501
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Shi S, Valle-Rodríguez JO, Siewers V, Nielsen J. Engineering of chromosomal wax ester synthase integrated Saccharomyces cerevisiae mutants for improved biosynthesis of fatty acid ethyl esters. Biotechnol Bioeng 2014; 111:1740-7. [PMID: 24752598 DOI: 10.1002/bit.25234] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2014] [Accepted: 03/13/2014] [Indexed: 01/03/2023]
Abstract
In recent years, significant advances have been made to engineer robust microbes for overproducing biochemical products from renewable resources. These accomplishments have to a large extend been based on plasmid based methods. However, plasmid maintenance may cause a metabolic burden on the host cell and plasmid-based overexpression of genes can result in genetically unstable strains, which contributes to loss in productivity. Here, a chromosome engineering method based on delta integration was applied in Saccharomyces cerevisiae for the production of fatty acid ethyl esters (FAEEs), which can be directly used as biodiesel and would be a possible substitute for conventional petroleum-based diesel. An integration construct was designed and integrated into chromosomal delta sequences by repetitive transformation, which resulted in 1-6 copies of the integration construct per genome. The corresponding FAEE production increased up to 34 mg/L, which is an about sixfold increase compared to the equivalent plasmid-based producer. The integrated cassette in the yeast genome was stably maintained in nonselective medium after deletion of RAD52 which is essential for efficient homologous recombination. To obtain a further increase of FAEE production, genes encoding endogenous acyl-CoA binding protein (ACB1) and a bacterial NADP(+)-dependent glyceraldehyde-3-phosphate dehydrogenase (gapN) were overexpressed in the final integration strain, which resulted in another 40% percent increase in FAEE production. Our integration strategy enables easy engineering of strains with adjustable gene copy numbers integrated into the genome and this allows for an easy evaluation of the effect of the gene copy number on pathway flux. It therefore represents a valuable tool for introducing and expressing a heterologous pathway in yeast.
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Affiliation(s)
- Shuobo Shi
- Department of Chemical and Biological Engineering, Chalmers University of Technology, SE-412 96, Göteborg, Sweden
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502
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A versatile framework for microbial engineering using synthetic non-coding RNAs. Nat Rev Microbiol 2014; 12:341-54. [DOI: 10.1038/nrmicro3244] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
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503
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Biopharmaceutical protein production bySaccharomyces cerevisiae: current state and future prospects. ACTA ACUST UNITED AC 2014. [DOI: 10.4155/pbp.14.8] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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504
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505
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Sakai Y, Abe K, Nakashima S, Yoshida W, Ferri S, Sode K, Ikebukuro K. Improving the gene-regulation ability of small RNAs by scaffold engineering in Escherichia coli. ACS Synth Biol 2014; 3:152-62. [PMID: 24328142 DOI: 10.1021/sb4000959] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Noncoding small RNAs are involved in transcriptional and post-transcriptional gene regulation of target mRNAs by modulating mRNA elongation, stability, or translational efficiency. Many natural trans-encoded small RNAs contain a scaffold that allows binding of the RNA chaperone protein Hfq for conditional gene regulation. Here, we improved the gene regulation abilities of small RNAs by directly fusing the natural Escherichia coli trans-encoded small RNA-derived scaffolds, including Hfq-binding and rho-independent transcription terminator sequences, to the 3' end of the small RNAs that mediate RNA-based gene regulation. As target small RNAs to improve their gene regulation abilities, we selected small RNAs of artificial post-transcriptional riboregulators and transcriptional attenuators. Four different small RNA scaffolds were fused to the riboregulator and attenuator-derived small RNAs. Mutations were introduced into the best small RNA scaffold to improve its gene-regulation ability further. As a result, mutations predicted to stabilize the secondary structures of the small RNA scaffolds dramatically increased its ability to regulate gene expression of both the post-transcriptional riboregulator and transcriptional attenuator systems. We believe our engineered small RNA scaffolds are applicable to other RNA regulators for improving regulatory activity, and engineered small RNA scaffolds may present a valuable strategy to regulate target gene expression strongly.
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Affiliation(s)
- Yuta Sakai
- Department
of Biotechnology and Life Science, Graduate School of Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
- Japan Science and Technology Agency, CREST, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
| | - Koichi Abe
- Department
of Biotechnology and Life Science, Graduate School of Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
- Japan Science and Technology Agency, CREST, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
| | - Saki Nakashima
- Department
of Biotechnology and Life Science, Graduate School of Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
- Japan Science and Technology Agency, CREST, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
| | - Wataru Yoshida
- Department
of Biotechnology and Life Science, Graduate School of Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
- Japan Science and Technology Agency, CREST, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
| | - Stefano Ferri
- Department
of Biotechnology and Life Science, Graduate School of Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
- Japan Science and Technology Agency, CREST, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
| | - Koji Sode
- Department
of Biotechnology and Life Science, Graduate School of Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
- Japan Science and Technology Agency, CREST, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
| | - Kazunori Ikebukuro
- Department
of Biotechnology and Life Science, Graduate School of Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
- Japan Science and Technology Agency, CREST, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
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506
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Elucidation of intrinsic biosynthesis yields using 13C-based metabolism analysis. Microb Cell Fact 2014; 13:42. [PMID: 24642094 PMCID: PMC3994946 DOI: 10.1186/1475-2859-13-42] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2013] [Accepted: 03/12/2014] [Indexed: 11/10/2022] Open
Abstract
This paper discusses the use of 13C-based metabolism analysis for the assessment of intrinsic product yields - the actual carbon contribution from a single carbon substrate to the final product via a specific biosynthesis route - in the following four cases. First, undefined nutrients (such as yeast extract) in fermentation may contribute significantly to product synthesis, which can be quantified through an isotopic dilution method. Second, product and biomass synthesis may be dependent on the co-metabolism of multiple-carbon sources. 13C labeling experiments can track the fate of each carbon substrate in the cell metabolism and identify which substrate plays a main role in product synthesis. Third, 13C labeling can validate and quantify the contribution of the engineered pathway (versus the native pathway) to the product synthesis. Fourth, the loss of catabolic energy due to cell maintenance (energy used for functions other than production of new cell components) and low P/O ratio (Phosphate/Oxygen Ratio) significantly reduces product yields. Therefore, 13C-metabolic flux analysis is needed to assess the influence of suboptimal energy metabolism on microbial productivity, and determine how ATP/NAD(P)H are partitioned among various cellular functions. Since product yield is a major determining factor in the commercialization of a microbial cell factory, we foresee that 13C-isotopic labeling experiments, even without performing extensive flux calculations, can play a valuable role in the development and verification of microbial cell factories.
