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Roehner N, Roberts J, Lapets A, Gould D, Akavoor V, Qin L, Gordon DB, Voigt C, Densmore D. GOLDBAR: A Framework for Combinatorial Biological Design. ACS Synth Biol 2024. [PMID: 39162314 DOI: 10.1021/acssynbio.4c00296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/21/2024]
Abstract
With the rise of new DNA part libraries and technologies for assembling DNA, synthetic biologists are increasingly constructing and screening combinatorial libraries to optimize their biological designs. As combinatorial libraries are used to generate data on design performance, new rules for composing biological designs will emerge. Most formal frameworks for combinatorial design, however, do not yet support formal comparison of design composition, which is needed to facilitate automated analysis and machine learning in massive biological design spaces. To address this need, we introduce a combinatorial design framework called GOLDBAR. Compared with existing frameworks, GOLDBAR enables synthetic biologists to intersect and merge the rules for entire classes of biological designs to extract common design motifs and infer new ones. Here, we demonstrate the application of GOLDBAR to refine/validate design spaces for TetR-homologue transcriptional logic circuits, verify the assembly of a partial nif gene cluster, and infer novel gene clusters for the biosynthesis of rebeccamycin. We also discuss how GOLDBAR could be used to facilitate grammar-based machine learning in synthetic biology.
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Affiliation(s)
- Nicholas Roehner
- RTX BBN Technologies, Cambridge, Massachusetts 02138, United States
| | - James Roberts
- Biological Design Center, Boston University, Boston, Massachusetts 02215, United States
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts 02215, United States
| | | | - Dany Gould
- Hariri Institute for Computing, Boston University, Boston, Massachusetts 02215, United States
| | - Vidya Akavoor
- Hariri Institute for Computing, Boston University, Boston, Massachusetts 02215, United States
| | - Lucy Qin
- Hariri Institute for Computing, Boston University, Boston, Massachusetts 02215, United States
| | - D Benjamin Gordon
- The Foundry, 75 Ames Street, Cambridge, Massachusetts 02142, United States
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Christopher Voigt
- The Foundry, 75 Ames Street, Cambridge, Massachusetts 02142, United States
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Douglas Densmore
- Biological Design Center, Boston University, Boston, Massachusetts 02215, United States
- Department of Electrical and Computer Engineering, Boston University, Boston, Massachusetts 02215, United States
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2
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Ji CH, Je HW, Kim H, Kang HS. Promoter engineering of natural product biosynthetic gene clusters in actinomycetes: concepts and applications. Nat Prod Rep 2024; 41:672-699. [PMID: 38259139 DOI: 10.1039/d3np00049d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Covering 2011 to 2022Low titers of natural products in laboratory culture or fermentation conditions have been one of the challenging issues in natural products research. Many natural product biosynthetic gene clusters (BGCs) are also transcriptionally silent in laboratory culture conditions, making it challenging to characterize the structures and activities of their metabolites. Promoter engineering offers a potential solution to this problem by providing tools for transcriptional activation or optimization of biosynthetic genes. In this review, we summarize the 10 years of progress in promoter engineering approaches in natural products research focusing on the most metabolically talented group of bacteria actinomycetes.
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Affiliation(s)
- Chang-Hun Ji
- Department of Biomedical Science and Engineering, Konkuk University, Seoul 05029, Korea.
| | - Hyun-Woo Je
- Department of Biomedical Science and Engineering, Konkuk University, Seoul 05029, Korea.
| | - Hiyoung Kim
- Department of Biomedical Science and Engineering, Konkuk University, Seoul 05029, Korea.
| | - Hahk-Soo Kang
- Department of Biomedical Science and Engineering, Konkuk University, Seoul 05029, Korea.
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3
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Rizzo P, Chavez BG, Leite Dias S, D'Auria JC. Plant synthetic biology: from inspiration to augmentation. Curr Opin Biotechnol 2023; 79:102857. [PMID: 36502769 DOI: 10.1016/j.copbio.2022.102857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 11/17/2022] [Indexed: 12/13/2022]
Abstract
Although it is still in its infancy, synthetic biology has the capacity to face scientific and societal problems related to modern agriculture. Innovations in cloning toolkits and genetic parts allow increased precision over gene expression in planta. We review the vast spectrum of available technologies providing a practical list of toolkits that take advantage of combinatorial power to introduce/alter metabolic pathways. We highlight that rational design is inspired by deep knowledge of natural and biochemical mechanisms. Finally, we provide several examples in which modern technologies have been applied to address these critical topics. Future applications in plants include not only pathway modifications but also prospects of augmenting plant anatomical features and developmental processes.
