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Berna AZ, Merriman JA, Mellett L, Parchment DK, Caparon MG, Odom John AR. Volatile profiling distinguishes Streptococcus pyogenes from other respiratory streptococcal species. mSphere 2023; 8:e0019423. [PMID: 37791788 PMCID: PMC10597408 DOI: 10.1128/msphere.00194-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 08/13/2023] [Indexed: 10/05/2023] Open
Abstract
Sore throat is one of the most common complaints encountered in the ambulatory clinical setting. Rapid, culture-independent diagnostic techniques that do not rely on pharyngeal swabs would be highly valuable as a point-of-care strategy to guide outpatient antibiotic treatment. Despite the promise of this approach, efforts to detect volatiles during oropharyngeal infection have yet been limited. In our research study, we sought to evaluate for specific bacterial volatile organic compounds (VOC) biomarkers in isolated cultures in vitro, in order to establish proof-of-concept prior to initial clinical studies of breath biomarkers. A particular challenge for the diagnosis of pharyngitis due to Streptococcus pyogenes is the likelihood that many metabolites may be shared by S. pyogenes and other related oropharyngeal colonizing bacterial species. Therefore, we evaluated whether sufficient metabolic differences are present, which distinguish the volatile metabolome of Group A streptococci from other streptococcal species that also colonize the respiratory mucosa, such as Streptococcus pneumoniae and Streptococcus intermedius. In this work, we identified 27 discriminatory VOCs (q-values < 0.05), composed of aldehydes, alcohols, nitrogen-containing compounds, hydrocarbons, ketones, aromatic compounds, esters, ethers, and carboxylic acid. From this group of volatiles, we identify candidate biomarkers that distinguish S. pyogenes from other species and establish highly produced VOCs that indicate the presence of S. pyogenes in vitro, supporting future breath-based diagnostic testing for streptococcal pharyngitis. IMPORTANCE Acute pharyngitis accounts for approximately 15 million ambulatory care visits in the United States. The most common and important bacterial cause of pharyngitis is Streptococcus pyogenesis, accounting for 15%-30% of pediatric pharyngitis. Distinguishing between bacterial and viral pharyngitis is key to management in US practice. The culture of a specimen obtained by a throat swab is the standard laboratory procedure for the microbiologic confirmation of pharyngitis; however, this method is time-consuming, which delays appropriate treatment. If left untreated, S. pyogenes pharyngitis may lead to local and distant complications. In this study, we characterized the volatile metabolomes of S. pyogenes and other related oropharyngeal colonizing bacterial species. We identify candidate biomarkers that distinguish S. pyogenes from other species and provide evidence to support future breath-based diagnostic testing for streptococcal pharyngitis.
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Affiliation(s)
- Amalia Z. Berna
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, USA
- Department of Pediatrics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Joseph A. Merriman
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, USA
- Microbiome Therapies Initiative, Stanford University, Palo Alto, California, USA
| | - Leah Mellett
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Danealle K. Parchment
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, USA
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland, USA
| | - Michael G. Caparon
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Audrey R. Odom John
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, USA
- Department of Pediatrics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
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2
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Su H, Lin J. Biosynthesis pathways of expanding carbon chains for producing advanced biofuels. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2023; 16:109. [PMID: 37400889 DOI: 10.1186/s13068-023-02340-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 05/11/2023] [Indexed: 07/05/2023]
Abstract
Because the thermodynamic property is closer to gasoline, advanced biofuels (C ≥ 6) are appealing for replacing non-renewable fossil fuels using biosynthesis method that has presented a promising approach. Synthesizing advanced biofuels (C ≥ 6), in general, requires the expansion of carbon chains from three carbon atoms to more than six carbon atoms. Despite some specific biosynthesis pathways that have been developed in recent years, adequate summary is still lacking on how to obtain an effective metabolic pathway. Review of biosynthesis pathways for expanding carbon chains will be conducive to selecting, optimizing and discovering novel synthetic route to obtain new advanced biofuels. Herein, we first highlighted challenges on expanding carbon chains, followed by presentation of two biosynthesis strategies and review of three different types of biosynthesis pathways of carbon chain expansion for synthesizing advanced biofuels. Finally, we provided an outlook for the introduction of gene-editing technology in the development of new biosynthesis pathways of carbon chain expansion.
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Affiliation(s)
- Haifeng Su
- Key Laboratory of Degraded and Unused Land Consolidation Engineering, The Ministry of Natural and Resources, Xian, 710075, Shanxi, China
| | - JiaFu Lin
- Antibiotics Research and Re-Evaluation Key Laboratory of Sichuan Province, Sichuan Industrial Institute of Antibiotics, School of Pharmacy, Chengdu University, Chengdu, 610106, China.
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Seo H, Giannone RJ, Yang YH, Trinh CT. Proteome reallocation enables the selective de novo biosynthesis of non-linear, branched-chain acetate esters. Metab Eng 2022; 73:38-49. [PMID: 35561848 DOI: 10.1016/j.ymben.2022.05.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 04/21/2022] [Accepted: 05/06/2022] [Indexed: 10/25/2022]
Abstract
The one-carbon recursive ketoacid elongation pathway is responsible for making various branched-chain amino acids, aldehydes, alcohols, and acetate esters in living cells. Controlling selective microbial biosynthesis of these target molecules at high efficiency is challenging due to enzyme promiscuity, regulation, and metabolic burden. In this study, we present a systematic modular design approach to control proteome reallocation for selective microbial biosynthesis of branched-chain acetate esters. Through pathway modularization, we partitioned the branched-chain ester pathways into four submodules including keto-isovalerate submodule for converting pyruvate to keto-isovalerate, ketoacid elongation submodule for producing longer carbon-chain keto-acids, ketoacid decarboxylase submodule for converting ketoacids to alcohols, and alcohol acyltransferase submodule for producing branched-chain acetate esters by condensing alcohols and acetyl-CoA. By systematic manipulation of pathway gene replication and transcription, enzyme specificity of the first committed steps of these submodules, and downstream competing pathways, we demonstrated selective microbial production of isoamyl acetate over isobutyl acetate. We found that the optimized isoamyl acetate pathway globally redistributed the amino acid fractions in the proteomes and required up to 23-31% proteome reallocation at the expense of other cellular resources, such as those required to generate precursor metabolites and energy for growth and amino acid biosynthesis. From glucose fed-batch fermentation, the engineered strains produced isoamyl acetate up to a titer of 8.8 g/L (>0.25 g/L toxicity limit), a yield of 0.22 g/g (61% of maximal theoretical value), and 86% selectivity, achieving the highest titers, yields and selectivity of isoamyl acetate reported to date.
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Affiliation(s)
- Hyeongmin Seo
- Department of Chemical and Biomolecular Engineering, The University of Tennessee, Knoxville, TN, USA; Center of Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Richard J Giannone
- Center of Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, USA; Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37830, USA
| | - Yung-Hun Yang
- Department of Biological Engineering, Konkuk University, Seoul, South Korea
| | - Cong T Trinh
- Department of Chemical and Biomolecular Engineering, The University of Tennessee, Knoxville, TN, USA; Center of Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, USA.
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Ranganathan S, Mahesh S, Suresh S, Nagarajan A, Z Sen T, M Yennamalli R. Experimental and computational studies of cellulases as bioethanol enzymes. Bioengineered 2022; 13:14028-14046. [PMID: 35730402 PMCID: PMC9345620 DOI: 10.1080/21655979.2022.2085541] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Bioethanol industries and bioprocesses have many challenges that constantly impede commercialization of the end product. One of the bottlenecks in the bioethanol industry is the challenge of discovering highly efficient catalysts that can improve biomass conversion. The current promising bioethanol conversion catalysts are microorganism-based cellulolytic enzymes, but lack optimization for high bioethanol conversion, due to biological and other factors. A better understanding of molecular underpinnings of cellulolytic enzyme mechanisms and significant ways to improve them can accelerate the bioethanol commercial production process. In order to do this, experimental methods are the primary choice to evaluate and characterize cellulase’s properties, but they are time-consuming and expensive. A time-saving, complementary approach involves computational methods that evaluate the same properties and improves our atomistic-level understanding of enzymatic mechanism of action. Theoretical methods in many cases have proposed research routes for subsequent experimental testing and validation, reducing the overall research cost. Having a plethora of tools to evaluate cellulases and the yield of the enzymatic process will aid in planning more optimized experimental setups. Thus, there is a need to connect the computational evaluation methods with the experimental methods to overcome the bottlenecks in the bioethanol industry. This review discusses various experimental and computational methods and their use in evaluating the multiple properties of cellulases.
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Affiliation(s)
- Shrivaishnavi Ranganathan
- Department of Biotechnology, School of Chemical and Biotechnology, SASTRA Deemed to be University, Tirumalaisamudram, Thanjavur, India
| | - Sankar Mahesh
- Department of Biotechnology, School of Chemical and Biotechnology, SASTRA Deemed to be University, Tirumalaisamudram, Thanjavur, India
| | - Sruthi Suresh
- Department of Biotechnology, School of Chemical and Biotechnology, SASTRA Deemed to be University, Tirumalaisamudram, Thanjavur, India
| | - Ayshwarya Nagarajan
- Department of Bioinformatics, School of Chemical and Biotechnology, SASTRA Deemed to be University, Tirumalaisamudram, Thanjavur, India
| | - Taner Z Sen
- S. Department of Agriculture, Agricultural Research Service, Crop Improvement and Genetics Research UnitU., California, USA
| | - Ragothaman M Yennamalli
- Department of Bioinformatics, School of Chemical and Biotechnology, SASTRA Deemed to be University, Tirumalaisamudram, Thanjavur, India
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Biosynthesizing structurally diverse diols via a general route combining oxidative and reductive formations of OH-groups. Nat Commun 2022; 13:1595. [PMID: 35332143 PMCID: PMC8948231 DOI: 10.1038/s41467-022-29216-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2021] [Accepted: 03/02/2022] [Indexed: 11/09/2022] Open
Abstract
Diols encompass important bulk and fine chemicals for the chemical, pharmaceutical and cosmetic industries. During the past decades, biological production of C3-C5 diols from renewable feedstocks has received great interest. Here, we elaborate a general principle for effectively synthesizing structurally diverse diols by expanding amino acid metabolism. Specifically, we propose to combine oxidative and reductive formations of hydroxyl groups from amino acids in a thermodynamically favorable order of four reactions catalyzed by amino acid hydroxylase, L-amino acid deaminase, α-keto acid decarboxylase and aldehyde reductase consecutively. The oxidative formation of hydroxyl group from an alkyl group is energetically more attractive than the reductive pathway, which is exclusively used in the synthetic pathways of diols reported so far. We demonstrate this general route for microbial production of branched-chain diols in E. coli. Ten C3-C5 diols are synthesized. Six of them, namely isopentyldiol (IPDO), 2-methyl-1,3-butanediol (2-M-1,3-BDO), 2-methyl-1,4-butanediol (2-M-1,4-BDO), 2-methyl-1,3-propanediol (MPO), 2-ethyl-1,3-propanediol (2-E-1,3-PDO), 1,4-pentanediol (1,4-PTD), have not been biologically synthesized before. This work opens up opportunities for synthesizing structurally diverse diols and triols, especially by genome mining, rational design or directed evolution of proper enzymes. Diols are important bulk and fine chemicals, but bioproduciton of branch-chain diols is hampered by the unknown biological route. Here, the authors report the expanding of amino acid metabolism for biosynthesis of branch-chain diols via a general route of combined oxidative and reductive formations of hydroxyl groups.