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507
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Liu H, Cheng T, Xian M, Cao Y, Fang F, Zou H. Fatty acid from the renewable sources: A promising feedstock for the production of biofuels and biobased chemicals. Biotechnol Adv 2014; 32:382-9. [DOI: 10.1016/j.biotechadv.2013.12.003] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2013] [Revised: 12/11/2013] [Accepted: 12/13/2013] [Indexed: 12/18/2022]
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508
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Tee TW, Chowdhury A, Maranas CD, Shanks JV. Systems metabolic engineering design: fatty acid production as an emerging case study. Biotechnol Bioeng 2014; 111:849-57. [PMID: 24481660 PMCID: PMC4241050 DOI: 10.1002/bit.25205] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2013] [Revised: 01/21/2014] [Accepted: 01/28/2014] [Indexed: 12/20/2022]
Abstract
Increasing demand for petroleum has stimulated industry to develop sustainable production of chemicals and biofuels using microbial cell factories. Fatty acids of chain lengths from C6 to C16 are propitious intermediates for the catalytic synthesis of industrial chemicals and diesel-like biofuels. The abundance of genetic information available for Escherichia coli and specifically, fatty acid metabolism in E. coli, supports this bacterium as a promising host for engineering a biocatalyst for the microbial production of fatty acids. Recent successes rooted in different features of systems metabolic engineering in the strain design of high-yielding medium chain fatty acid producing E. coli strains provide an emerging case study of design methods for effective strain design. Classical metabolic engineering and synthetic biology approaches enabled different and distinct design paths towards a high-yielding strain. Here we highlight a rational strain design process in systems biology, an integrated computational and experimental approach for carboxylic acid production, as an alternative method. Additional challenges inherent in achieving an optimal strain for commercialization of medium chain-length fatty acids will likely require a collection of strategies from systems metabolic engineering. Not only will the continued advancement in systems metabolic engineering result in these highly productive strains more quickly, this knowledge will extend more rapidly the carboxylic acid platform to the microbial production of carboxylic acids with alternate chain-lengths and functionalities.
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Affiliation(s)
- Ting Wei Tee
- Department of Chemical and Biological Engineering, Iowa State University, Ames, Iowa
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509
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Xu P, Wang W, Li L, Bhan N, Zhang F, Koffas MAG. Design and kinetic analysis of a hybrid promoter-regulator system for malonyl-CoA sensing in Escherichia coli. ACS Chem Biol 2014; 9:451-8. [PMID: 24191643 DOI: 10.1021/cb400623m] [Citation(s) in RCA: 103] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Malonyl-CoA is the rate-limiting precursor involved in the chain elongation reaction of a range of value-added pharmaceuticals and biofuels. Development of malonyl-CoA responsive sensors holds great promise in overcoming critical pathway limitations and optimizing production titers and yields. By incorporating the Bacillus subtilis trans-regulatory protein FapR and the cis-regulatory element fapO, we constructed a hybrid promoter-regulatory system that responds to a broad range of intracellular malonyl-CoA concentrations (from 0.1 to 1.1 nmol/mgDW) in Escherichia coli. Elimination of regulatory protein and nonspecific DNA cross-communication leads to a sensor construct that exhibits malonyl-CoA-dependent linear phase kinetics with increased dynamic response range. The sensors reported in this study could potentially control and optimize carbon flux leading to robust biosynthetic pathways for the production of malonyl-CoA-derived compounds.
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Affiliation(s)
- Peng Xu
- Department
of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, New York 12180, United States
- Center
for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York 12180, United States
| | - Wenya Wang
- Center
for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York 12180, United States
- College
of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Lingyun Li
- Center
for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York 12180, United States
- Department
of Biological Sciences, Rensselaer Polytechnic Institute, Troy, New York 12180, United States
| | - Namita Bhan
- Department
of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, New York 12180, United States
- Center
for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York 12180, United States
| | - Fuming Zhang
- Department
of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, New York 12180, United States
- Center
for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York 12180, United States
| | - Mattheos A. G. Koffas
- Department
of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, New York 12180, United States
- Center
for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York 12180, United States
- Department
of Biological Sciences, Rensselaer Polytechnic Institute, Troy, New York 12180, United States
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510
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Roquet N, Lu TK. Digital and analog gene circuits for biotechnology. Biotechnol J 2014; 9:597-608. [PMID: 24677719 DOI: 10.1002/biot.201300258] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2013] [Revised: 12/05/2013] [Accepted: 01/08/2014] [Indexed: 11/08/2022]
Abstract
Biotechnology offers the promise of valuable chemical production via microbial processing of renewable and inexpensive substrates. Thus far, static metabolic engineering strategies have enabled this field to advance industrial applications. However, the industrial scaling of statically engineered microbes inevitably creates inefficiencies due to variable conditions present in large-scale microbial cultures. Synthetic gene circuits that dynamically sense and regulate different molecules can resolve this issue by enabling cells to continuously adapt to variable conditions. These circuits also have the potential to enable next-generation production programs capable of autonomous transitioning between steps in a bioprocess. Here, we review the design and application of two main classes of dynamic gene circuits, digital and analog, for biotechnology. Within the context of these classes, we also discuss the potential benefits of digital-analog interconversion, memory, and multi-signal integration. Though synthetic gene circuits have largely been applied for cellular computation to date, we envision that utilizing them in biotechnology will enhance the efficiency and scope of biochemical production with living cells.
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Affiliation(s)
- Nathaniel Roquet
- Synthetic Biology Group, Research Lab of Electronics, Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA, USA; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA; Harvard Biophysics Program, Boston, MA, USA
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511
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Zhuo Y, Zhang T, Wang Q, Cruz-Morales P, Zhang B, Liu M, Barona-Gómez F, Zhang L. Synthetic biology of avermectin for production improvement and structure diversification. Biotechnol J 2014; 9:316-25. [PMID: 24478271 DOI: 10.1002/biot.201200383] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2013] [Revised: 10/26/2013] [Accepted: 12/24/2013] [Indexed: 01/15/2023]
Abstract
Natural products are still key sources of current clinical drugs and innovative therapeutic agents. Since wild-type microorganisms only produce natural products in very small quantities, yields of production strains need to be improved by breaking down the precise genetic and biochemical circuitry. Herein, we use avermectins as an example of production improvement and chemical structure diversification by synthetic biology. Avermectins are macrocyclic lactones produced by Streptomyces avermitilis and are well known and widely used for antiparasitic therapy. Given the importance of this molecule and its derivatives, many efforts and strategies were employed to improve avermectin production and generate new active analogues. This review describes the current status of synthetic strategies successfully applied for developing natural-product-producing strains and discusses future prospects for the application of enhanced avermectin production.