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Affiliation(s)
- Paride Rizzo
- Metabolite Diversity Group, Department of Molecular Genetics, Leibniz Institute for Plant Genetics and Crop Plant Research (IPK) OT Gatersleben, Correnstr. 3, D-06466 Seeland, Germany
| | - Benjamin G Chavez
- Metabolite Diversity Group, Department of Molecular Genetics, Leibniz Institute for Plant Genetics and Crop Plant Research (IPK) OT Gatersleben, Correnstr. 3, D-06466 Seeland, Germany
| | - Sara Leite Dias
- Metabolite Diversity Group, Department of Molecular Genetics, Leibniz Institute for Plant Genetics and Crop Plant Research (IPK) OT Gatersleben, Correnstr. 3, D-06466 Seeland, Germany
| | - John C D'Auria
- Metabolite Diversity Group, Department of Molecular Genetics, Leibniz Institute for Plant Genetics and Crop Plant Research (IPK) OT Gatersleben, Correnstr. 3, D-06466 Seeland, Germany.
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4
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Guidi C, De Wannemaeker L, De Baets J, Demeester W, Maertens J, De Paepe B, De Mey M. Dynamic feedback regulation for efficient membrane protein production using a small RNA-based genetic circuit in Escherichia coli. Microb Cell Fact 2022; 21:260. [PMID: 36522655 PMCID: PMC9753035 DOI: 10.1186/s12934-022-01983-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Accepted: 12/05/2022] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Membrane proteins (MPs) are an important class of molecules with a wide array of cellular functions and are part of many metabolic pathways. Despite their great potential-as therapeutic drug targets or in microbial cell factory optimization-many challenges remain for efficient and functional expression in a host such as Escherichia coli. RESULTS A dynamically regulated small RNA-based circuit was developed to counter membrane stress caused by overexpression of different MPs. The best performing small RNAs were able to enhance the maximum specific growth rate with 123%. On culture level, the total MP production was increased two-to three-fold compared to a system without dynamic control. This strategy not only improved cell growth and production of the studied MPs, it also suggested the potential use for countering metabolic burden in general. CONCLUSIONS A dynamically regulated feedback circuit was developed that can sense metabolic stress caused by, in casu, the overexpression of an MP and responds to it by balancing the metabolic state of the cell and more specifically by downregulating the expression of the MP of interest. This negative feedback mechanism was established by implementing and optimizing simple-to-use genetic control elements based on post-transcriptional regulation: small non-coding RNAs. In addition to membrane-related stress when the MP accumulated in the cytoplasm as aggregates, the sRNA-based feedback control system was still effective for improving cell growth but resulted in a decreased total protein production. This result suggests promiscuity of the MP sensor for more than solely membrane stress.
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Affiliation(s)
- Chiara Guidi
- Centre for Synthetic Biology, Ghent University, 9000, Ghent, Belgium
| | | | - Jasmine De Baets
- Centre for Synthetic Biology, Ghent University, 9000, Ghent, Belgium
| | - Wouter Demeester
- Centre for Synthetic Biology, Ghent University, 9000, Ghent, Belgium
| | - Jo Maertens
- Centre for Synthetic Biology, Ghent University, 9000, Ghent, Belgium
| | - Brecht De Paepe
- Centre for Synthetic Biology, Ghent University, 9000, Ghent, Belgium
| | - Marjan De Mey
- Centre for Synthetic Biology, Ghent University, 9000, Ghent, Belgium.