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Bracalente F, Sabatini M, Arabolaza A, Gramajo H. Escherichia coli coculture for de novo production of esters derived of methyl-branched alcohols and multi-methyl branched fatty acids. Microb Cell Fact 2022; 21:10. [PMID: 35033081 PMCID: PMC8760833 DOI: 10.1186/s12934-022-01737-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 12/31/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND A broad diversity of natural and non-natural esters have now been made in bacteria, and in other microorganisms, as a result of original metabolic engineering approaches. However, the fact that the properties of these molecules, and therefore their applications, are largely defined by the structural features of the fatty acid and alcohol moieties, has driven a persistent interest in generating novel structures of these chemicals. RESULTS In this research, we engineered Escherichia coli to synthesize de novo esters composed of multi-methyl-branched-chain fatty acids and short branched-chain alcohols (BCA), from glucose and propionate. A coculture engineering strategy was developed to avoid metabolic burden generated by the reconstitution of long heterologous biosynthetic pathways. The cocultures were composed of two independently optimized E. coli strains, one dedicated to efficiently achieve the biosynthesis and release of the BCA, and the other to synthesize the multi methyl-branched fatty acid and the corresponding multi-methyl-branched esters (MBE) as the final products. Response surface methodology, a cost-efficient multivariate statistical technique, was used to empirical model the BCA-derived MBE production landscape of the coculture and to optimize its productivity. Compared with the monoculture strategy, the utilization of the designed coculture improved the BCA-derived MBE production in 45%. Finally, the coculture was scaled up in a high-cell density fed-batch fermentation in a 2 L bioreactor by fine-tuning the inoculation ratio between the two engineered E. coli strains. CONCLUSION Previous work revealed that esters containing multiple methyl branches in their molecule present favorable physicochemical properties which are superior to those of linear esters. Here, we have successfully engineered an E. coli strain to broaden the diversity of these molecules by incorporating methyl branches also in the alcohol moiety. The limited production of these esters by a monoculture was considerable improved by a design of a coculture system and its optimization using response surface methodology. The possibility to scale-up this process was confirmed in high-cell density fed-batch fermentations.
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Affiliation(s)
- Fernando Bracalente
- Microbiology Division, Facultad de Ciencias Bioquímicas Y Farmacéuticas, IBR (Instituto de Biología Molecular Y Celular de Rosario), Consejo Nacional de Investigaciones Científicas Y Técnicas, Universidad Nacional de Rosario, Ocampo y Esmeralda, 2000, Rosario, Argentina
| | - Martín Sabatini
- Microbiology Division, Facultad de Ciencias Bioquímicas Y Farmacéuticas, IBR (Instituto de Biología Molecular Y Celular de Rosario), Consejo Nacional de Investigaciones Científicas Y Técnicas, Universidad Nacional de Rosario, Ocampo y Esmeralda, 2000, Rosario, Argentina
| | - Ana Arabolaza
- Microbiology Division, Facultad de Ciencias Bioquímicas Y Farmacéuticas, IBR (Instituto de Biología Molecular Y Celular de Rosario), Consejo Nacional de Investigaciones Científicas Y Técnicas, Universidad Nacional de Rosario, Ocampo y Esmeralda, 2000, Rosario, Argentina.
| | - Hugo Gramajo
- Microbiology Division, Facultad de Ciencias Bioquímicas Y Farmacéuticas, IBR (Instituto de Biología Molecular Y Celular de Rosario), Consejo Nacional de Investigaciones Científicas Y Técnicas, Universidad Nacional de Rosario, Ocampo y Esmeralda, 2000, Rosario, Argentina.
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7
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Bahls MO, Platz L, Morgado G, Schmidt GW, Panke S. Directed evolution of biofuel-responsive biosensors for automated optimization of branched-chain alcohol biosynthesis. Metab Eng 2021; 69:98-111. [PMID: 34767976 DOI: 10.1016/j.ymben.2021.10.014] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 10/21/2021] [Accepted: 10/31/2021] [Indexed: 12/18/2022]
Abstract
The biosynthesis of short-chain alcohols is a carbon-neutral alternative to petroleum-derived production, but strain screening operations are encumbered by laborious analytics. Here, we built, characterized and applied whole cell biosensors by directed evolution of the transcription factor AlkS for screening microbial strain libraries producing industrially relevant alcohols. A selected AlkS variant was applied for in situ product detection in two screening applications concerning key steps in alcohol production. Further, the biosensor strains enabled the implementation of an automated, robotic platform-based workflow with data clustering, which readily allowed the identification of significantly improved strain variants for isopentanol production.
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Affiliation(s)
- Maximilian O Bahls
- Department of Biosystems Science and Engineering, ETH Zurich, Switzerland
| | - Lukas Platz
- Department of Biosystems Science and Engineering, ETH Zurich, Switzerland
| | - Gaspar Morgado
- Department of Biosystems Science and Engineering, ETH Zurich, Switzerland
| | - Gregor W Schmidt
- Department of Biosystems Science and Engineering, ETH Zurich, Switzerland
| | - Sven Panke
- Department of Biosystems Science and Engineering, ETH Zurich, Switzerland.
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8
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Dynamic metabolic engineering of Escherichia coli improves fermentation for the production of pyruvate and its derivatives. J Biosci Bioeng 2021; 133:56-63. [PMID: 34674961 DOI: 10.1016/j.jbiosc.2021.09.015] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 09/14/2021] [Accepted: 09/14/2021] [Indexed: 11/23/2022]
Abstract
Pyruvate is a key intermediate that is involved in various synthetic metabolic pathways for microbial chemical and fuel production. It is widely used in the food, chemical, and pharmaceutical industries. However, the microbial production of pyruvate and its derivatives compete with microbial cell growth, as pyruvate is an important metabolic intermediate that serves as a hub for various endogenous metabolic pathways, including gluconeogenesis, amino acid synthesis, TCA cycle, and fatty acid biosynthesis. To achieve a more efficient bioprocess for the production of pyruvate and its derivatives, it is necessary to reduce the metabolic imbalance between cell growth and target chemical production. For this purpose, we devised a dynamic metabolic engineering strategy within an Escherichia coli model, in which a metabolic toggle switch (MTS) was employed to redirect metabolic flux from the endogenous pathway toward the target synthetic pathway. Through a combination of TCA cycle interruption through MTS and reduction of pyruvate consumption in endogenous pathways, we achieved a drastic improvement (163 mM, 26-fold) in pyruvate production. In addition, we demonstrated the redirection of metabolic flux from excess pyruvate toward isobutanol production. The final isobutanol production titer of the strain harboring MTS was 26% improved compared with that of the control strain.
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Zhao Y, Liu S, Lu Z, Zhao B, Wang S, Zhang C, Xiao D, Foo JL, Yu A. Hybrid promoter engineering strategies in Yarrowia lipolytica: isoamyl alcohol production as a test study. BIOTECHNOLOGY FOR BIOFUELS 2021; 14:149. [PMID: 34215293 PMCID: PMC8252286 DOI: 10.1186/s13068-021-02002-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 06/22/2021] [Indexed: 05/11/2023]
Abstract
BACKGROUND In biological cells, promoters drive gene expression by specific binding of RNA polymerase. They determine the starting position, timing and level of gene expression. Therefore, rational fine-tuning of promoters to regulate the expression levels of target genes for optimizing biosynthetic pathways in metabolic engineering has recently become an active area of research. RESULTS In this study, we systematically detected and characterized the common promoter elements in the unconventional yeast Yarrowia lipolytica, and constructed an artificial hybrid promoter library that covers a wide range of promoter strength. The results indicate that the hybrid promoter strength can be fine-tuned by promoter elements, namely, upstream activation sequences (UAS), TATA box and core promoter. Notably, the UASs of Saccharomyces cerevisiae promoters were reported for the first time to be functionally transferred to Y. lipolytica. Subsequently, using the production of a versatile platform chemical isoamyl alcohol as a test study, the hybrid promoter library was applied to optimize the biosynthesis pathway expression in Y. lipolytica. By expressing the key pathway gene, ScARO10, with the promoter library, 1.1-30.3 folds increase in the isoamyl alcohol titer over that of the control strain Y. lipolytica Po1g KU70∆ was achieved. Interestingly, the highest titer increase was attained with a weak promoter PUAS1B4-EXPm to express ScARO10. These results suggest that our hybrid promoter library can be a powerful toolkit for identifying optimum promoters for expressing metabolic pathways in Y. lipolytica. CONCLUSION We envision that this promoter engineering strategy and the rationally engineered promoters constructed in this study could also be extended to other non-model fungi for strain improvement.