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Affiliation(s)
- Ying Zhuo
- Chinese Academy of Sciences Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, P.R. China
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512
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Schallmey M, Frunzke J, Eggeling L, Marienhagen J. Looking for the pick of the bunch: high-throughput screening of producing microorganisms with biosensors. Curr Opin Biotechnol 2014; 26:148-54. [PMID: 24480185 DOI: 10.1016/j.copbio.2014.01.005] [Citation(s) in RCA: 106] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2013] [Revised: 12/31/2013] [Accepted: 01/07/2014] [Indexed: 11/25/2022]
Abstract
The engineering of microbial strains for the production of small molecules of biotechnological interest is a time-consuming, laborious and expensive process. This can be mostly attributed to the fact that good producers cannot be readily obtained by high-throughput screening approaches since increased product formation usually does not confer a clear phenotype to producing strain variants. Recently, advances were made in the design and construction of genetically encoded RNA aptamer-based or transcription factor-based biosensors for detecting small molecules at the single-cell level. The first promising examples for the application of these molecular biosensors in combination with fluorescent-activated cell sorting as a high-throughput screening device demonstrated the value and potential of these new tools for microbial strain development.
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Affiliation(s)
- Marcus Schallmey
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich D-52425, Germany
| | - Julia Frunzke
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich D-52425, Germany
| | - Lothar Eggeling
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich D-52425, Germany
| | - Jan Marienhagen
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich D-52425, Germany.
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513
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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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514
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Janßen HJ, Steinbüchel A. Fatty acid synthesis in Escherichia coli and its applications towards the production of fatty acid based biofuels. BIOTECHNOLOGY FOR BIOFUELS 2014; 7:7. [PMID: 24405789 PMCID: PMC3896788 DOI: 10.1186/1754-6834-7-7] [Citation(s) in RCA: 180] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2013] [Accepted: 12/24/2013] [Indexed: 05/04/2023]
Abstract
The idea of renewable and regenerative resources has inspired research for more than a hundred years. Ideally, the only spent energy will replenish itself, like plant material, sunlight, thermal energy or wind. Biodiesel or ethanol are examples, since their production relies mainly on plant material. However, it has become apparent that crop derived biofuels will not be sufficient to satisfy future energy demands. Thus, especially in the last decade a lot of research has focused on the production of next generation biofuels. A major subject of these investigations has been the microbial fatty acid biosynthesis with the aim to produce fatty acids or derivatives for substitution of diesel. As an industrially important organism and with the best studied microbial fatty acid biosynthesis, Escherichia coli has been chosen as producer in many of these studies and several reviews have been published in the fields of E. coli fatty acid biosynthesis or biofuels. However, most reviews discuss only one of these topics in detail, despite the fact, that a profound understanding of the involved enzymes and their regulation is necessary for efficient genetic engineering of the entire pathway. The first part of this review aims at summarizing the knowledge about fatty acid biosynthesis of E. coli and its regulation, and it provides the connection towards the production of fatty acids and related biofuels. The second part gives an overview about the achievements by genetic engineering of the fatty acid biosynthesis towards the production of next generation biofuels. Finally, the actual importance and potential of fatty acid-based biofuels will be discussed.
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Affiliation(s)
- Helge Jans Janßen
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität Münster, Corrensstrasse 3, D-48149, Münster, Germany
| | - Alexander Steinbüchel
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität Münster, Corrensstrasse 3, D-48149, Münster, Germany
- Environmental Sciences Department, King Abdulaziz University, Jeddah, Saudi Arabia
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515
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Janßen HJ, Steinbüchel A. Production of triacylglycerols in Escherichia coli by deletion of the diacylglycerol kinase gene and heterologous overexpression of atfA from Acinetobacter baylyi ADP1. Appl Microbiol Biotechnol 2014; 98:1913-24. [PMID: 24389701 DOI: 10.1007/s00253-013-5460-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2013] [Revised: 12/03/2013] [Accepted: 12/05/2013] [Indexed: 12/20/2022]
Abstract
This study investigated the production of triacylglycerols in cells of the wild type of Escherichia coli and of a strain with a deleted diacylglycerol kinase gene (dgkA). By overexpression of atfA from Acinetobacter baylyi ADP1 and fadD from E. coli in the dgkA deletion mutant, cellular contents of up to 4.9% (w/w) triacylglycerols could be achieved in batch cultivation. Furthermore, heterologous expression of atfA relieves the negative effects of dgkA deletion on growth. Process optimization and fed-batch fermentation resulted in the production of 530 mg l (-1) triacylglycerols and a maximal content of 8.5% (w/w) triacylglycerols of the cell dry mass. This clearly exceeded all previous results concerning triacylglycerol production in E. coli. Furthermore, the production of extracellular free fatty acids and fatty acid ethyl esters was investigated. Like triacylglycerols, both products are potential biofuels, and we show their continuous production in a repeated batch process, with recovery of the production cells.
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Affiliation(s)
- Helge Jans Janßen
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität Münster, Corrensstrasse 3, 48149, Münster, Germany,
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516
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Blazeck J, Hill A, Liu L, Knight R, Miller J, Pan A, Otoupal P, Alper HS. Harnessing Yarrowia lipolytica lipogenesis to create a platform for lipid and biofuel production. Nat Commun 2014; 5:3131. [PMID: 24445655 DOI: 10.1038/ncomms4131] [Citation(s) in RCA: 386] [Impact Index Per Article: 38.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2013] [Accepted: 12/17/2013] [Indexed: 12/12/2022] Open
Abstract
Economic feasibility of biosynthetic fuel and chemical production hinges upon harnessing metabolism to achieve high titre and yield. Here we report a thorough genotypic and phenotypic optimization of an oleaginous organism to create a strain with significant lipogenesis capability. Specifically, we rewire Yarrowia lipolytica's native metabolism for superior de novo lipogenesis by coupling combinatorial multiplexing of lipogenesis targets with phenotypic induction. We further complete direct conversion of lipid content into biodiesel. Tri-level metabolic control results in saturated cells containing upwards of 90% lipid content and titres exceeding 25 g l(-1) lipids, which represents a 60-fold improvement over parental strain and conditions. Through this rewiring effort, we advance fundamental understanding of lipogenesis, demonstrate non-canonical environmental and intracellular stimuli and uncouple lipogenesis from nitrogen starvation. The high titres and carbon-source independent nature of this lipogenesis in Y. lipolytica highlight the potential of this organism as a platform for efficient oleochemical production.