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5
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Grewal J, Woła̧cewicz M, Pyter W, Joshi N, Drewniak L, Pranaw K. Colorful Treasure From Agro-Industrial Wastes: A Sustainable Chassis for Microbial Pigment Production. Front Microbiol 2022; 13:832918. [PMID: 35173704 PMCID: PMC8841802 DOI: 10.3389/fmicb.2022.832918] [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] [Received: 12/10/2021] [Accepted: 01/10/2022] [Indexed: 12/16/2022] Open
Abstract
Colors with their attractive appeal have been an integral part of human lives and the easy cascade of chemical catalysis enables fast, bulk production of these synthetic colorants with low costs. However, the resulting hazardous impacts on the environment and human health has stimulated an interest in natural pigments as a safe and ecologically clean alternative. Amidst sources of natural producers, the microbes with their diversity, ease of all-season production and peculiar bioactivities are attractive entities for industrial production of these marketable natural colorants. Further, in line with circular bioeconomy and environmentally clean technologies, the use of agro-industrial wastes as feedstocks for carrying out the microbial transformations paves way for sustainable and cost-effective production of these valuable secondary metabolites with simultaneous waste management. The present review aims to comprehensively cover the current green workflow of microbial colorant production by encompassing the potency of waste feedstocks and fermentation technologies. The commercially important pigments viz. astaxanthin, prodigiosin, canthaxanthin, lycopene, and β-carotene produced by native and engineered bacterial, fungal, or yeast strains have been elaborately discussed with their versatile applications in food, pharmaceuticals, textiles, cosmetics, etc. The limitations and their economic viability to meet the future market demands have been envisaged. The most recent advances in various molecular approaches to develop engineered microbiological systems for enhanced pigment production have been included to provide new perspectives to this burgeoning field of research.
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Affiliation(s)
| | | | | | | | | | - Kumar Pranaw
- Department of Environmental Microbiology and Biotechnology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
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6
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Evolution-aided engineering of plant specialized metabolism. ABIOTECH 2021; 2:240-263. [PMID: 36303885 PMCID: PMC9590541 DOI: 10.1007/s42994-021-00052-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 06/04/2021] [Indexed: 02/07/2023]
Abstract
The evolution of new traits in living organisms occurs via the processes of mutation, recombination, genetic drift, and selection. These processes that have resulted in the immense biological diversity on our planet are also being employed in metabolic engineering to optimize enzymes and pathways, create new-to-nature reactions, and synthesize complex natural products in heterologous systems. In this review, we discuss two evolution-aided strategies for metabolic engineering-directed evolution, which improves upon existing genetic templates using the evolutionary process, and combinatorial pathway reconstruction, which brings together genes evolved in different organisms into a single heterologous host. We discuss the general principles of these strategies, describe the technologies involved and the molecular traits they influence, provide examples of their use, and discuss the roadblocks that need to be addressed for their wider adoption. A better understanding of these strategies can provide an impetus to research on gene function discovery and biochemical evolution, which is foundational for improved metabolic engineering. These evolution-aided approaches thus have a substantial potential for improving our understanding of plant metabolism in general, for enhancing the production of plant metabolites, and in sustainable agriculture.
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7
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Otero-Muras I, Carbonell P. Automated engineering of synthetic metabolic pathways for efficient biomanufacturing. Metab Eng 2020; 63:61-80. [PMID: 33316374 DOI: 10.1016/j.ymben.2020.11.012] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2020] [Revised: 11/15/2020] [Accepted: 11/20/2020] [Indexed: 12/19/2022]
Abstract
Metabolic engineering involves the engineering and optimization of processes from single-cell to fermentation in order to increase production of valuable chemicals for health, food, energy, materials and others. A systems approach to metabolic engineering has gained traction in recent years thanks to advances in strain engineering, leading to an accelerated scaling from rapid prototyping to industrial production. Metabolic engineering is nowadays on track towards a truly manufacturing technology, with reduced times from conception to production enabled by automated protocols for DNA assembly of metabolic pathways in engineered producer strains. In this review, we discuss how the success of the metabolic engineering pipeline often relies on retrobiosynthetic protocols able to identify promising production routes and dynamic regulation strategies through automated biodesign algorithms, which are subsequently assembled as embedded integrated genetic circuits in the host strain. Those approaches are orchestrated by an experimental design strategy that provides optimal scheduling planning of the DNA assembly, rapid prototyping and, ultimately, brings forward an accelerated Design-Build-Test-Learn cycle and the overall optimization of the biomanufacturing process. Achieving such a vision will address the increasingly compelling demand in our society for delivering valuable biomolecules in an affordable, inclusive and sustainable bioeconomy.