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Affiliation(s)
- Yu Zhao
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, No. 29 the 13th Street TEDA, Tianjin, 300457 People’s Republic of China
| | - Shiqi Liu
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, No. 29 the 13th Street TEDA, Tianjin, 300457 People’s Republic of China
| | - Zhihui Lu
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, No. 29 the 13th Street TEDA, Tianjin, 300457 People’s Republic of China
| | - Baixiang Zhao
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, No. 29 the 13th Street TEDA, Tianjin, 300457 People’s Republic of China
| | - Shuhui Wang
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, No. 29 the 13th Street TEDA, Tianjin, 300457 People’s Republic of China
| | - Cuiying Zhang
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, No. 29 the 13th Street TEDA, Tianjin, 300457 People’s Republic of China
| | - Dongguang Xiao
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, No. 29 the 13th Street TEDA, Tianjin, 300457 People’s Republic of China
| | - Jee Loon Foo
- Synthetic Biology Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 119228 Singapore
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, Singapore, 117456 Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117597 Singapore
| | - Aiqun Yu
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, No. 29 the 13th Street TEDA, Tianjin, 300457 People’s Republic of China
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Runguphan W, Sae-Tang K, Tanapongpipat S. Recent advances in the microbial production of isopentanol (3-Methyl-1-butanol). World J Microbiol Biotechnol 2021; 37:107. [PMID: 34043086 DOI: 10.1007/s11274-021-03074-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Accepted: 05/17/2021] [Indexed: 10/21/2022]
Abstract
As the effects of climate change become increasingly severe, metabolic engineers and synthetic biologists are looking towards greener sources for transportation fuels. The design and optimization of microorganisms to produce gasoline, diesel, and jet fuel compounds from renewable feedstocks can significantly reduce dependence on fossil fuels and thereby produce fewer emissions. Over the past two decades, a tremendous amount of research has contributed to the development of microbial strains to produce advanced fuel compounds, including branched-chain higher alcohols (BCHAs) such as isopentanol (3-methyl-1-butanol; 3M1B) and isobutanol (2-methyl-1-propanol). In this review, we provide an overview of recent advances in the development of microbial strains for the production of isopentanol in both conventional and non-conventional hosts. We also highlight metabolic engineering strategies that may be employed to enhance product titers, reduce end-product toxicity, and broaden the substrate range to non-sugar carbon sources. Finally, we offer glimpses into some promising future directions in the development of isopentanol producing microbial strains.
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Affiliation(s)
- Weerawat Runguphan
- National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Paholyothin Road, Klong 1, Klong Luang, 12120, Pathumthani, Thailand.
| | - Kittapong Sae-Tang
- National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Paholyothin Road, Klong 1, Klong Luang, 12120, Pathumthani, Thailand
| | - Sutipa Tanapongpipat
- National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Paholyothin Road, Klong 1, Klong Luang, 12120, Pathumthani, Thailand
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Development of a Simple Colorimetric Assay for Determination of the Isoamyl Alcohol-Producing Strain. Appl Biochem Biotechnol 2020; 192:632-642. [PMID: 32500427 DOI: 10.1007/s12010-020-03353-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Accepted: 05/22/2020] [Indexed: 01/13/2023]
Abstract
Like other branched-chain higher alcohols used as biofuels, isoamyl alcohol has attracted considerable attention because of its advantages, which include high energy density, low hygroscopicity, and compatibility with the current infrastructure. Previous attempts to increase the microbial production of isoamyl alcohol have yielded great progress, but the existing methods of detecting isoamyl alcohol based on gas chromatography and high-performance liquid chromatography are laborious and time-consuming. In this study, we developed a simple colorimetric assay to determine high isoamyl alcohol-producing strains. The assay was based on isoamyl alcohol oxidase and peroxidase (IAOP assay) and could be performed in microplate with high throughput and had a specific detection range of 0-20 mM. Characterization analysis revealed that the developed IAOP assay was highly specific for isoamyl alcohol relative to other branched-chain alcohols. Little interference with the assay was observed from the fermentation media, microorganisms, and fermentation byproducts (e.g., lactic acid, acetic acid). We conclude that the enzyme-based IAOP assay can be used for high-throughput monitoring of strains that produce isoamyl alcohol and could be adjusted to screen for strains that produce many other metabolites.
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Enriching the Production of 2-Methyl-1-Butanol in Fermentation Process Using Corynebacterium crenatum. Curr Microbiol 2020; 77:1699-1706. [PMID: 32300924 DOI: 10.1007/s00284-020-01961-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Accepted: 03/21/2020] [Indexed: 10/24/2022]
Abstract
Non-natural 2-methyl-1-butanol (2 MB) has been biosynthesized through the modification of metabolic pathways using Corynebacterium crenatum, a non-model host. However, its production capacity is not effectively improved. In this study, the fermentation process was strengthened through factor combination design (FCD) for enhancing the production of 2 MB. Our results showed that the highest production of 2 MB, 3-methyl-1-butanol (3 MB), ethanol, and total solvent was 4.87 ± 0.39 g/L, 3.57 ± 0.21 g/L, 5.74 ± 0.43 g/L, and 14.18 g/L, respectively, under the optimal fermentation conditions. The optimal fermentation conditions were determined through the FCD to be as follows: pH of 6.5, IPTG concentration of 1.2 mM, fermentation temperature of 32 °C, and fermentation time of 96 h. This study provides a significant guidance for the optimal control technology of the genetically engineered C. crenatum, and also a useful reference for the industrial production of 2 MB via the microbial fermentation approach.
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Huang M, Zhao Y, Feng L, Zhu L, Zhan L, Chen X. Role of the ClpX from Corynebacterium crenatum involved in stress responses and energy metabolism. Appl Microbiol Biotechnol 2020; 104:5505-5517. [PMID: 32300856 DOI: 10.1007/s00253-020-10597-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 03/24/2020] [Accepted: 03/31/2020] [Indexed: 02/04/2023]
Abstract
ClpX and ClpP are involved in many important functions, including stress responses and energy metabolism, in microorganisms. However, the ClpX and ClpP of microbes used in industrial scale have rarely been studied. Industrial bacterial fermentation experiences a variety of stresses, and energy metabolism is extremely important for industrial bacteria. Thus, the role played by the ClpX and ClpP of industrial bacteria in fermentation should be investigated. Most microorganisms have a single clpP gene, while Corynebacterium crenatum AS 1.542 possesses two clpPs. Herein, the clpX, clpP1, and clpP2 of C. crenatum were cloned, and its fusion protein was expressed and characterized. We also constructed clpX deletion mutant and complementation strain. Results indicate that ClpX serves an important function in thermal, pH, and ethanol stresses. It is also involved in NADPH synthesis and glucose consumption during fermentation.
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Affiliation(s)
- Mingzhu Huang
- Department of Life Science, Jiangxi Normal University, Nanchang, 330096, People's Republic of China.,School of Life Science, Key Laboratory of Functional Small Organic Molecule of Ministry of Education, Jiangxi Normal University, 99 Ziyang Road, Nanchang, 330096, People's Republic of China
| | - Yue Zhao
- Department of Life Science, Jiangxi Normal University, Nanchang, 330096, People's Republic of China
| | - Lin Feng
- Department of Life Science, Jiangxi Normal University, Nanchang, 330096, People's Republic of China
| | - Lingfeng Zhu
- Department of Life Science, Jiangxi Normal University, Nanchang, 330096, People's Republic of China
| | - Li Zhan
- Department of Life Science, Jiangxi Normal University, Nanchang, 330096, People's Republic of China
| | - Xuelan Chen
- Department of Life Science, Jiangxi Normal University, Nanchang, 330096, People's Republic of China. .,School of Life Science, Key Laboratory of Functional Small Organic Molecule of Ministry of Education, Jiangxi Normal University, 99 Ziyang Road, Nanchang, 330096, People's Republic of China.
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Lee SM, Kim SB, Kim YS. Determination of Key Volatile Compounds Related to Long-Term Fermentation of Soy Sauce. J Food Sci 2019; 84:2758-2776. [PMID: 31509249 DOI: 10.1111/1750-3841.14771] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Revised: 07/08/2019] [Accepted: 07/25/2019] [Indexed: 11/27/2022]
Abstract
The changes of volatile compounds in soy sauce during long-term fermentation (12 months) were investigated using solid-phase microextraction (SPME) and stir bar sorptive extraction (SBSE). A total of 144 and 129 compounds were identified in soy sauce with long-term fermentation by SPME and SBSE, respectively. The contents of most compounds, such as acids, aldehydes, benzene and benzene derivatives, esters, lactones, pyrazines, pyrones, and pyrroles, showed a tendency to increase, whereas those of alcohols and ketones decreased according to long-term fermentation. In addition, principal component analysis and partial least squares discriminant analysis were applied to discriminate soy sauce samples according to fermentation periods and determine key volatile compounds related to long-term fermentation. The initial fermentation stages were mainly associated with some alcohols, ketones, and lactones, whereas the later stages were strongly associated with most esters, some phenols, benzene and benzene derivatives, and pyrroles. Moreover, the key volatile compounds associated with long-term fermentation in soy sauce samples were ethyl 3-methylbutanoate (ethyl isovalerate), ethyl pentanoate (ethyl valerate), 1-octen-3-yl acetate, 3-(methylthio)-1-propanol (methionol), ethyl benzoate, ethyl 2-phenylacetate, 1-(1H-pyrrol-2-yl)ethanone (2-acetylpyrrole), and 5-pentyl-2-oxolanone (γ-nonalactone). PRACTICAL APPLICATION: This study investigated changes of volatile compounds in soy sauce during long-term fermentation (12 months) using solid-phase microextraction and stir bar sorptive extraction. In addition, the key volatile compounds associated with long-term fermentation in soy sauce samples were determined. These results may help to predict the effective contributors related to long-term fermentation of soy sauce and improve the quality of soy sauce during long-term fermentation.