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Affiliation(s)
- John Blazeck
- 1] McKetta Department of Chemical Engineering, The University of Texas at Austin, 200 E Dean Keeton St. Stop C0400, Austin, Texas 78712, USA [2]
| | - Andrew Hill
- 1] McKetta Department of Chemical Engineering, The University of Texas at Austin, 200 E Dean Keeton St. Stop C0400, Austin, Texas 78712, USA [2]
| | - Leqian Liu
- 1] McKetta Department of Chemical Engineering, The University of Texas at Austin, 200 E Dean Keeton St. Stop C0400, Austin, Texas 78712, USA [2]
| | - Rebecca Knight
- Section of Molecular, Cell and Developmental Biology, The University of Texas at Austin, 1 University Station Stop A6700, Austin, Texas 78712, USA
| | - Jarrett Miller
- McKetta Department of Chemical Engineering, The University of Texas at Austin, 200 E Dean Keeton St. Stop C0400, Austin, Texas 78712, USA
| | - Anny Pan
- McKetta Department of Chemical Engineering, The University of Texas at Austin, 200 E Dean Keeton St. Stop C0400, Austin, Texas 78712, USA
| | - Peter Otoupal
- McKetta Department of Chemical Engineering, The University of Texas at Austin, 200 E Dean Keeton St. Stop C0400, Austin, Texas 78712, USA
| | - Hal S Alper
- 1] McKetta Department of Chemical Engineering, The University of Texas at Austin, 200 E Dean Keeton St. Stop C0400, Austin, Texas 78712, USA [2] Institute for Cellular and Molecular Biology, The University of Texas at Austin, 2500 Speedway Avenue, Austin, Texas 78712, USA
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517
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Tseng HW, Tsai YJ, Yen JH, Chen PH, Yeh YC. A fluorescence-based microbial sensor for the selective detection of gold. Chem Commun (Camb) 2014; 50:1735-7. [DOI: 10.1039/c3cc48028c] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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518
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Zhang L, Chen Y, He N, Lu C. Acetone Cataluminescence as an Indicator for Evaluation of Heterogeneous Base Catalysts in Biodiesel Production. Anal Chem 2013; 86:870-5. [DOI: 10.1021/ac4034399] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Lijuan Zhang
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Yingchun Chen
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Nan He
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Chao Lu
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, China
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519
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Jin G, Zhang Y, Shen H, Yang X, Xie H, Zhao ZK. Fatty acid ethyl esters production in aqueous phase by the oleaginous yeast Rhodosporidium toruloides. BIORESOURCE TECHNOLOGY 2013; 150:266-270. [PMID: 24177160 DOI: 10.1016/j.biortech.2013.10.023] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2013] [Revised: 10/05/2013] [Accepted: 10/07/2013] [Indexed: 06/02/2023]
Abstract
Fatty acid ethyl esters (FAEEs) are attractive biofuel molecules. Conventional FAEEs production process uses triglycerides and ethanol as feedstocks and is sensitive to water contents. In this work, we show that the oleaginous yeast Rhodosporidium toruloides cells are capable of converting lipids into FAEEs intracellularly in aqueous phase. Up to 73% of cellular neutral glycerides could be converted into FAEEs when lipid-rich cells were incubated for 84 h at 35°C, pH 6.0 in a broth containing 10 vol% ethanol. It was found that neutral glycerides were first hydrolyzed to free fatty acids followed by esterification and that lipid droplets played important roles in the process. This new process provides a novel opportunity for integration of microbial lipid production technology with bioethanol fermentation for more efficient production of drop-in biofuels from renewable resources.
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Affiliation(s)
- Guojie Jin
- Dalian Institute of Chemical Physics, CAS, 457 Zhongshan Road, Dalian 116023, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China
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520
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Nielsen DR, Moon TS. From promise to practice. The role of synthetic biology in green chemistry. EMBO Rep 2013; 14:1034-8. [PMID: 24201977 DOI: 10.1038/embor.2013.178] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Affiliation(s)
- David R Nielsen
- School for Engineering of Matter, Transport, and Energy, Arizona State University in Tempe, Arizona, USA
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521
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Computational evaluation of cellular metabolic costs successfully predicts genes whose expression is deleterious. Proc Natl Acad Sci U S A 2013; 110:19166-71. [PMID: 24198337 DOI: 10.1073/pnas.1312361110] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Gene suppression and overexpression are both fundamental tools in linking genotype to phenotype in model organisms. Computational methods have proven invaluable in studying and predicting the deleterious effects of gene deletions, and yet parallel computational methods for overexpression are still lacking. Here, we present Expression-Dependent Gene Effects (EDGE), an in silico method that can predict the deleterious effects resulting from overexpression of either native or foreign metabolic genes. We first test and validate EDGE's predictive power in bacteria through a combination of small-scale growth experiments that we performed and analysis of extant large-scale datasets. Second, a broad cross-species analysis, ranging from microorganisms to multiple plant and human tissues, shows that genes that EDGE predicts to be deleterious when overexpressed are indeed typically down-regulated. This reflects a universal selection force keeping the expression of potentially deleterious genes in check. Third, EDGE-based analysis shows that cancer genetic reprogramming specifically suppresses genes whose overexpression impedes proliferation. The magnitude of this suppression is large enough to enable an almost perfect distinction between normal and cancerous tissues based solely on EDGE results. We expect EDGE to advance our understanding of human pathologies associated with up-regulation of particular transcripts and to facilitate the utilization of gene overexpression in metabolic engineering.
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522
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Dahl RH, Zhang F, Alonso-Gutierrez J, Baidoo E, Batth TS, Redding-Johanson AM, Petzold CJ, Mukhopadhyay A, Lee TS, Adams PD, Keasling JD. Engineering dynamic pathway regulation using stress-response promoters. Nat Biotechnol 2013; 31:1039-46. [DOI: 10.1038/nbt.2689] [Citation(s) in RCA: 352] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2013] [Accepted: 08/09/2013] [Indexed: 12/20/2022]
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523
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Lim JH, Seo SW, Kim SY, Jung GY. Model-driven rebalancing of the intracellular redox state for optimization of a heterologous n-butanol pathway in Escherichia coli. Metab Eng 2013; 20:56-62. [DOI: 10.1016/j.ymben.2013.09.003] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2013] [Revised: 08/07/2013] [Accepted: 09/11/2013] [Indexed: 12/23/2022]
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524
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525
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Szmidt-Middleton HL, Ouellet M, Adams PD, Keasling JD, Mukhopadhyay A. Utilizing a highly responsive gene, yhjX, in E. coli based production of 1,4-butanediol. Chem Eng Sci 2013. [DOI: 10.1016/j.ces.2013.06.044] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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526
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Seo SW, Yang J, Min BE, Jang S, Lim JH, Lim HG, Kim SC, Kim SY, Jeong JH, Jung GY. Synthetic biology: Tools to design microbes for the production of chemicals and fuels. Biotechnol Adv 2013; 31:811-7. [DOI: 10.1016/j.biotechadv.2013.03.012] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2012] [Revised: 03/14/2013] [Accepted: 03/28/2013] [Indexed: 10/27/2022]
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527
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528
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Rhodius VA, Segall-Shapiro TH, Sharon BD, Ghodasara A, Orlova E, Tabakh H, Burkhardt DH, Clancy K, Peterson TC, Gross CA, Voigt CA. Design of orthogonal genetic switches based on a crosstalk map of σs, anti-σs, and promoters. Mol Syst Biol 2013; 9:702. [PMID: 24169405 PMCID: PMC3817407 DOI: 10.1038/msb.2013.58] [Citation(s) in RCA: 123] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2013] [Accepted: 09/26/2013] [Indexed: 01/22/2023] Open
Abstract
Cells react to their environment through gene regulatory networks. Network integrity requires minimization of undesired crosstalk between their biomolecules. Similar constraints also limit the use of regulators when building synthetic circuits for engineering applications. Here, we mapped the promoter specificities of extracytoplasmic function (ECF) σs as well as the specificity of their interaction with anti-σs. DNA synthesis was used to build 86 ECF σs (two from every subgroup), their promoters, and 62 anti-σs identified from the genomes of diverse bacteria. A subset of 20 σs and promoters were found to be highly orthogonal to each other. This set can be increased by combining the -35 and -10 binding domains from different subgroups to build chimeras that target sequences unrepresented in any subgroup. The orthogonal σs, anti-σs, and promoters were used to build synthetic genetic switches in Escherichia coli. This represents a genome-scale resource of the properties of ECF σs and a resource for synthetic biology, where this set of well-characterized regulatory parts will enable the construction of sophisticated gene expression programs.