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Affiliation(s)
- Irene Otero-Muras
- BioProcess Engineering Group, IIM-CSIC, Spanish National Research Council, Vigo, 36208, Spain.
| | - Pablo Carbonell
- Institute of Industrial Control Systems and Computing (ai2), Universitat Politècnica de València, 46022, Spain.
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8
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Naseri G, Koffas MAG. Application of combinatorial optimization strategies in synthetic biology. Nat Commun 2020; 11:2446. [PMID: 32415065 PMCID: PMC7229011 DOI: 10.1038/s41467-020-16175-y] [Citation(s) in RCA: 71] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2019] [Accepted: 04/15/2020] [Indexed: 12/26/2022] Open
Abstract
In the first wave of synthetic biology, genetic elements, combined into simple circuits, are used to control individual cellular functions. In the second wave of synthetic biology, the simple circuits, combined into complex circuits, form systems-level functions. However, efforts to construct complex circuits are often impeded by our limited knowledge of the optimal combination of individual circuits. For example, a fundamental question in most metabolic engineering projects is the optimal level of enzymes for maximizing the output. To address this point, combinatorial optimization approaches have been established, allowing automatic optimization without prior knowledge of the best combination of expression levels of individual genes. This review focuses on current combinatorial optimization methods and emerging technologies facilitating their applications.
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Affiliation(s)
- Gita Naseri
- Institut für Chemie, Humboldt Universität zu Berlin, 12489, Berlin, Germany.
| | - Mattheos A G Koffas
- Center for Biotechnology, Rensselaer Polytechnic Institute, Troy, NY, USA.
- Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, NY, USA.
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, NY, USA.
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9
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Coussement P, Bauwens D, Peters G, Maertens J, De Mey M. Mapping and refactoring pathway control through metabolic and protein engineering: The hexosamine biosynthesis pathway. Biotechnol Adv 2020; 40:107512. [DOI: 10.1016/j.biotechadv.2020.107512] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Revised: 08/07/2019] [Accepted: 09/30/2019] [Indexed: 01/14/2023]
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10
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Wiltschi B, Cernava T, Dennig A, Galindo Casas M, Geier M, Gruber S, Haberbauer M, Heidinger P, Herrero Acero E, Kratzer R, Luley-Goedl C, Müller CA, Pitzer J, Ribitsch D, Sauer M, Schmölzer K, Schnitzhofer W, Sensen CW, Soh J, Steiner K, Winkler CK, Winkler M, Wriessnegger T. Enzymes revolutionize the bioproduction of value-added compounds: From enzyme discovery to special applications. Biotechnol Adv 2020; 40:107520. [DOI: 10.1016/j.biotechadv.2020.107520] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Revised: 10/18/2019] [Accepted: 01/13/2020] [Indexed: 12/11/2022]
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11
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Genome engineering of E. coli for improved styrene production. Metab Eng 2020; 57:74-84. [DOI: 10.1016/j.ymben.2019.09.007] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Revised: 08/18/2019] [Accepted: 09/12/2019] [Indexed: 01/01/2023]
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12
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Eichmann J, Oberpaul M, Weidner T, Gerlach D, Czermak P. Selection of High Producers From Combinatorial Libraries for the Production of Recombinant Proteins in Escherichia coli and Vibrio natriegens. Front Bioeng Biotechnol 2019; 7:254. [PMID: 31637238 PMCID: PMC6788121 DOI: 10.3389/fbioe.2019.00254] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Accepted: 09/20/2019] [Indexed: 11/13/2022] Open
Abstract
The optimization of recombinant protein production in bacteria is an important stage of process development, especially for difficult-to-express proteins that are particularly sensitive or recalcitrant. The optimal expression level must be neither too low, which would limit yields, nor too high, which would promote the formation of insoluble inclusion bodies. Expression can be optimized by testing different combinations of elements such as ribosome binding sites and N-terminal affinity tags, but the rate of protein synthesis is strongly dependent on mRNA secondary structures so the combined effects of these elements must be taken into account. This substantially increases the complexity of high-throughput expression screening. To address this limitation, we generated libraries of constructs systematically combining different ribosome binding sites, N-terminal affinity tags, and periplasmic translocation sequences representing two secretion pathways. Each construct also contained a green fluorescent protein (GFP) tag to allow the identification of high producers and a thrombin cleavage site enabling the removal of fusion tags. To achieve proof of principle, we generated libraries of 200 different combinations of elements for the expression of an antimicrobial peptide (AMPs), an antifungal peptide, and the enzyme urate oxidase (uricase) in Escherichia coli and Vibrio natriegens. High producers for all three difficult-to-express products were enriched by fluorescence-activated cell sorting. Our results indicated that the E. coli ssYahJ secretion signal is recognized in V. natriegens and efficiently mediates translocation to the periplasm. Our combinatorial library approach therefore allows the cross-species direct selection of high-producer clones for difficult-to-express proteins by systematically evaluating the combined impact of multiple construct elements.