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Affiliation(s)
- Sang Mi Lee
- Dept. of Food Science and Engineering, Ewha Womans Univ., 11-1 Daehyun-dong, Seodaemun-gu, Seoul, 120-750, Republic of Korea
| | - Sa-Bin Kim
- Dept. of Food Science and Engineering, Ewha Womans Univ., 11-1 Daehyun-dong, Seodaemun-gu, Seoul, 120-750, Republic of Korea
| | - Young-Suk Kim
- Dept. of Food Science and Engineering, Ewha Womans Univ., 11-1 Daehyun-dong, Seodaemun-gu, Seoul, 120-750, Republic of Korea
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15
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Lee JW, Trinh CT. Microbial biosynthesis of lactate esters. BIOTECHNOLOGY FOR BIOFUELS 2019; 12:226. [PMID: 31548868 PMCID: PMC6753613 DOI: 10.1186/s13068-019-1563-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Accepted: 09/07/2019] [Indexed: 05/18/2023]
Abstract
BACKGROUND Green organic solvents such as lactate esters have broad industrial applications and favorable environmental profiles. Thus, manufacturing and use of these biodegradable solvents from renewable feedstocks help benefit the environment. However, to date, the direct microbial biosynthesis of lactate esters from fermentable sugars has not yet been demonstrated. RESULTS In this study, we present a microbial conversion platform for direct biosynthesis of lactate esters from fermentable sugars. First, we designed a pyruvate-to-lactate ester module, consisting of a lactate dehydrogenase (ldhA) to convert pyruvate to lactate, a propionate CoA-transferase (pct) to convert lactate to lactyl-CoA, and an alcohol acyltransferase (AAT) to condense lactyl-CoA and alcohol(s) to make lactate ester(s). By generating a library of five pyruvate-to-lactate ester modules with divergent AATs, we screened for the best module(s) capable of producing a wide range of linear, branched, and aromatic lactate esters with an external alcohol supply. By co-introducing a pyruvate-to-lactate ester module and an alcohol (i.e., ethanol, isobutanol) module into a modular Escherichia coli (chassis) cell, we demonstrated for the first time the microbial biosynthesis of ethyl and isobutyl lactate esters directly from glucose. In an attempt to enhance ethyl lactate production as a proof-of-study, we re-modularized the pathway into (1) the upstream module to generate the ethanol and lactate precursors and (2) the downstream module to generate lactyl-CoA and condense it with ethanol to produce the target ethyl lactate. By manipulating the metabolic fluxes of the upstream and downstream modules through plasmid copy numbers, promoters, ribosome binding sites, and environmental perturbation, we were able to probe and alleviate the metabolic bottlenecks by improving ethyl lactate production by 4.96-fold. We found that AAT is the most rate-limiting step in biosynthesis of lactate esters likely due to its low activity and specificity toward the non-natural substrate lactyl-CoA and alcohols. CONCLUSIONS We have successfully established the biosynthesis pathway of lactate esters from fermentable sugars and demonstrated for the first time the direct fermentative production of lactate esters from glucose using an E. coli modular cell. This study defines a cornerstone for the microbial production of lactate esters as green solvents from renewable resources with novel industrial applications.
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Affiliation(s)
- Jong-Won Lee
- Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee, Knoxville, TN USA
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN USA
| | - Cong T. Trinh
- Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee, Knoxville, TN USA
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN USA
- Department of Chemical and Biomolecular Engineering, University of Tennessee, 1512 Middle Dr., DO#432, Knoxville, TN 37996 USA
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16
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Yu H, Wang N, Huo W, Zhang Y, Zhang W, Yang Y, Chen Z, Huo YX. Establishment of BmoR-based biosensor to screen isobutanol overproducer. Microb Cell Fact 2019; 18:30. [PMID: 30732651 PMCID: PMC6366067 DOI: 10.1186/s12934-019-1084-2] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Accepted: 01/31/2019] [Indexed: 11/12/2022] Open
Abstract
Background Isobutanol, a C4 branched-chain higher alcohol, is regarded as an attractive next-generation transport fuel. Metabolic engineering for efficient isobutanol production has been achieved in many studies. BmoR, an alcohol-regulated transcription factor, mediates a σ54-dependent promoter Pbmo of alkane monooxygenase in n-alkane metabolism of Thauera butanivorans and displays high sensitivity to C4–C6 linear alcohols and C3–C5 branched-chain alcohols. In this study, to achieve the high-level production of isobutanol, we established a screening system which relied on the combination of BmoR-based biosensor and isobutanol biosynthetic pathway and then employed it to screen isobutanol overproduction strains from an ARTP mutagenesis library. Results Firstly, we constructed and verified a GFP-based BmoR-Pbmo device responding to the isobutanol produced by the host. Then, this screening system was employed to select three mutants which exhibited higher GFP/OD600 values than that of wild type. Significantly, GFP/OD600 of mutant 10 was 190.7 ± 4.8, a 1.4-fold higher value than that of wild type. Correspondingly, the isobutanol titer of that strain was 1597.6 ± 129.6 mg/L, 2.0-fold higher than the wild type. With the overexpression of upstream pathway genes, the isobutanol production from mutant 10 reached 14.0 ± 1.0 g/L after medium optimization in shake flask. The isobutanol titer reached 56.5 ± 1.8 g/L in a fed-batch production experiment. Conclusions This work screened out isobutanol overproduction strains from a mutagenesis library by using a screening system which depended on the combination of BmoR-based biosensor and isobutanol biosynthetic pathway. Optimizing fermentation condition and reinforcing upstream pathway could realize the increase of isobutanol production from the overproducer. Lastly, fed-batch fermentation of the mutant enhanced the isobutanol production to 56.5 ± 1.8 g/L.
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Affiliation(s)
- Huan Yu
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, No. 5 South Zhongguancun Street, Beijing, 100081, China
| | - Ning Wang
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, No. 5 South Zhongguancun Street, Beijing, 100081, China
| | - Wenbo Huo
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, No. 5 South Zhongguancun Street, Beijing, 100081, China
| | - Yuhong Zhang
- Biotechnology Research Institute of Chinese Academy of Agricultural Sciences, No. 12 South Zhongguancun Street, Beijing, 100081, China
| | - Wei Zhang
- Biotechnology Research Institute of Chinese Academy of Agricultural Sciences, No. 12 South Zhongguancun Street, Beijing, 100081, China
| | - Yu Yang
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, No. 5 South Zhongguancun Street, Beijing, 100081, China
| | - Zhenya Chen
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, No. 5 South Zhongguancun Street, Beijing, 100081, China.
| | - Yi-Xin Huo
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, No. 5 South Zhongguancun Street, Beijing, 100081, China.
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17
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Acedos MG, de la Torre I, Santos VE, Garcia-Ochoa F. Kinetic Modeling of the Isobutanol Production from Glucose Using Shimwellia blattae (p424IbPSO) Strain: Effect of Initial Substrate Concentration. Ind Eng Chem Res 2019. [DOI: 10.1021/acs.iecr.8b05121] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Miguel G. Acedos
- Chemical & Materials Engineering Department, Universidad Complutense, 28040 Madrid, Spain
| | - Isabel de la Torre
- Chemical & Materials Engineering Department, Universidad Complutense, 28040 Madrid, Spain
| | - Victoria E. Santos
- Chemical & Materials Engineering Department, Universidad Complutense, 28040 Madrid, Spain
| | - Felix Garcia-Ochoa
- Chemical & Materials Engineering Department, Universidad Complutense, 28040 Madrid, Spain
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18
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Black WB, King E, Wang Y, Jenic A, Rowley AT, Seki K, Luo R, Li H. Engineering a Coenzyme A Detour To Expand the Product Scope and Enhance the Selectivity of the Ehrlich Pathway. ACS Synth Biol 2018; 7:2758-2764. [PMID: 30433765 DOI: 10.1021/acssynbio.8b00358] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The Ehrlich pathway is a major route for the renewable production of higher alcohols. However, the product scope of the Ehrlich pathway is restricted, and the product selectivity is suboptimal. Here, we demonstrate that a Coenzyme A (CoA) detour, which involves conversion of the 2-keto acids into acyl-CoAs, expands the biological toolkit of reaction chemistries available in the Ehrlich pathway to include the gamut of CoA-dependent enzymes. As a proof-of-concept, we demonstrated the first biosynthesis of a tertiary branched-alcohol, pivalcohol, at a level of ∼10 mg/L from glucose in Escherichia coli, using a pivalyl-CoA mutase from Xanthobacter autotrophicus. Furthermore, engineering an enzyme in the CoA detour, the Lactobacillus brevis CoA-acylating aldehyde dehydrogenase, allowed stringent product selectivity. Targeted production of 3-methyl-1-butanol (3-MB) in E. coli mediated by the CoA detour showed a 3-MB:side-product (isobutanol) ratio of >20, an increase over the ratios previously achieved using the conventional Ehrlich pathway.
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19
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Bioformation of Volatile and Nonvolatile Metabolites by Saccharomycopsis fibuligera KJJ81 Cultivated under Different Conditions-Carbon Sources and Cultivation Times. Molecules 2018; 23:molecules23112762. [PMID: 30366381 PMCID: PMC6278445 DOI: 10.3390/molecules23112762] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Revised: 10/18/2018] [Accepted: 10/23/2018] [Indexed: 11/17/2022] Open
Abstract
Saccharomycopsis fibuligera KJJ81 isolated from nuruk is an amylolytic yeast that is widely used as a microbial starter in various fermented foods. Volatile and nonvolatile metabolites of S. fibuligera KJJ81 were investigated according to different carbon sources and cultivation times using a nontargeted metabolomic approach. Partial-least-squares discriminant analysis was applied to determine the major metabolites, which were found to be closely related to the clustering and discrimination of S. fibuligera KJJ81 samples. Some volatile metabolites derived from phenylalanine, such as 2-phenylethanol, 2-phenylethyl acetate, and ethyl phenylacetate, were predominantly found in cultivation medium containing glucose (YPD medium). In addition, the level of 2-phenylethanol increased continuously with the cultivation time. In terms of nonvolatile metabolites, carbohydrates (mannose, arabitol, and mannitol), fatty acids (palmitic acid and stearic acid), organic acids (oxalic acid and succinic acid), and amino acids (isoleucine, serine, alanine, glutamic acid, glycine, proline, phenylalanine, and threonine) were the main contributors to S. fibuligera KJJ81 samples cultivated in YPD medium according to cultivation time. These results show that the formation of volatile and nonvolatile metabolites of S. fibuligera KJJ81 can be significantly affected by both the carbon sources and the cultivation time.
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20
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Acedos MG, Santos VE, Garcia-Ochoa F. Resting cells isobutanol production by Shimwellia blattae (p424IbPSO): Influence of growth culture conditions. Biotechnol Prog 2018; 34:1073-1080. [PMID: 30281946 DOI: 10.1002/btpr.2705] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Revised: 05/31/2018] [Accepted: 08/08/2018] [Indexed: 01/19/2023]
Abstract
Isobutanol is a promising gasoline additive and could even be a potential substitute used directly as combustible. In this work, the production of isobutanol from glucose by Shimwellia blattae (p424IbPSO) in resting cell cultures is studied. This production has two stages, involving a resting cell phase that has not been studied before. The cell growth was carried out under different operating conditions: temperature and medium composition (YE, ammonium, and IPTG concentrations), looking for the highest isobutanol production. Moreover, the cells were collected at three different growth times checking their isobutanol production capacity. The best operating conditions have been determined as: 30°C of temperature, a medium containing 1.5 g L-1 YE and 1.4 g L-1 of ammonium as nitrogen sources, adding 0.5 mM IPTG as inducer. The cells collected at early growth times are significantly more active. The use of S. blattae (p424IbPSO) in resting cells is a good strategy for the production of isobutanol from glucose yielding better results than in batch growth cultures, a yield of 60% attainment of theoretical maximum yield is obtained under optimal conditions. In addition, it has been demonstrated that if the cells are cultured at higher temperatures and with high IPTG concentrations, inclusion bodies are formed in the cytoplasm inhibiting the isobutanol production in the resting cell stage.