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Affiliation(s)
- Virgil A Rhodius
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA, USA
| | - Thomas H Segall-Shapiro
- Department of Biological Engineering, Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Brian D Sharon
- Graduate Group in Biophysics, University of California San Francisco, San Francisco, CA, USA
| | - Amar Ghodasara
- Department of Biological Engineering, Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Ekaterina Orlova
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA, USA
| | - Hannah Tabakh
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA, USA
| | - David H Burkhardt
- Graduate Group in Biophysics, University of California San Francisco, San Francisco, CA, USA
| | - Kevin Clancy
- Synthetic Biology Research and Development, Life Technologies, Carlsbad, CA, USA
| | - Todd C Peterson
- Synthetic Biology Research and Development, Life Technologies, Carlsbad, CA, USA
| | - Carol A Gross
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA, USA
- Department of Cell and Tissue Biology, University of California San Francisco, San Francisco, CA, USA
| | - Christopher A Voigt
- Department of Biological Engineering, Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, USA
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529
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Lin F, Chen Y, Levine R, Lee K, Yuan Y, Lin XN. Improving fatty acid availability for bio-hydrocarbon production in Escherichia coli by metabolic engineering. PLoS One 2013; 8:e78595. [PMID: 24147139 PMCID: PMC3798384 DOI: 10.1371/journal.pone.0078595] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2013] [Accepted: 09/22/2013] [Indexed: 02/03/2023] Open
Abstract
Previous studies have demonstrated the feasibility of producing fatty-acid-derived hydrocarbons in Escherichia coli. However, product titers and yields remain low. In this work, we demonstrate new methods for improving fatty acid production by modifying central carbon metabolism and storing fatty acids in triacylglycerol. Based on suggestions from a computational model, we deleted seven genes involved in aerobic respiration, mixed-acid fermentation, and glyoxylate bypass (in the order of cyoA, nuoA, ndh, adhE, dld, pta, and iclR) to modify the central carbon metabolic/regulatory networks. These gene deletions led to increased total fatty acids, which were the highest in the mutants containing five or six gene knockouts. Additionally, when two key enzymes in the fatty acid biosynthesis pathway were over-expressed, we observed further increase in strain △cyoA△adhE△nuoA△ndh△pta△dld, leading to 202 mg/g dry cell weight of total fatty acids, ~250% of that in the wild-type strain. Meanwhile, we successfully introduced a triacylglycerol biosynthesis pathway into E. coli through heterologous expression of wax ester synthase/acyl-coenzyme:diacylglycerol acyltransferase (WS/DGAT) enzymes. The added pathway improved both the amount and fuel quality of the fatty acids. These new metabolic engineering strategies are providing promising directions for future investigation.
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Affiliation(s)
- Fengming Lin
- Department of Chemical Engineering, University of Michigan, Ann Arbor, Michigan, United States of America
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, P.R. China
| | - Yu Chen
- Department of Chemical Engineering, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Robert Levine
- Department of Chemical Engineering, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Kilho Lee
- Department of Chemical Engineering, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Yingjin Yuan
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, P.R. China
| | - Xiaoxia Nina Lin
- Department of Chemical Engineering, University of Michigan, Ann Arbor, Michigan, United States of America
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, Michigan, United States of America
- Center for Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, United States of America
- * E-mail:
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530
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Microbial production of short-chain alkanes. Nature 2013; 502:571-4. [DOI: 10.1038/nature12536] [Citation(s) in RCA: 356] [Impact Index Per Article: 32.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2013] [Accepted: 08/08/2013] [Indexed: 12/19/2022]
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531
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Single-cell measurements of enzyme levels as a predictive tool for cellular fates during organic acid production. Appl Environ Microbiol 2013; 79:7569-82. [PMID: 24038690 DOI: 10.1128/aem.01749-13] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Organic acids derived from engineered microbes can replace fossil-derived chemicals in many applications. Fungal hosts are preferred for organic acid production because they tolerate lignocellulosic hydrolysates and low pH, allowing economic production and recovery of the free acid. However, cell death caused by cytosolic acidification constrains productivity. Cytosolic acidification affects cells asynchronously, suggesting that there is an underlying cell-to-cell heterogeneity in acid productivity and/or in resistance to toxicity. We used fluorescence microscopy to investigate the relationship between enzyme concentration, cytosolic pH, and viability at the single-cell level in Saccharomyces cerevisiae engineered to synthesize xylonic acid. We found that cultures producing xylonic acid accumulate cells with cytosolic pH below 5 (referred to here as "acidified"). Using live-cell time courses, we found that the probability of acidification was related to the initial levels of xylose dehydrogenase and sharply increased from 0.2 to 0.8 with just a 60% increase in enzyme abundance (Hill coefficient, >6). This "switch-like" relationship likely results from an enzyme level threshold above which the produced acid overwhelms the cell's pH buffering capacity. Consistent with this hypothesis, we showed that expression of xylose dehydrogenase from a chromosomal locus yields ∼20 times fewer acidified cells and ∼2-fold more xylonic acid relative to expression of the enzyme from a plasmid with variable copy number. These results suggest that strategies that further reduce cell-to-cell heterogeneity in enzyme levels could result in additional gains in xylonic acid productivity. Our results demonstrate a generalizable approach that takes advantage of the cell-to-cell variation of a clonal population to uncover causal relationships in the toxicity of engineered pathways.
