other recursively synthesized hydrocarbons for which chain-length control is desired.
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45
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Liu A, Tan X, Yao L, Lu X. Fatty alcohol production in engineered E. coli expressing Marinobacter fatty acyl-CoA reductases. Appl Microbiol Biotechnol 2013; 97:7061-71. [PMID: 23793343 DOI: 10.1007/s00253-013-5027-2] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2013] [Revised: 05/21/2013] [Accepted: 05/30/2013] [Indexed: 12/28/2022]
Abstract
Although successful production of fatty alcohols in metabolically engineered Escherichia coli with heterologous expression of fatty acyl-CoA reductase has been reported, low biosynthetic efficiency is still a hurdle to be overcome. In this study, we examined the characteristics of two fatty acyl-CoA reductases encoded by Maqu_2220 and Maqu_2507 genes from Marinobacter aquaeolei VT8 on fatty alcohol production in E. coli. Fatty alcohols with diversified carbon chain length were obtained by co-expressing Maqu_2220 with different carbon chain length-specific acyl-ACP thioesterases. Both fatty acyl-CoA reductases displayed broad substrate specificities for C12-C18 fatty acyl chains in vivo. The optimized mutant strain of E. coli carrying the modified tesA gene and fadD gene from E. coli and Maqu_2220 gene from Marinobacter aquaeolei VT8 produced fatty alcohols at a remarkable level of 1.725 g/L under the fermentation condition.
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Affiliation(s)
- Aiqiu Liu
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Qingdao, 266101, China
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46
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Kaiser BK, Carleton M, Hickman JW, Miller C, Lawson D, Budde M, Warrener P, Paredes A, Mullapudi S, Navarro P, Cross F, Roberts JM. Fatty aldehydes in cyanobacteria are a metabolically flexible precursor for a diversity of biofuel products. PLoS One 2013; 8:e58307. [PMID: 23505484 PMCID: PMC3594298 DOI: 10.1371/journal.pone.0058307] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2012] [Accepted: 02/01/2013] [Indexed: 11/19/2022] Open
Abstract
We describe how pathway engineering can be used to convert a single intermediate derived from lipid biosynthesis, fatty aldehydes, into a variety of biofuel precursors including alkanes, free fatty acids and wax esters. In cyanobacteria, long-chain acyl-ACPs can be reduced to fatty aldehydes, and then decarbonylated to alkanes. We discovered a cyanobacteria class-3 aldehyde-dehydrogenase, AldE, that was necessary and sufficient to instead oxidize fatty aldehyde precursors into fatty acids. Overexpression of enzymes in this pathway resulted in production of 50 to 100 fold more fatty acids than alkanes, and the fatty acids were secreted from the cell. Co-expression of acyl-ACP reductase, an alcohol-dehydrogenase and a wax-ester-synthase resulted in a third fate for fatty aldehydes: conversion to wax esters, which accumulated as intracellular lipid bodies. Conversion of acyl-ACP to fatty acids using endogenous cyanobacterial enzymes may allow biofuel production without transgenesis.
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Affiliation(s)
- Brett K. Kaiser
- Matrix Genetics, Seattle, Washington, United States of America
| | | | | | - Cameron Miller
- Matrix Genetics, Seattle, Washington, United States of America
| | - David Lawson
- Matrix Genetics, Seattle, Washington, United States of America
| | - Mark Budde
- Matrix Genetics, Seattle, Washington, United States of America
| | - Paul Warrener
- Matrix Genetics, Seattle, Washington, United States of America
| | - Angel Paredes
- Department of Pathology and Laboratory Medicine, University of Texas Health Science Center, Houston, Texas, United States of America
| | - Srinivas Mullapudi
- Department of Pathology and Laboratory Medicine, University of Texas Health Science Center, Houston, Texas, United States of America
| | - Patricia Navarro
- Department of Pathology and Laboratory Medicine, University of Texas Health Science Center, Houston, Texas, United States of America
| | - Fred Cross
- The Rockefeller University, New York, New York, United States of America
| | - James M. Roberts
- Department of Biochemistry, University of Washington, Seattle, Washington, United States of America
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- * E-mail:
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48
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Lin H, Wang Q, Shen Q, Zhan J, Zhao Y. Genetic engineering of microorganisms for biodiesel production. Bioengineered 2012; 4:292-304. [PMID: 23222170 DOI: 10.4161/bioe.23114] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Biodiesel, as one type of renewable energy, is an ideal substitute for petroleum-based diesel fuel and is usually made from triacylglycerides by transesterification with alcohols. Biodiesel production based on microbial fermentation aiming to establish more efficient, less-cost and sustainable biodiesel production strategies is under current investigation by various start-up biotechnology companies and research centers. Genetic engineering plays a key role in the transformation of microbes into the desired cell factories with high efficiency of biodiesel production. Here, we present an overview of principal microorganisms used in the microbial biodiesel production and recent advances in metabolic engineering for the modification required. Overexpression or deletion of the related enzymes for de novo synthesis of biodiesel is highlighted with relevant examples.
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Affiliation(s)
- Hui Lin
- Institute of Microbiology; College of Life Sciences; Zhejiang University; Hangzhou, China; Institute of Plant Science; College of Life Sciences; Zhejiang University; Hangzhou, China
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49
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Lennen RM, Pfleger BF. Engineering Escherichia coli to synthesize free fatty acids. Trends Biotechnol 2012; 30:659-67. [PMID: 23102412 PMCID: PMC3856887 DOI: 10.1016/j.tibtech.2012.09.006] [Citation(s) in RCA: 125] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2012] [Revised: 09/21/2012] [Accepted: 09/24/2012] [Indexed: 12/15/2022]
Abstract
Fatty acid metabolism has received significant attention as a route for producing high-energy density, liquid transportation fuels and high-value oleochemicals from renewable feedstocks. If microbes can be engineered to produce these compounds at yields that approach the theoretical limits of 0.3-0.4 g/g glucose, then processes can be developed to replace current petrochemical technologies. Here, we review recent metabolic engineering efforts to maximize production of free fatty acids (FFA) in Escherichia coli, the first step towards production of downstream products. To date, metabolic engineers have succeeded in achieving higher yields of FFA than any downstream products. Regulation of fatty acid metabolism and the physiological effects of fatty acid production will also be reviewed from the perspective of identifying future engineering targets.
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Affiliation(s)
- Rebecca M Lennen
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI 53706, USA
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Machado IM, Atsumi S. Cyanobacterial biofuel production. J Biotechnol 2012; 162:50-6. [DOI: 10.1016/j.jbiotec.2012.03.005] [Citation(s) in RCA: 209] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2011] [Revised: 01/28/2012] [Accepted: 03/08/2012] [Indexed: 12/31/2022]
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