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Affiliation(s)
- Miguel G Acedos
- Dept. of Chemical and Materials Engineering, Universidad Complutense, Madrid, 28040, Spain
| | - Victoria E Santos
- Dept. of Chemical and Materials Engineering, Universidad Complutense, Madrid, 28040, Spain
| | - Felix Garcia-Ochoa
- Dept. of Chemical and Materials Engineering, Universidad Complutense, Madrid, 28040, Spain
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21
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Rahman MM, Andberg M, Koivula A, Rouvinen J, Hakulinen N. The crystal structure of D-xylonate dehydratase reveals functional features of enzymes from the Ilv/ED dehydratase family. Sci Rep 2018; 8:865. [PMID: 29339766 PMCID: PMC5770437 DOI: 10.1038/s41598-018-19192-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Accepted: 12/22/2017] [Indexed: 01/06/2023] Open
Abstract
The Ilv/ED dehydratase protein family includes dihydroxy acid-, gluconate-, 6-phosphogluconate- and pentonate dehydratases. The members of this family are involved in various biosynthetic and carbohydrate metabolic pathways. Here, we describe the first crystal structure of D-xylonate dehydratase from Caulobacter crescentus (CcXyDHT) at 2.7 Å resolution and compare it with other available enzyme structures from the IlvD/EDD protein family. The quaternary structure of CcXyDHT is a tetramer, and each monomer is composed of two domains in which the N-terminal domain forms a binding site for a [2Fe-2S] cluster and a Mg2+ ion. The active site is located at the monomer-monomer interface and contains residues from both the N-terminal recognition helix and the C-terminus of the dimeric counterpart. The active site also contains a conserved Ser490, which probably acts as a base in catalysis. Importantly, the cysteines that participate in the binding and formation of the [2Fe-2S] cluster are not all conserved within the Ilv/ED dehydratase family, which suggests that some members of the IlvD/EDD family may bind different types of [Fe-S] clusters.
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Affiliation(s)
- Mohammad Mubinur Rahman
- Department of Chemistry, University of Eastern Finland, PO Box 111, FIN-80101, Joensuu, Finland
| | - Martina Andberg
- VTT Technical Research Centre of Finland Ltd, PO Box 1000, FIN-02044 VTT, Espoo, Finland
| | - Anu Koivula
- VTT Technical Research Centre of Finland Ltd, PO Box 1000, FIN-02044 VTT, Espoo, Finland
| | - Juha Rouvinen
- Department of Chemistry, University of Eastern Finland, PO Box 111, FIN-80101, Joensuu, Finland
| | - Nina Hakulinen
- Department of Chemistry, University of Eastern Finland, PO Box 111, FIN-80101, Joensuu, Finland.
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22
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Sangavai C, Chellapandi P. Amino acid catabolism-directed biofuel production in Clostridium sticklandii: An insight into model-driven systems engineering. ACTA ACUST UNITED AC 2017; 16:32-43. [PMID: 29167757 PMCID: PMC5686429 DOI: 10.1016/j.btre.2017.11.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Revised: 10/17/2017] [Accepted: 11/03/2017] [Indexed: 01/01/2023]
Abstract
Model-driven systems engineering has been more fascinating process for microbial biofuel production. Clostridium sticklandii is a potential strain for the solventogenesis and acidogenesis. The present review provides an insight for the protein catabolism-directed biofuel production.
Model-driven systems engineering has been more fascinating process for the microbial production of biofuel and bio-refineries in chemical and pharmaceutical industries. Genome-scale modeling and simulations have been guided for metabolic engineering of Clostridium species for the production of organic solvents and organic acids. Among them, Clostridium sticklandii is one of the potential organisms to be exploited as a microbial cell factory for biofuel production. It is a hyper-ammonia producing bacterium and is able to catabolize amino acids as important carbon and energy sources via Stickland reactions and the development of the specific pathways. Current genomic and metabolic aspects of this bacterium are comprehensively reviewed herein, which provided information for learning about protein catabolism-directed biofuel production. It has a metabolic potential to drive energy and direct solventogenesis as well as acidogenesis from protein catabolism. It produces by-products such as ethanol, acetate, n-butanol, n-butyrate and hydrogen from amino acid catabolism. Model-driven systems engineering of this organism would improve the performance of the industrial sectors and enhance the industrial economy by using protein-based waste in environment-friendly ways.
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Affiliation(s)
- C Sangavai
- Molecular Systems Engineering Lab, Department of Bioinformatics, School of Life Sciences, Bharathidasan University, Tiruchirappalli, 620 024, Tamil Nadu, India
| | - P Chellapandi
- Molecular Systems Engineering Lab, Department of Bioinformatics, School of Life Sciences, Bharathidasan University, Tiruchirappalli, 620 024, Tamil Nadu, India
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23
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Su H, Lin J, Wang Y, Chen Q, Wang G, Tan F. Engineering Brevibacterium flavum
for the production of renewable bioenergy: C4-C5 advanced alcohols. Biotechnol Bioeng 2017; 114:1946-1958. [DOI: 10.1002/bit.26324] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Revised: 04/18/2017] [Accepted: 04/26/2017] [Indexed: 12/30/2022]
Affiliation(s)
- HaiFeng Su
- Chongqing Institute of Green and Interligent Technology; Chinese Academy of Science; 266, Fangzheng Avenue, Shuitu High-Tech Park, Beibei Chongqing 400714 P. R. China
| | - JiaFu Lin
- Antibiotics Research and Re-evaluation Key Laboratory of Sichuan Province; Sichuan Industrial Institute of Antibiotics, Chengdu University; Chengdu P. R. China
| | - YuanHong Wang
- Center of Analysis and Testing; School of Public Health; Institute of Analytical Chemistry for Life Science; Nantong University; Nantong P. R. China
| | - Qiao Chen
- Chongqing Institute of Green and Interligent Technology; Chinese Academy of Science; 266, Fangzheng Avenue, Shuitu High-Tech Park, Beibei Chongqing 400714 P. R. China
| | - GuangWei Wang
- Chongqing Institute of Green and Interligent Technology; Chinese Academy of Science; 266, Fangzheng Avenue, Shuitu High-Tech Park, Beibei Chongqing 400714 P. R. China
| | - FuRong Tan
- Biogas Institute of Ministry of Agriculture; Chengdu 610041 Sichuan P. R. China
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24
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Soh LMJ, Mak WS, Lin PP, Mi L, Chen FYH, Damoiseaux R, Siegel JB, Liao JC. Engineering a Thermostable Keto Acid Decarboxylase Using Directed Evolution and Computationally Directed Protein Design. ACS Synth Biol 2017; 6:610-618. [PMID: 28052191 DOI: 10.1021/acssynbio.6b00240] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Keto acid decarboxylase (Kdc) is a key enzyme in producing keto acid derived higher alcohols, like isobutanol. The most active Kdc's are found in mesophiles; the only reported Kdc activity in thermophiles is 2 orders of magnitude less active. Therefore, the thermostability of mesophilic Kdc limits isobutanol production temperature. Here, we report development of a thermostable 2-ketoisovalerate decarboxylase (Kivd) with 10.5-fold increased residual activity after 1h preincubation at 60 °C. Starting with mesophilic Lactococcus lactis Kivd, a library was generated using random mutagenesis and approximately 8,000 independent variants were screened. The top single-mutation variants were recombined. To further improve thermostability, 16 designs built using Rosetta Comparative Modeling were screened and the most active was recombined to form our best variant, LLM4. Compared to wild-type Kivd, a 13 °C increase in melting temperature and over 4-fold increase in half-life at 60 °C were observed. LLM4 will be useful for keto acid derived alcohol production in lignocellulosic thermophiles.
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Affiliation(s)
| | - Wai Shun Mak
- Department of Chemistry, Biochemistry & Molecular Medicine, and the Genome Center, University of California Davis, One Shields Avenue, Davis, California 95616, United States
| | | | | | | | - Robert Damoiseaux
- California NanoSystems Institute, 420 Westwood Plaza, Los Angeles, California 90095, United States
| | - Justin B. Siegel
- Department of Chemistry, Biochemistry & Molecular Medicine, and the Genome Center, University of California Davis, One Shields Avenue, Davis, California 95616, United States
| | - James C. Liao
- UCLA-DOE Institute of Genomics and Proteomics, 420 Westwood Plaza, Los Angeles, California 90095, United States
- Academia Sinica, 128 Academia
Road, Section 2, Nankang, Taipei 115, Taiwan, R.O.C
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25
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Engineering the leucine biosynthetic pathway for isoamyl alcohol overproduction in Saccharomyces cerevisiae. ACTA ACUST UNITED AC 2017; 44:107-117. [DOI: 10.1007/s10295-016-1855-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Accepted: 10/30/2016] [Indexed: 10/20/2022]
Abstract
Abstract
Isoamyl alcohol can be used not only as a biofuel, but also as a precursor for various chemicals. Saccharomyces cerevisiae inherently produces a small amount of isoamyl alcohol via the leucine degradation pathway, but the yield is very low. In the current study, several strategies were devised to overproduce isoamyl alcohol in budding yeast. The engineered yeast cells with the cytosolic isoamyl alcohol biosynthetic pathway produced significantly higher amounts of isobutanol over isoamyl alcohol, suggesting that the majority of the metabolic flux was diverted to the isobutanol biosynthesis due to the broad substrate specificity of Ehrlich pathway enzymes. To channel the key intermediate 2-ketosiovalerate (KIV) towards α-IPM biosynthesis, we introduced an artificial protein scaffold to pull dihydroxyacid dehydratase and α-IPM synthase into the close proximity, and the resulting strain yielded more than twofold improvement of isoamyl alcohol. The best isoamyl alcohol producer yielded 522.76 ± 38.88 mg/L isoamyl alcohol, together with 540.30 ± 48.26 mg/L isobutanol and 82.56 ± 8.22 mg/L 2-methyl-1-butanol. To our best knowledge, our work represents the first study to bypass the native compartmentalized α-IPM biosynthesis pathway for the isoamyl alcohol overproduction in budding yeast. More importantly, artificial protein scaffold based on the feature of quaternary structure of enzymes would be useful in improving the catalytic efficiency and the product specificity of other enzymatic reactions.