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Affiliation(s)
- Joel Eichmann
- Institute of Bioprocess Engineering and Pharmaceutical Technology, University of Applied Sciences Mittelhessen, Giessen, Germany.,Faculty of Biology and Chemistry, Justus-Liebig University of Giessen, Giessen, Germany
| | - Markus Oberpaul
- Branch for Bioresources, Fraunhofer Institute for Molecular Biology and Applied Ecology, Giessen, Germany
| | - Tobias Weidner
- Institute of Bioprocess Engineering and Pharmaceutical Technology, University of Applied Sciences Mittelhessen, Giessen, Germany
| | - Doreen Gerlach
- Branch for Bioresources, Fraunhofer Institute for Molecular Biology and Applied Ecology, Giessen, Germany
| | - Peter Czermak
- Institute of Bioprocess Engineering and Pharmaceutical Technology, University of Applied Sciences Mittelhessen, Giessen, Germany.,Faculty of Biology and Chemistry, Justus-Liebig University of Giessen, Giessen, Germany.,Branch for Bioresources, Fraunhofer Institute for Molecular Biology and Applied Ecology, Giessen, Germany
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13
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Taylor GM, Mordaka PM, Heap JT. Start-Stop Assembly: a functionally scarless DNA assembly system optimized for metabolic engineering. Nucleic Acids Res 2019; 47:e17. [PMID: 30462270 PMCID: PMC6379671 DOI: 10.1093/nar/gky1182] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Revised: 11/02/2018] [Accepted: 11/07/2018] [Indexed: 12/20/2022] Open
Abstract
DNA assembly allows individual DNA constructs or libraries to be assembled quickly and reliably. Most methods are either: (i) Modular, easily scalable and suitable for combinatorial assembly, but leave undesirable 'scar' sequences; or (ii) bespoke (non-modular), scarless but less suitable for construction of combinatorial libraries. Both have limitations for metabolic engineering. To overcome this trade-off we devised Start-Stop Assembly, a multi-part, modular DNA assembly method which is both functionally scarless and suitable for combinatorial assembly. Crucially, 3 bp overhangs corresponding to start and stop codons are used to assemble coding sequences into expression units, avoiding scars at sensitive coding sequence boundaries. Building on this concept, a complete DNA assembly framework was designed and implemented, allowing assembly of up to 15 genes from up to 60 parts (or mixtures); monocistronic, operon-based or hybrid configurations; and a new streamlined assembly hierarchy minimizing the number of vectors. Only one destination vector is required per organism, reflecting our optimization of the system for metabolic engineering in diverse organisms. Metabolic engineering using Start-Stop Assembly was demonstrated by combinatorial assembly of carotenoid pathways in Escherichia coli resulting in a wide range of carotenoid production and colony size phenotypes indicating the intended exploration of design space.