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532
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Berla BM, Saha R, Immethun CM, Maranas CD, Moon TS, Pakrasi HB. Synthetic biology of cyanobacteria: unique challenges and opportunities. Front Microbiol 2013; 4:246. [PMID: 24009604 PMCID: PMC3755261 DOI: 10.3389/fmicb.2013.00246] [Citation(s) in RCA: 176] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2013] [Accepted: 08/05/2013] [Indexed: 12/31/2022] Open
Abstract
Photosynthetic organisms, and especially cyanobacteria, hold great promise as sources of renewably-produced fuels, bulk and specialty chemicals, and nutritional products. Synthetic biology tools can help unlock cyanobacteria's potential for these functions, but unfortunately tool development for these organisms has lagged behind that for S. cerevisiae and E. coli. While these organisms may in many cases be more difficult to work with as “chassis” strains for synthetic biology than certain heterotrophs, the unique advantages of autotrophs in biotechnology applications as well as the scientific importance of improved understanding of photosynthesis warrant the development of these systems into something akin to a “green E. coli.” In this review, we highlight unique challenges and opportunities for development of synthetic biology approaches in cyanobacteria. We review classical and recently developed methods for constructing targeted mutants in various cyanobacterial strains, and offer perspective on what genetic tools might most greatly expand the ability to engineer new functions in such strains. Similarly, we review what genetic parts are most needed for the development of cyanobacterial synthetic biology. Finally, we highlight recent methods to construct genome-scale models of cyanobacterial metabolism and to use those models to measure properties of autotrophic metabolism. Throughout this paper, we discuss some of the unique challenges of a diurnal, autotrophic lifestyle along with how the development of synthetic biology and biotechnology in cyanobacteria must fit within those constraints.
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Affiliation(s)
- Bertram M Berla
- Department of Energy, Environmental, and Chemical Engineering, Washington University St. Louis, MO, USA
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533
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Development of Synechocystis sp. PCC 6803 as a phototrophic cell factory. Mar Drugs 2013; 11:2894-916. [PMID: 23945601 PMCID: PMC3766872 DOI: 10.3390/md11082894] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2013] [Revised: 06/14/2013] [Accepted: 07/15/2013] [Indexed: 01/08/2023] Open
Abstract
Cyanobacteria (blue-green algae) play profound roles in ecology and biogeochemistry. One model cyanobacterial species is the unicellular cyanobacterium Synechocystis sp. PCC 6803. This species is highly amenable to genetic modification. Its genome has been sequenced and many systems biology and molecular biology tools are available to study this bacterium. Recently, researchers have put significant efforts into understanding and engineering this bacterium to produce chemicals and biofuels from sunlight and CO2. To demonstrate our perspective on the application of this cyanobacterium as a photosynthesis-based chassis, we summarize the recent research on Synechocystis 6803 by focusing on five topics: rate-limiting factors for cell cultivation; molecular tools for genetic modifications; high-throughput system biology for genome wide analysis; metabolic modeling for physiological prediction and rational metabolic engineering; and applications in producing diverse chemicals. We also discuss the particular challenges for systems analysis and engineering applications of this microorganism, including precise characterization of versatile cell metabolism, improvement of product rates and titers, bioprocess scale-up, and product recovery. Although much progress has been achieved in the development of Synechocystis 6803 as a phototrophic cell factory, the biotechnology for “Compounds from Synechocystis” is still significantly lagging behind those for heterotrophic microbes (e.g., Escherichia coli).
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534
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Teo WS, Chang MW. Development and characterization of AND-gate dynamic controllers with a modular synthetic GAL1 core promoter in Saccharomyces cerevisiae. Biotechnol Bioeng 2013; 111:144-51. [PMID: 23860786 DOI: 10.1002/bit.25001] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2013] [Revised: 07/02/2013] [Accepted: 07/11/2013] [Indexed: 01/10/2023]
Abstract
Expression of heterologous proteins in metabolic engineering endeavors can be detrimental to host cells due to increased usage of cellular resources. Dynamic controls, where protein expression can be triggered on-demand, are effective for the engineering and optimization of bio-catalysts towards robust cell growth and enhanced biochemical productivity. Here, we describe the development and characterization of AND-gate dynamic controllers in Saccharomyces cerevisiae which combine two dynamic control strategies, inducible promoters and sensing-regulation. These dynamic controllers were constructed based on synthetic hybrid promoters. Promoter enhancer sequences were fused to a synthetic GAL1 core promoter containing DNA binding sites for the binding of a repressor that reduced DNA affinity upon interaction with key intermediates in a biochemical pathway. As fatty acids are key intermediates for production of fatty alcohols, fatty acid esters, alkenes, and alkanes, which are advanced biofuels, we used the fatty acid responsive FadR repressor and its operator sequence to demonstrate the functionality of the dynamic controllers. We established that the synthetic GAL1 core promoter can be used as a modular promoter part for constructing synthetic hybrid promoters and conferring fatty acid inducibility. We further showed the performance of the AND-gate dynamic controllers, where two inputs (fatty acid and copper presence/phosphate starvation) were required to switch the AND-gate ON. This work provides a convenient platform for constructing AND-gate dynamic controllers, that is, promoters that combine inducible functionality with regulation of protein expression levels upon detection of key intermediates towards the engineering and optimization of bio-catalytic yeast cells.
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Affiliation(s)
- Wei Suong Teo
- Division of Chemical and Biomolecular Engineering, School of Chemical and Biomedical Engineering, Nanyang Technological University, 62 Nanyang Drive, Singapore, 637459, Singapore
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535
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Liu D, Hoynes-O'Connor A, Zhang F. Bridging the gap between systems biology and synthetic biology. Front Microbiol 2013; 4:211. [PMID: 23898328 PMCID: PMC3722476 DOI: 10.3389/fmicb.2013.00211] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2013] [Accepted: 07/07/2013] [Indexed: 12/24/2022] Open
Abstract
Systems biology is an inter-disciplinary science that studies the complex interactions and the collective behavior of a cell or an organism. Synthetic biology, as a technological subject, combines biological science and engineering, allowing the design and manipulation of a system for certain applications. Both systems and synthetic biology have played important roles in the recent development of microbial platforms for energy, materials, and environmental applications. More importantly, systems biology provides the knowledge necessary for the development of synthetic biology tools, which in turn facilitates the manipulation and understanding of complex biological systems. Thus, the combination of systems and synthetic biology has huge potential for studying and engineering microbes, especially to perform advanced tasks, such as producing biofuels. Although there have been very few studies in integrating systems and synthetic biology, existing examples have demonstrated great power in extending microbiological capabilities. This review focuses on recent efforts in microbiological genomics, transcriptomics, proteomics, and metabolomics, aiming to fill the gap between systems and synthetic biology.
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Affiliation(s)
- Di Liu
- Department of Energy, Environmental and Chemical Engineering, Washington University St. Louis, MO, USA
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536
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Design-driven, multi-use research agendas to enable applied synthetic biology for global health. SYSTEMS AND SYNTHETIC BIOLOGY 2013; 7:79-86. [PMID: 24432145 DOI: 10.1007/s11693-013-9118-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2012] [Revised: 04/24/2013] [Accepted: 07/09/2013] [Indexed: 01/03/2023]
Abstract
Many of the synthetic biological devices, pathways and systems that can be engineered are multi-use, in the sense that they could be used both for commercially-important applications and to help meet global health needs. The on-going development of models and simulation tools for assembling component parts into functionally-complex devices and systems will enable successful engineering with much less trial-and-error experimentation and laboratory infrastructure. As illustrations, I draw upon recent examples from my own work and the broader Keasling research group at the University of California Berkeley and the Joint BioEnergy Institute, of which I was formerly a part. By combining multi-use synthetic biology research agendas with advanced computer-aided design tool creation, it may be possible to more rapidly engineer safe and effective synthetic biology technologies that help address a wide range of global health problems.