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Jiang W, Qiao JB, Bentley GJ, Liu D, Zhang F. Modular pathway engineering for the microbial production of branched-chain fatty alcohols. BIOTECHNOLOGY FOR BIOFUELS 2017; 10:244. [PMID: 29090017 PMCID: PMC5658922 DOI: 10.1186/s13068-017-0936-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2017] [Accepted: 10/19/2017] [Indexed: 05/08/2023]
Abstract
The intrinsic structural properties of branched long-chain fatty alcohols (BLFLs) in the range of C12 to C18 make them more suitable as diesel fuel replacements and for other industrial applications than their straight-chain counterparts. While microbial production of straight long-chain fatty alcohols has been achieved, biosynthesis of BLFLs has never been reported. In this work, we engineered four different biosynthetic pathways in Escherichia coli to produce BLFLs. We then employed a modular engineering approach to optimize the supply of α-keto acid precursors and produced either odd-chain or even-chain BLFLs with high selectivity, reaching 70 and 75% of total fatty alcohols, respectively. The acyl-ACP and alcohol-producing modules were also extensively optimized to balance enzyme expression level and ratio, resulting in a 6.5-fold improvement in BLFL titers. The best performing strain overexpressed 14 genes from 6 engineered operons and produced 350 mg/L of BLFLs in fed-batch fermenter. The modular engineering strategy successfully facilitated microbial production of BLFLs and allowed us to quickly optimize new BLFL pathway with high titers and product specificity. More generally, this work provides pathways and knowledge for the production of BLFLs and BLFL-related, industry-relevant chemicals in high titers and yields.
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Affiliation(s)
- Wen Jiang
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, 1 Brookings Drive, Campus Box 1180, Saint Louis, MO 63130 USA
| | - James B. Qiao
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, 1 Brookings Drive, Campus Box 1180, Saint Louis, MO 63130 USA
| | - Gayle J. Bentley
- Division of Biological & Biomedical Sciences, Washington University in St. Louis, Saint Louis, MO 63130 USA
- Present Address: National Bioenergy Center, National Renewable Energy Laboratory, Golden, CO 80401 USA
| | - Di Liu
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, 1 Brookings Drive, Campus Box 1180, Saint Louis, MO 63130 USA
| | - Fuzhong Zhang
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, 1 Brookings Drive, Campus Box 1180, Saint Louis, MO 63130 USA
- Division of Biological & Biomedical Sciences, Washington University in St. Louis, Saint Louis, MO 63130 USA
- Institute of Materials Science & Engineering, Washington University in St. Louis, Saint Louis, MO 63130 USA
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Metabolically engineered Saccharomyces cerevisiae for enhanced isoamyl alcohol production. Appl Microbiol Biotechnol 2016; 101:465-474. [DOI: 10.1007/s00253-016-7970-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2016] [Accepted: 10/21/2016] [Indexed: 11/26/2022]
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Engineering Escherichia coli to produce branched-chain fatty acids in high percentages. Metab Eng 2016; 38:148-158. [DOI: 10.1016/j.ymben.2016.07.003] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Revised: 06/04/2016] [Accepted: 07/12/2016] [Indexed: 12/18/2022]
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Anderhuber N, Fladischer P, Gruber-Khadjawi M, Mairhofer J, Striedner G, Wiltschi B. High-level biosynthesis of norleucine in E. coli for the economic labeling of proteins. J Biotechnol 2016; 235:100-11. [PMID: 27107466 DOI: 10.1016/j.jbiotec.2016.04.033] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Revised: 04/14/2016] [Accepted: 04/19/2016] [Indexed: 10/21/2022]
Abstract
The residue-specific labeling of proteins with non-canonical amino acids (ncAA) is well established in shake flask cultures. A key aspect for the transfer of the methodology to larger scales for biotechnological applications is the cost of the supplemented ncAAs. Therefore, we established a scalable bioprocess using an engineered host strain for the biosynthesis of the methionine analog norleucine at titers appropriate for the efficient and economic labeling of proteins. To enhance the biosynthesis of norleucine, which is a side-product of the branched chain amino acid pathway, we deleted all three acetolactate synthase isoforms of the methionine auxotrophic Escherichia coli expression strain B834(DE3). Additionally, we overexpressed leuABCD to boost the biosynthesis of norleucine. We systematically analyzed the production of norleucine under the conditions for its residue-specific incorporation in bioreactor cultures that had a 30-fold higher cell density than shake flask cultures. Under optimized conditions, 5g/L norleucine was biosynthesized. This titer is two times higher than the standard supplementation with norleucine of a culture with comparable cell density. We expect that our metabolically engineered strain for the improved biosynthesis of norleucine in combination with the proposed bioprocess will facilitate the efficient residue-specific labeling of proteins at a reasonable price in scales beyond the shake flask.
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Affiliation(s)
- Niklaus Anderhuber
- acib-Austrian Centre of Industrial Biotechnology, Petersgasse 14, A-8010 Graz, Austria
| | - Patrik Fladischer
- acib-Austrian Centre of Industrial Biotechnology, Petersgasse 14, A-8010 Graz, Austria; Institute of Molecular Biotechnology, Graz University of Technology, Petersgasse 14, A-8010 Graz, Austria
| | - Mandana Gruber-Khadjawi
- acib-Austrian Centre of Industrial Biotechnology, Petersgasse 14, A-8010 Graz, Austria; Department of Organic Chemistry, Graz University of Technology, Stremayrgasse 9/4, A-8010 Graz, Austria
| | - Juergen Mairhofer
- Department of Biotechnology, University of Natural Resources and Life Sciences, and Department of Biotechnology, Muthgasse 18, A-1190 Vienna, Austria; enGenes Biotech GmbH, Mooslackengasse 17, A-1190 Vienna, Austria
| | - Gerald Striedner
- acib-Austrian Centre of Industrial Biotechnology, Petersgasse 14, A-8010 Graz, Austria; Department of Biotechnology, University of Natural Resources and Life Sciences, and Department of Biotechnology, Muthgasse 18, A-1190 Vienna, Austria
| | - Birgit Wiltschi
- acib-Austrian Centre of Industrial Biotechnology, Petersgasse 14, A-8010 Graz, Austria.
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Isopentenyl diphosphate (IPP)-bypass mevalonate pathways for isopentenol production. Metab Eng 2016; 34:25-35. [DOI: 10.1016/j.ymben.2015.12.002] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Revised: 11/02/2015] [Accepted: 12/07/2015] [Indexed: 11/20/2022]
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Sun X, Shen X, Jain R, Lin Y, Wang J, Sun J, Wang J, Yan Y, Yuan Q. Synthesis of chemicals by metabolic engineering of microbes. Chem Soc Rev 2016; 44:3760-85. [PMID: 25940754 DOI: 10.1039/c5cs00159e] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Metabolic engineering is a powerful tool for the sustainable production of chemicals. Over the years, the exploration of microbial, animal and plant metabolism has generated a wealth of valuable genetic information. The prudent application of this knowledge on cellular metabolism and biochemistry has enabled the construction of novel metabolic pathways that do not exist in nature or enhance existing ones. The hand in hand development of computational technology, protein science and genetic manipulation tools has formed the basis of powerful emerging technologies that make the production of green chemicals and fuels a reality. Microbial production of chemicals is more feasible compared to plant and animal systems, due to simpler genetic make-up and amenable growth rates. Here, we summarize the recent progress in the synthesis of biofuels, value added chemicals, pharmaceuticals and nutraceuticals via metabolic engineering of microbes.
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Affiliation(s)
- Xinxiao Sun
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, 15#, Beisanhuan East Road, Chaoyang District, Beijing 100029, China.
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Yamamoto K, Tsuchisaka A, Yukawa H. Branched-Chain Amino Acids. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2016; 159:103-128. [PMID: 27872960 DOI: 10.1007/10_2016_28] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
Branched-chain amino acids (BCAAs), viz., L-isoleucine, L-leucine, and L-valine, are essential amino acids that cannot be synthesized in higher organisms and are important nutrition for humans as well as livestock. They are also valued as synthetic intermediates for pharmaceuticals. Therefore, the demand for BCAAs in the feed and pharmaceutical industries is increasing continuously. Traditional industrial fermentative production of BCAAs was performed using microorganisms isolated by random mutagenesis. A collection of these classical strains was also scientifically useful to clarify the details of the BCAA biosynthetic pathways, which are tightly regulated by feedback inhibition and transcriptional attenuation. Based on this understanding of the metabolism of BCAAs, it is now possible for us to pursue strains with higher BCAA productivity using rational design and advanced molecular biology techniques. Additionally, systems biology approaches using augmented omics information help us to optimize carbon flux toward BCAA production. Here, we describe the biosynthetic pathways of BCAAs and their regulation and then overview the microorganisms developed for BCAA production. Other chemicals, including isobutanol, i.e., a second-generation biofuel, can be synthesized by branching the BCAA biosynthetic pathways, which are also outlined.
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Affiliation(s)
- Keisuke Yamamoto
- Green Earth Institute Co., Ltd, Hongo, Tokyo, Japan
- Green Earth Research Center, Kisarazu, Chiba, Japan
| | - Atsunari Tsuchisaka
- Green Earth Institute Co., Ltd, Hongo, Tokyo, Japan
- Green Earth Research Center, Kisarazu, Chiba, Japan
| | - Hideaki Yukawa
- Green Earth Institute Co., Ltd, Hongo, Tokyo, Japan.
- Green Earth Research Center, Kisarazu, Chiba, Japan.