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Affiliation(s)
- George M Taylor
- Imperial College Centre for Synthetic Biology, Department of Life Sciences, Imperial College London, London SW7 2AZ, UK
| | - Paweł M Mordaka
- Imperial College Centre for Synthetic Biology, Department of Life Sciences, Imperial College London, London SW7 2AZ, UK
| | - John T Heap
- Imperial College Centre for Synthetic Biology, Department of Life Sciences, Imperial College London, London SW7 2AZ, UK
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14
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Systems Metabolic Engineering Strategies: Integrating Systems and Synthetic Biology with Metabolic Engineering. Trends Biotechnol 2019; 37:817-837. [DOI: 10.1016/j.tibtech.2019.01.003] [Citation(s) in RCA: 226] [Impact Index Per Article: 45.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Revised: 01/07/2019] [Accepted: 01/10/2019] [Indexed: 12/12/2022]
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15
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Ma X, Liang H, Cui X, Liu Y, Lu H, Ning W, Poon NY, Ho B, Zhou K. A standard for near-scarless plasmid construction using reusable DNA parts. Nat Commun 2019; 10:3294. [PMID: 31337759 PMCID: PMC6650416 DOI: 10.1038/s41467-019-11263-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Accepted: 07/04/2019] [Indexed: 12/25/2022] Open
Abstract
Here we report GT (Guanin/Thymine) standard (GTS) for plasmid construction under which DNA sequences are defined as two types of standard, reusable parts (fragment and barcode). We develop a technology that can efficiently add any two barcodes to two ends of any fragment without leaving scars in most cases. We can assemble up to seven such barcoded fragments into one plasmid by using one of the existing DNA assembly methods, including CLIVA, Gibson assembly, In-fusion cloning, and restriction enzyme-based methods. Plasmids constructed under GTS can be easily edited, and/or be further assembled into more complex plasmids by using standard DNA oligonucleotides (oligos). Based on 436 plasmids we constructed under GTS, the averaged accuracy of the workflow was 85.9%. GTS can also construct a library of plasmids from a set of fragments and barcodes combinatorically, which has been demonstrated to be useful for optimizing metabolic pathways. Construction of plasmids from multiple fragments often uses customised parts and leaves scars where fragments are joined. Here the authors develop a method for barcoding fragments and constructing plasmids in a scarless manner from a collection of standard parts.
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Affiliation(s)
- Xiaoqiang Ma
- Department of Chemical and Biomolecular Engineering, National University of Singapore, Singapore, 119077, Singapore.,Disruptive & Sustainable Technologies for Agricultural Precision, Singapore-MIT Alliance for Research and Technology, Singapore, 138602, Singapore
| | - Hong Liang
- Department of Chemical and Biomolecular Engineering, National University of Singapore, Singapore, 119077, Singapore.,Disruptive & Sustainable Technologies for Agricultural Precision, Singapore-MIT Alliance for Research and Technology, Singapore, 138602, Singapore
| | - Xiaoyi Cui
- Department of Chemical and Biomolecular Engineering, National University of Singapore, Singapore, 119077, Singapore.,Disruptive & Sustainable Technologies for Agricultural Precision, Singapore-MIT Alliance for Research and Technology, Singapore, 138602, Singapore
| | - Yurou Liu
- Department of Chemical and Biomolecular Engineering, National University of Singapore, Singapore, 119077, Singapore.,Disruptive & Sustainable Technologies for Agricultural Precision, Singapore-MIT Alliance for Research and Technology, Singapore, 138602, Singapore
| | - Hongyuan Lu
- Department of Chemical and Biomolecular Engineering, National University of Singapore, Singapore, 119077, Singapore
| | - Wenbo Ning
- Department of Chemical and Biomolecular Engineering, National University of Singapore, Singapore, 119077, Singapore
| | - Nga Yu Poon
- Disruptive & Sustainable Technologies for Agricultural Precision, Singapore-MIT Alliance for Research and Technology, Singapore, 138602, Singapore
| | - Benjamin Ho
- Department of Chemical and Biomolecular Engineering, National University of Singapore, Singapore, 119077, Singapore
| | - Kang Zhou
- Department of Chemical and Biomolecular Engineering, National University of Singapore, Singapore, 119077, Singapore. .,Disruptive & Sustainable Technologies for Agricultural Precision, Singapore-MIT Alliance for Research and Technology, Singapore, 138602, Singapore.
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16
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Bervoets I, Van Brempt M, Van Nerom K, Van Hove B, Maertens J, De Mey M, Charlier D. A sigma factor toolbox for orthogonal gene expression in Escherichia coli. Nucleic Acids Res 2019; 46:2133-2144. [PMID: 29361130 PMCID: PMC5829568 DOI: 10.1093/nar/gky010] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Accepted: 01/08/2018] [Indexed: 11/18/2022] Open
Abstract
Synthetic genetic sensors and circuits enable programmable control over timing and conditions of gene expression and, as a result, are increasingly incorporated into the control of complex and multi-gene pathways. Size and complexity of genetic circuits are growing, but stay limited by a shortage of regulatory parts that can be used without interference. Therefore, orthogonal expression and regulation systems are needed to minimize undesired crosstalk and allow for dynamic control of separate modules. This work presents a set of orthogonal expression systems for use in Escherichia coli based on heterologous sigma factors from Bacillus subtilis that recognize specific promoter sequences. Up to four of the analyzed sigma factors can be combined to function orthogonally between each other and toward the host. Additionally, the toolbox is expanded by creating promoter libraries for three sigma factors without loss of their orthogonal nature. As this set covers a wide range of transcription initiation frequencies, it enables tuning of multiple outputs of the circuit in response to different sensory signals in an orthogonal manner. This sigma factor toolbox constitutes an interesting expansion of the synthetic biology toolbox and may contribute to the assembly of more complex synthetic genetic systems in the future.