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537
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Event report: SynBio Workshop (Paris 2012) – Risk assessment challenges of Synthetic Biology. J Verbrauch Lebensm 2013. [DOI: 10.1007/s00003-013-0829-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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538
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Tailored fatty acid synthesis via dynamic control of fatty acid elongation. Proc Natl Acad Sci U S A 2013; 110:11290-5. [PMID: 23798438 DOI: 10.1073/pnas.1307129110] [Citation(s) in RCA: 135] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Medium-chain fatty acids (MCFAs, 4-12 carbons) are valuable as precursors to industrial chemicals and biofuels, but are not canonical products of microbial fatty acid synthesis. We engineered microbial production of the full range of even- and odd-chain-length MCFAs and found that MCFA production is limited by rapid, irreversible elongation of their acyl-ACP precursors. To address this limitation, we programmed an essential ketoacyl synthase to degrade in response to a chemical inducer, thereby slowing acyl-ACP elongation and redirecting flux from phospholipid synthesis to MCFA production. Our results show that induced protein degradation can be used to dynamically alter metabolic flux, and thereby increase the yield of a desired compound. The strategy reported herein should be widely useful in a range of metabolic engineering applications in which essential enzymes divert flux away from a desired product, as well as in the production of polyketides, bioplastics, and other recursively synthesized hydrocarbons for which chain-length control is desired.
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539
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Glasgow JE, Tullman-Ercek D. Synthetic biologists spring into action at the 245th American Chemical Society National Meeting. ACS Synth Biol 2013; 2:293-5. [PMID: 24884108 DOI: 10.1021/sb400046t] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
As the field of synthetic biology continues to define itself, it has merged concepts from many related areas of research: molecular biology, genetics, bioengineering, and chemistry. At the 2013 Spring American Chemical Society National Meeting in New Orleans, LA, this mixture was manifested in a wealth of sessions emphasizing the use of modern synthetic biological approaches to solve many of today's biggest chemical problems. As a result of the field's diverse yet pervasive nature, synthetic biology concepts were present in several of the conferences many divisions, including Biological Chemistry, Biochemical Technology, Cellulose and Renewable Materials, and several others. Here we offer a snapshot of some of the exciting research discussed in the dedicated synthetic biology sessions throughout the week.
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Affiliation(s)
- Jeff E. Glasgow
- Department
of Chemistry and ‡Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720,
United States
| | - Danielle Tullman-Ercek
- Department
of Chemistry and ‡Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720,
United States
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540
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Ortiz-Marquez JCF, Do Nascimento M, Zehr JP, Curatti L. Genetic engineering of multispecies microbial cell factories as an alternative for bioenergy production. Trends Biotechnol 2013; 31:521-9. [PMID: 23791304 DOI: 10.1016/j.tibtech.2013.05.006] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2013] [Revised: 05/20/2013] [Accepted: 05/21/2013] [Indexed: 01/01/2023]
Abstract
There is currently much interest in developing technology to use microlgae or cyanobacteria for the production of bioenergy and biomaterials. Here, we summarize some remarkable achievements in strains improvement by traditional genetic engineering and discuss common drawbacks for further progress. We present general knowledge on natural microalgal-bacterial mutualistic interactions and discuss the potential of recent developments in genetic engineering of multispecies microbial cell factories. This synthetic biology approach would rely on the assembly of complex metabolic networks from optimized metabolic modules such as photosynthetic or nitrogen-fixing parts.
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Affiliation(s)
- Juan Cesar Federico Ortiz-Marquez
- Instituto de Investigaciones en Biodiversidad y Biotecnología - Consejo Nacional de Investigaciones Científicas y Técnicas. Mar del Plata, Buenos Aires, Argentina
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541
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Fu P. Grand Challenges in Synthetic Biology to be Accomplished. Front Bioeng Biotechnol 2013; 1:2. [PMID: 25024167 PMCID: PMC4090911 DOI: 10.3389/fbioe.2013.00002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2013] [Accepted: 05/30/2013] [Indexed: 11/13/2022] Open
Affiliation(s)
- Pengcheng Fu
- State Key Laboratory of Heavy Oil Processing, Faculty of Chemical Engineering, China University of Petroleum Beijing, China
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542
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Affiliation(s)
- Benjamin M. Woolston
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139; , ,
| | - Steven Edgar
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139; , ,
| | - Gregory Stephanopoulos
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139; , ,
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543
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Teo WS, Hee KS, Chang MW. Bacterial FadR and synthetic promoters function as modular fatty acid sensor- regulators inSaccharomyces cerevisiae. Eng Life Sci 2013. [DOI: 10.1002/elsc.201200113] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Affiliation(s)
- Wei Suong Teo
- Division of Chemical and Biomolecular Engineering; School of Chemical and Biomedical Engineering; Nanyang Technological University; Singapore Singapore
| | - Kai Sheng Hee
- Division of Chemical and Biomolecular Engineering; School of Chemical and Biomedical Engineering; Nanyang Technological University; Singapore Singapore
| | - Matthew Wook Chang
- Division of Chemical and Biomolecular Engineering; School of Chemical and Biomedical Engineering; Nanyang Technological University; Singapore Singapore
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544
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Wen M, Bond-Watts BB, Chang MCY. Production of advanced biofuels in engineered E. coli. Curr Opin Chem Biol 2013; 17:472-9. [PMID: 23659832 DOI: 10.1016/j.cbpa.2013.03.034] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2012] [Revised: 03/01/2013] [Accepted: 03/28/2013] [Indexed: 12/21/2022]
Abstract
Commercial fermentation processes have long taken advantage of the synthetic power of living systems to rapidly and efficiently transform simple carbon sources into complex molecules. In this regard, the ability of yeasts to produce ethanol from glucose at exceptionally high yields has served as a key feature in its use as a fuel, but is also limited by the poor molecular properties of ethanol as a fuel such as high water miscibility and low energy density. Advances in metabolic engineering and synthetic biology allow us to begin constructing new high-flux pathways for production of next generation biofuels that are key to building a sustainable pipeline for liquid transportation fuels.
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Affiliation(s)
- Miao Wen
- Department of Chemistry, University of California, Berkeley, CA 94720-1460, USA
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545
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Lim JH, Seo SW, Kim SY, Jung GY. Refactoring redox cofactor regeneration for high-yield biocatalysis of glucose to butyric acid in Escherichia coli. BIORESOURCE TECHNOLOGY 2013; 135:568-73. [PMID: 23127832 DOI: 10.1016/j.biortech.2012.09.091] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2012] [Revised: 09/23/2012] [Accepted: 09/25/2012] [Indexed: 05/20/2023]
Abstract
In this study, the native redox cofactor regeneration system in Escherichia coli was engineered for the production of butyric acid. The synthetic butyrate pathway, which regenerates NAD(+) from NADH using butyrate as the only final electron acceptor, enabled high-yield production of butyric acid from glucose (83.4% of the molar theoretical yield). The high selectivity for butyrate, with a butyrate/acetate ratio of 41, suggests dramatically improved industrial potential for the production of butyric acid from nonnative hosts compared to the native producers (Clostridium species). Furthermore, this strategy could be broadly utilized for the production of various other useful chemicals in the fields of metabolic engineering and synthetic biology.