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Recent advances in microbial production of fuels and chemicals using tools and strategies of systems metabolic engineering. Biotechnol Adv 2015; 33:1455-66. [DOI: 10.1016/j.biotechadv.2014.11.006] [Citation(s) in RCA: 84] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2014] [Revised: 10/23/2014] [Accepted: 11/09/2014] [Indexed: 11/22/2022]
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35
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Pearsall SM, Rowley CN, Berry A. Advances in Pathway Engineering for Natural Product Biosynthesis. ChemCatChem 2015. [DOI: 10.1002/cctc.201500602] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Sarah M. Pearsall
- Astbury Centre for Structural Molecular Biology; University of Leeds; Leeds LS2 9JT UK
| | - Christopher N. Rowley
- Astbury Centre for Structural Molecular Biology; University of Leeds; Leeds LS2 9JT UK
| | - Alan Berry
- Astbury Centre for Structural Molecular Biology; University of Leeds; Leeds LS2 9JT UK
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Chen X, Xu J, Yang L, Yuan Z, Xiao S, Zhang Y, Liang C, He M, Guo Y. Production of C4 and C5 branched-chain alcohols by engineered Escherichia. coli. J Ind Microbiol Biotechnol 2015; 42:1473-9. [PMID: 26350079 DOI: 10.1007/s10295-015-1656-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2015] [Accepted: 07/22/2015] [Indexed: 11/26/2022]
Abstract
Higher alcohols, longer chain alcohols, contain more than 3 carbon atoms, showed close energy advantages as gasoline, and were considered as the next generation substitution for chemical fuels. Higher alcohol biosynthesis by native microorganisms mainly needs gene expression of heterologous keto acid decarboxylase and alcohol dehydrogenases. In the present study, branched-chain α-keto acid decarboxylase gene from Lactococcus lactis subsp. lactis CICC 6246 (Kivd) and alcohol dehydrogenases gene from Zymomonas mobilis CICC 41465 (AdhB) were transformed into Escherichia coli for higher alcohol production. SDS-PAGE results showed these two proteins were expressed in the recombinant strains. The resulting strain was incubated in LB medium at 37 °C in Erlenmeyer flasks and much more 3-methyl-1-butanol (104 mg/L) than isobutanol (24 mg/L) was produced. However, in 5 g/L glucose-containing medium, the production of two alcohols was similar, 156 and 161 mg/L for C4 (isobutanol) and C5 (3-methyl-1-butanol) alcohol, respectively. Effects of fermentation factors including temperature, glucose content, and α-keto acid on alcohol production were also investigated. The increase of glucose content and the adding of α-keto acids facilitated the production of C4 and C5 alcohols. The enzyme activities of pure Kivd on α-ketoisovalerate and α-ketoisocaproate were 26.77 and 21.24 μmol min(-1) mg(-1), respectively. Due to its ability on decarboxylation of α-ketoisovalerate and α-ketoisocaproate, the recombinant E. coli strain showed potential application on isoamyl alcohol and isobutanol production.
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Affiliation(s)
- Xiaoyan Chen
- Key Laboratory of Renewable Energy and Gas Hydrate, Chinese Academy of Sciences, Guangzhou, 510640, China
| | - Jingliang Xu
- Key Laboratory of Renewable Energy and Gas Hydrate, Chinese Academy of Sciences, Guangzhou, 510640, China
| | - Liu Yang
- Key Laboratory of Renewable Energy and Gas Hydrate, Chinese Academy of Sciences, Guangzhou, 510640, China
| | - Zhenhong Yuan
- Key Laboratory of Renewable Energy and Gas Hydrate, Chinese Academy of Sciences, Guangzhou, 510640, China.
| | - Shiyuan Xiao
- Key Laboratory of Renewable Energy and Gas Hydrate, Chinese Academy of Sciences, Guangzhou, 510640, China
| | - Yu Zhang
- Key Laboratory of Renewable Energy and Gas Hydrate, Chinese Academy of Sciences, Guangzhou, 510640, China
| | - Cuiyi Liang
- Key Laboratory of Renewable Energy and Gas Hydrate, Chinese Academy of Sciences, Guangzhou, 510640, China
| | - Minchao He
- Key Laboratory of Renewable Energy and Gas Hydrate, Chinese Academy of Sciences, Guangzhou, 510640, China
| | - Ying Guo
- Key Laboratory of Renewable Energy and Gas Hydrate, Chinese Academy of Sciences, Guangzhou, 510640, China
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37
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Mukhopadhyay A. Tolerance engineering in bacteria for the production of advanced biofuels and chemicals. Trends Microbiol 2015; 23:498-508. [DOI: 10.1016/j.tim.2015.04.008] [Citation(s) in RCA: 163] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Revised: 04/17/2015] [Accepted: 04/23/2015] [Indexed: 02/06/2023]
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38
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Jiang W, Jiang Y, Bentley GJ, Liu D, Xiao Y, Zhang F. Enhanced production of branched-chain fatty acids by replacing β-ketoacyl-(acyl-carrier-protein) synthase III (FabH). Biotechnol Bioeng 2015; 112:1613-22. [DOI: 10.1002/bit.25583] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Revised: 02/09/2015] [Accepted: 02/23/2015] [Indexed: 01/13/2023]
Affiliation(s)
- Wen Jiang
- Department of Energy, Environmental, and Chemical Engineering; Washington University in St. Louis; 1 Brookings Drive, Saint Louis Missouri 63130
| | - Yanfang Jiang
- Department of Energy, Environmental, and Chemical Engineering; Washington University in St. Louis; 1 Brookings Drive, Saint Louis Missouri 63130
| | - Gayle J. Bentley
- Division of Biological & Biomedical Sciences; Washington University in St. Louis; Saint Louis Missouri
| | - Di Liu
- Division of Biological & Biomedical Sciences; Washington University in St. Louis; Saint Louis Missouri
| | - Yi Xiao
- Department of Energy, Environmental, and Chemical Engineering; Washington University in St. Louis; 1 Brookings Drive, Saint Louis Missouri 63130
| | - Fuzhong Zhang
- Department of Energy, Environmental, and Chemical Engineering; Washington University in St. Louis; 1 Brookings Drive, Saint Louis Missouri 63130
- Division of Biological & Biomedical Sciences; Washington University in St. Louis; Saint Louis Missouri
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39
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Miller DM, Gulbis JM. Engineering protocells: prospects for self-assembly and nanoscale production-lines. Life (Basel) 2015; 5:1019-53. [PMID: 25815781 PMCID: PMC4500129 DOI: 10.3390/life5021019] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2015] [Revised: 03/09/2015] [Accepted: 03/16/2015] [Indexed: 11/16/2022] Open
Abstract
The increasing ease of producing nucleic acids and proteins to specification offers potential for design and fabrication of artificial synthetic "organisms" with a myriad of possible capabilities. The prospects for these synthetic organisms are significant, with potential applications in diverse fields including synthesis of pharmaceuticals, sources of renewable fuel and environmental cleanup. Until now, artificial cell technology has been largely restricted to the modification and metabolic engineering of living unicellular organisms. This review discusses emerging possibilities for developing synthetic protocell "machines" assembled entirely from individual biological components. We describe a host of recent technological advances that could potentially be harnessed in design and construction of synthetic protocells, some of which have already been utilized toward these ends. More elaborate designs include options for building self-assembling machines by incorporating cellular transport and assembly machinery. We also discuss production in miniature, using microfluidic production lines. While there are still many unknowns in the design, engineering and optimization of protocells, current technologies are now tantalizingly close to the capabilities required to build the first prototype protocells with potential real-world applications.
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Affiliation(s)
- David M Miller
- The Walter and Eliza Hall Institute of Medical Research, Parkville VIC 3052, Australia.
- Department of Medical Biology, The University of Melbourne, Parkville VIC 3052, Australia.
| | - Jacqueline M Gulbis
- The Walter and Eliza Hall Institute of Medical Research, Parkville VIC 3052, Australia.
- Department of Medical Biology, The University of Melbourne, Parkville VIC 3052, Australia.
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Honjo H, Tsuruno K, Tatsuke T, Sato M, Hanai T. Dual synthetic pathway for 3-hydroxypropionic acid production in engineered Escherichia coli. J Biosci Bioeng 2015; 120:199-204. [PMID: 25650075 DOI: 10.1016/j.jbiosc.2014.12.023] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Revised: 12/16/2014] [Accepted: 12/24/2014] [Indexed: 10/24/2022]
Abstract
3-Hydroxypropionic acid (3-HP) is an important platform C3 chemical; production of 3-HP in recombinant Escherichia coli by synthetic pathways has been the focus of a lot of research. When glycerol is used as a substrate to produce 3-HP in E. coli, only the ALDH pathway (employing aldehyde dehydrogenase (ALDH) for conversion of 3-hydroxypropionaldehyde (3-HPA) into 3-HP) has been utilized as a synthetic pathway. However, several bacteria (including Klebsiella pneumoniae) are known to have the ability to produce 3-HP by the Pdu pathway (employing the PduP, PduL, and PduW enzymes). Here, we report the production of 3-HP in E. coli by using the Pdu pathway from K. pneumoniae as a synthetic pathway. Moreover, a strain harboring a dual synthetic pathways (ALDH and Pdu) exhibited a 70% increase in 3-HP titer compared to one harboring the ALDH pathway alone (56.1 ± 0.736 mM and 33.1 ± 0.920 mM, respectively). To our knowledge, this is the first report of 3-HP production by E. coli harboring the Pdu pathway, with the dual synthetic pathway showing the highest yield ever reported by batch culture [54.1% (mol/mol)].
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Affiliation(s)
- Hiroshi Honjo
- Laboratory for Bioinformatics, Graduate School of Systems Life Sciences, Kyushu University, 804 Westwing, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Keigo Tsuruno
- Laboratory for Bioinformatics, Graduate School of Systems Life Sciences, Kyushu University, 804 Westwing, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Tsuneyuki Tatsuke
- Laboratory for Bioinformatics, Graduate School of Systems Life Sciences, Kyushu University, 804 Westwing, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Masaki Sato
- Laboratory for Bioinformatics, Graduate School of Systems Life Sciences, Kyushu University, 804 Westwing, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Taizo Hanai
- Laboratory for Bioinformatics, Graduate School of Systems Life Sciences, Kyushu University, 804 Westwing, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan.
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41
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Nazem-Bokaee H, S. Senger R. ToMI-FBA: A genome-scale metabolic flux based algorithm to select optimum hosts and media formulations for expressing pathways of interest. AIMS BIOENGINEERING 2015. [DOI: 10.3934/bioeng.2015.4.335] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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42
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Tao H, Guo D, Zhang Y, Deng Z, Liu T. Metabolic engineering of microbes for branched-chain biodiesel production with low-temperature property. BIOTECHNOLOGY FOR BIOFUELS 2015; 8:92. [PMID: 26120362 PMCID: PMC4483204 DOI: 10.1186/s13068-015-0270-7] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Accepted: 06/05/2015] [Indexed: 05/08/2023]
Abstract
BACKGROUND The steadily increasing demand for diesel fuels calls for renewable energy sources. This has attracted a growing amount of research to develop advanced, alternative biodiesel worldwide. Several major disadvantages of current biodiesels are the undesirable physical properties such as high viscosity and poor low-temperature operability. Therefore, there is an urgent need to develop novel and advanced biodiesels. RESULTS Inspired by the proven capability of wax ester synthase/acyl-coenzyme A, diacylglycerol acyltransferase (WS/DGAT) to generate fatty acid esters, de novo biosynthesis of fatty acid branched-chain esters (FABCEs) and branched fatty acid branched-chain esters (BFABCEs) was performed in engineered Escherichia coli through combination of the (branched) fatty acid biosynthetic pathway and the branched-chain amino acid biosynthetic pathway. Furthermore, by modifying the fatty acid pathway, we improved FABCE production to 273 mg/L and achieved a high proportion of FABCEs at 99.3 % of total fatty acid esters. In order to investigate the universality of this strategy, Pichia pastoris yeast was engineered and produced desirable levels of FABCEs for the first time with a good starting point of 169 mg/L. CONCLUSIONS We propose new pathways of fatty acid ester biosynthesis and establish proof of concept through metabolic engineering of E. coli and P. pastoris yeast. We were able to produce advanced biodiesels with high proportions FABCEs and BFABCEs. Furthermore, this new strategy promises to achieve advanced biodiesels with beneficial low-temperature properties.
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Affiliation(s)
- Hui Tao
- />Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education and Wuhan University School of Pharmaceutical Sciences, Wuhan, 430071 China
- />Hubei Engineering Laboratory for Synthetic Microbiology, Wuhan Institute of Biotechnology, Wuhan, 430075 China
| | - Daoyi Guo
- />Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education and Wuhan University School of Pharmaceutical Sciences, Wuhan, 430071 China
| | - Yuchen Zhang
- />Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education and Wuhan University School of Pharmaceutical Sciences, Wuhan, 430071 China
- />Hubei Engineering Laboratory for Synthetic Microbiology, Wuhan Institute of Biotechnology, Wuhan, 430075 China
| | - Zixin Deng
- />Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education and Wuhan University School of Pharmaceutical Sciences, Wuhan, 430071 China
- />Hubei Engineering Laboratory for Synthetic Microbiology, Wuhan Institute of Biotechnology, Wuhan, 430075 China
- />State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240 China
| | - Tiangang Liu
- />Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education and Wuhan University School of Pharmaceutical Sciences, Wuhan, 430071 China
- />Hubei Engineering Laboratory for Synthetic Microbiology, Wuhan Institute of Biotechnology, Wuhan, 430075 China
- />Hubei Provincial Cooperative Innovation Center of Industrial Fermentation, Wuhan, 430068 China
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Tashiro Y, Rodriguez GM, Atsumi S. 2-Keto acids based biosynthesis pathways for renewable fuels and chemicals. J Ind Microbiol Biotechnol 2014; 42:361-73. [PMID: 25424696 DOI: 10.1007/s10295-014-1547-8] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2014] [Accepted: 11/11/2014] [Indexed: 11/30/2022]
Abstract
Global energy and environmental concerns have driven the development of biological chemical production from renewable sources. Biological processes using microorganisms are efficient and have been traditionally utilized to convert biomass (i.e., glucose) to useful chemicals such as amino acids. To produce desired fuels and chemicals with high yield and rate, metabolic pathways have been enhanced and expanded with metabolic engineering and synthetic biology approaches. 2-Keto acids, which are key intermediates in amino acid biosynthesis, can be converted to a wide range of chemicals. 2-Keto acid pathways were engineered in previous research efforts and these studies demonstrated that 2-keto acid pathways have high potential for novel metabolic routes with high productivity. In this review, we discuss recently developed 2-keto acid-based pathways.
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Affiliation(s)
- Yohei Tashiro
- Department of Chemistry, University of California-Davis, Davis, CA, USA
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Tai YS, Xiong M, Zhang K. Engineered biosynthesis of medium-chain esters in Escherichia coli. Metab Eng 2014; 27:20-28. [PMID: 25447641 DOI: 10.1016/j.ymben.2014.10.004] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2013] [Revised: 09/28/2014] [Accepted: 10/20/2014] [Indexed: 01/17/2023]
Abstract
Medium-chain esters such as isobutyl acetate (IBAc) and isoamyl acetate (IAAc) are high-volume solvents, flavors and fragrances. In this work, we engineered synthetic metabolic pathways in Escherichia coli for the total biosynthesis of IBAc and IAAc directly from glucose. Our pathways harnessed the power of natural amino acid biosynthesis. In particular, the native valine and leucine pathways in E. coli were utilized to supply the precursors. Then alcohol acyltransferases from various organisms were investigated on their capability to catalyze esterification reactions. It was discovered that ATF1 from Saccharomyces cerevisiae was the best enzyme for the formation of both IBAc and IAAc in E. coli. In vitro biochemical characterization of ATF1 confirmed the fermentation results and provided rational guidance for future enzyme engineering. We also performed strain improvement by removing byproduct pathways (Δldh, ΔpoxB, Δpta) and increased the production of both target chemicals. Then the best IBAc producing strain was used for scale-up fermentation in a 1.3-L benchtop bioreactor. 36g/L of IBAc was produced after 72h fermentation. This work demonstrates the feasibility of total biosynthesis of medium-chain esters as renewable chemicals.
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Affiliation(s)
- Yi-Shu Tai
- Department of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, MN 55455, USA
| | - Mingyong Xiong
- Department of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, MN 55455, USA
| | - Kechun Zhang
- Department of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, MN 55455, USA.
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45
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Park SH, Kim S, Hahn JS. Metabolic engineering of Saccharomyces cerevisiae for the production of isobutanol and 3-methyl-1-butanol. Appl Microbiol Biotechnol 2014; 98:9139-47. [DOI: 10.1007/s00253-014-6081-0] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2014] [Revised: 08/19/2014] [Accepted: 09/09/2014] [Indexed: 11/28/2022]
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46
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Nozzi NE, Desai SH, Case AE, Atsumi S. Metabolic engineering for higher alcohol production. Metab Eng 2014; 25:174-82. [DOI: 10.1016/j.ymben.2014.07.007] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2014] [Revised: 07/16/2014] [Accepted: 07/16/2014] [Indexed: 10/25/2022]
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47
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Wendisch VF. Microbial production of amino acids and derived chemicals: synthetic biology approaches to strain development. Curr Opin Biotechnol 2014; 30:51-8. [PMID: 24922334 DOI: 10.1016/j.copbio.2014.05.004] [Citation(s) in RCA: 96] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2014] [Revised: 05/15/2014] [Accepted: 05/18/2014] [Indexed: 10/25/2022]
Abstract
Amino acids are produced at the multi-million-ton-scale with fermentative production of l-glutamate and l-lysine alone being estimated to amount to more than five million tons in the year 2013. Metabolic engineering constantly improves productivities of amino acid producing strains, mainly Corynebacterium glutamicum and Escherichia coli strains. Classical mutagenesis and screening have been accelerated by combination with intracellular metabolite sensing. Synthetic biology approaches have allowed access to new carbon sources to realize a flexible feedstock concept. Moreover, new pathways for amino acid production as well as fermentative production of non-native compounds derived from amino acids or their metabolic precursors were developed. These include dipeptides, α,ω-diamines, α,ω-diacids, keto acids, acetylated amino acids and ω-amino acids.
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Affiliation(s)
- Volker F Wendisch
- Chair of Genetics of Prokaryotes, Faculty of Biology & CeBiTec, Bielefeld University, Germany.
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48
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Latendresse M, Krummenacker M, Karp PD. Optimal metabolic route search based on atom mappings. Bioinformatics 2014; 30:2043-50. [DOI: 10.1093/bioinformatics/btu150] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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49
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Jambunathan P, Zhang K. Novel pathways and products from 2-keto acids. Curr Opin Biotechnol 2014; 29:1-7. [PMID: 24492019 DOI: 10.1016/j.copbio.2014.01.008] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2013] [Accepted: 01/13/2014] [Indexed: 01/23/2023]
Abstract
Since traditional chemical processes are non-renewable and environmentally unfriendly, biosynthesis is emerging as an attractive alternative for the production of advanced biofuels, chemicals, pharmaceuticals and polymers. Cost-competitive biomanufacturing requires the design of metabolic pathways that can achieve high production yields and rates. Recent advances in natural amino acid production have motivated the use of 2-ketoacid intermediates for the production of important chemicals. These 2-ketoacids undergo a wide range of efficient biochemical reactions leading to an array of industrially useful products. In this review, recently developed novel pathways based on 2-ketoacids will be described along with representative examples.
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Affiliation(s)
- Pooja Jambunathan
- Department of Chemical Engineering and Materials Science, University of Minnesota, Twin Cities, MN 55455, USA
| | - Kechun Zhang
- Department of Chemical Engineering and Materials Science, University of Minnesota, Twin Cities, MN 55455, USA.
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50
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Metabolic engineering of Escherichia coli for production of fatty acid short-chain esters through combination of the fatty acid and 2-keto acid pathways. Metab Eng 2014; 22:69-75. [PMID: 24440714 DOI: 10.1016/j.ymben.2014.01.003] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2013] [Revised: 12/30/2013] [Accepted: 01/08/2014] [Indexed: 01/22/2023]
Abstract
Fatty acid short-chain esters (FASEs) are biodiesels that are renewable, nontoxic, and biodegradable biofuels. A novel approach for the biosynthesis of FASEs has been developed using metabolically-engineered E. coli through combination of the fatty acid and 2-keto acid pathways. Several genetic engineering strategies were also developed to increase fatty acyl-CoA availability to improve FASEs production. Fed-batch cultivation of the engineered E. coli resulted in a titer of 1008 mg/L FASEs. Since the fatty acid and 2-keto acid pathways are native microbial synthesis pathways, this strategy can be implemented in a variety of microorganisms to produce various FASEs from cheap and readily-available, renewable, raw materials such as sugars and cellulose in the future.
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