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Affiliation(s)
- Jae Hyung Lim
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, San 31, Hyoja-dong, Nam-gu, Pohang, Gyeongbuk 790-784, South Korea
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546
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Next generation biofuel engineering in prokaryotes. Curr Opin Chem Biol 2013; 17:462-71. [PMID: 23623045 DOI: 10.1016/j.cbpa.2013.03.037] [Citation(s) in RCA: 129] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2012] [Revised: 02/23/2013] [Accepted: 03/28/2013] [Indexed: 12/15/2022]
Abstract
Next-generation biofuels must be compatible with current transportation infrastructure and be derived from environmentally sustainable resources that do not compete with food crops. Many bacterial species have unique properties advantageous to the production of such next-generation fuels. However, no single species possesses all characteristics necessary to make high quantities of fuels from plant waste or CO2. Species containing a subset of the desired characteristics are used as starting points for engineering organisms with all desired attributes. Metabolic engineering of model organisms has yielded high titer production of advanced fuels, including alcohols, isoprenoids, and fatty acid derivatives. Technical developments now allow engineering of native fuel producers, as well as lignocellulolytic and autotrophic bacteria, for the production of biofuels. Continued research on multiple fronts is required to engineer organisms for truly sustainable and economical biofuel production.
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547
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Synthesis of customized petroleum-replica fuel molecules by targeted modification of free fatty acid pools in Escherichia coli. Proc Natl Acad Sci U S A 2013; 110:7636-41. [PMID: 23610415 DOI: 10.1073/pnas.1215966110] [Citation(s) in RCA: 147] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Biofuels are the most immediate, practical solution for mitigating dependence on fossil hydrocarbons, but current biofuels (alcohols and biodiesels) require significant downstream processing and are not fully compatible with modern, mass-market internal combustion engines. Rather, the ideal biofuels are structurally and chemically identical to the fossil fuels they seek to replace (i.e., aliphatic n- and iso-alkanes and -alkenes of various chain lengths). Here we report on production of such petroleum-replica hydrocarbons in Escherichia coli. The activity of the fatty acid (FA) reductase complex from Photorhabdus luminescens was coupled with aldehyde decarbonylase from Nostoc punctiforme to use free FAs as substrates for alkane biosynthesis. This combination of genes enabled rational alterations to hydrocarbon chain length (Cn) and the production of branched alkanes through upstream genetic and exogenous manipulations of the FA pool. Genetic components for targeted manipulation of the FA pool included expression of a thioesterase from Cinnamomum camphora (camphor) to alter alkane Cn and expression of the branched-chain α-keto acid dehydrogenase complex and β-keto acyl-acyl carrier protein synthase III from Bacillus subtilis to synthesize branched (iso-) alkanes. Rather than simply reconstituting existing metabolic routes to alkane production found in nature, these results demonstrate the ability to design and implement artificial molecular pathways for the production of renewable, industrially relevant fuel molecules.
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548
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Chen Z, Zeng AP. Protein design in systems metabolic engineering for industrial strain development. Biotechnol J 2013; 8:523-33. [PMID: 23589416 DOI: 10.1002/biot.201200238] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2012] [Revised: 01/24/2013] [Accepted: 02/27/2013] [Indexed: 12/20/2022]
Abstract
Accelerating the process of industrial bacterial host strain development, aimed at increasing productivity, generating new bio-products or utilizing alternative feedstocks, requires the integration of complementary approaches to manipulate cellular metabolism and regulatory networks. Systems metabolic engineering extends the concept of classical metabolic engineering to the systems level by incorporating the techniques used in systems biology and synthetic biology, and offers a framework for the development of the next generation of industrial strains. As one of the most useful tools of systems metabolic engineering, protein design allows us to design and optimize cellular metabolism at a molecular level. Here, we review the current strategies of protein design for engineering cellular synthetic pathways, metabolic control systems and signaling pathways, and highlight the challenges of this subfield within the context of systems metabolic engineering.
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Affiliation(s)
- Zhen Chen
- Institute of Bioprocess and Biosystems Engineering, Hamburg University of Technology, Hamburg, Germany
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549
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Chen S, Harrigan P, Heineike B, Stewart-Ornstein J, El-Samad H. Building robust functionality in synthetic circuits using engineered feedback regulation. Curr Opin Biotechnol 2013; 24:790-6. [PMID: 23566378 DOI: 10.1016/j.copbio.2013.02.025] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2013] [Revised: 02/11/2013] [Accepted: 02/25/2013] [Indexed: 01/02/2023]
Abstract
The ability to engineer novel functionality within cells, to quantitatively control cellular circuits, and to manipulate the behaviors of populations, has many important applications in biotechnology and biomedicine. These applications are only beginning to be explored. In this review, we advocate the use of feedback control as an essential strategy for the engineering of robust homeostatic control of biological circuits and cellular populations. We also describe recent works where feedback control, implemented in silico or with biological components, was successfully employed for this purpose.
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Affiliation(s)
- Susan Chen
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA, USA
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550
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Eriksen DT, Lian J, Zhao H. Protein design for pathway engineering. J Struct Biol 2013; 185:234-42. [PMID: 23558037 DOI: 10.1016/j.jsb.2013.03.011] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2012] [Revised: 02/23/2013] [Accepted: 03/21/2013] [Indexed: 02/02/2023]
Abstract
Design and construction of biochemical pathways has increased the complexity of biosynthetically-produced compounds when compared to single enzyme biocatalysis. However, the coordination of multiple enzymes can introduce a complicated set of obstacles to overcome in order to achieve a high titer and yield of the desired compound. Metabolic engineering has made great strides in developing tools to optimize the flux through a target pathway, but the inherent characteristics of a particular enzyme within the pathway can still limit the productivity. Thus, judicious protein design is critical for metabolic and pathway engineering. This review will describe various strategies and examples of applying protein design to pathway engineering to optimize the flux through the pathway. The proteins can be engineered for altered substrate specificity/selectivity, increased catalytic activity, reduced mass transfer limitations through specific protein localization, and reduced substrate/product inhibition. Protein engineering can also be expanded to design biosensors to enable high through-put screening and to customize cell signaling networks. These strategies have successfully engineered pathways for significantly increased productivity of the desired product or in the production of novel compounds.
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Affiliation(s)
- Dawn T Eriksen
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States
| | - Jiazhang Lian
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States
| | - Huimin Zhao
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States; Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States; Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States; Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States.
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