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Affiliation(s)
- Indra Bervoets
- Research Group of Microbiology, Department of Bioengineering Sciences, Vrije Universiteit Brussel (VUB), Pleinlaan 2, 1050 Brussels, Belgium
| | - Maarten Van Brempt
- Centre for Synthetic Biology (CSB), Department of Biotechnology, Ghent University, 9000 Ghent, Belgium
| | - Katleen Van Nerom
- Research Group of Microbiology, Department of Bioengineering Sciences, Vrije Universiteit Brussel (VUB), Pleinlaan 2, 1050 Brussels, Belgium
| | - Bob Van Hove
- Centre for Synthetic Biology (CSB), Department of Biotechnology, Ghent University, 9000 Ghent, Belgium
| | - Jo Maertens
- Centre for Synthetic Biology (CSB), Department of Biotechnology, Ghent University, 9000 Ghent, Belgium
| | - Marjan De Mey
- Centre for Synthetic Biology (CSB), Department of Biotechnology, Ghent University, 9000 Ghent, Belgium
| | - Daniel Charlier
- Research Group of Microbiology, Department of Bioengineering Sciences, Vrije Universiteit Brussel (VUB), Pleinlaan 2, 1050 Brussels, Belgium
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17
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Combinatorial Assembly of Multigene Pathways by Combining Single-Strand Assembly with Golden Gate Assembly. Methods Mol Biol 2019; 1927:111-123. [PMID: 30788788 DOI: 10.1007/978-1-4939-9142-6_8] [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: 12/12/2022]
Abstract
Biotechnological production routes for fine and bulk chemicals are progressively explored and developed. Yet this development is hampered by the many constraints determining the metabolic sweet spot, such as optimal expression levels, metabolic stress, feedback regulation, etc.In this regard, we introduce a novel, highly reliable, and rapid single-strand assembly (SSA) methods for combinatorial pathway engineering. In this contribution, SSA is elucidated which enables one to modulate the expression via promoter and/or RBS randomization. Moreover, a new combinatorial multigene pathway assembly scheme based on single-strand assembly (SSA) methods and Golden Gate Assembly is introduced, exploiting the strengths of both assembly techniques.
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18
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Garcia-Ruiz E, HamediRad M, Zhao H. Pathway Design, Engineering, and Optimization. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2018; 162:77-116. [PMID: 27629378 DOI: 10.1007/10_2016_12] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Abstract
The microbial metabolic versatility found in nature has inspired scientists to create microorganisms capable of producing value-added compounds. Many endeavors have been made to transfer and/or combine pathways, existing or even engineered enzymes with new function to tractable microorganisms to generate new metabolic routes for drug, biofuel, and specialty chemical production. However, the success of these pathways can be impeded by different complications from an inherent failure of the pathway to cell perturbations. Pursuing ways to overcome these shortcomings, a wide variety of strategies have been developed. This chapter will review the computational algorithms and experimental tools used to design efficient metabolic routes, and construct and optimize biochemical pathways to produce chemicals of high interest.
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Affiliation(s)
- Eva Garcia-Ruiz
- Department of Chemical and Biomolecular Engineering, Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Mohammad HamediRad
- Department of Chemical and Biomolecular Engineering, Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Huimin Zhao
- Department of Chemical and Biomolecular Engineering, Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
- Departments of Chemistry, Biochemistry, and Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
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19
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Eriksen DT, Chao R, Zhao H. Applying Advanced DNA Assembly Methods to Generate Pathway Libraries. Synth Biol (Oxf) 2018. [DOI: 10.1002/9783527688104.ch16] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Affiliation(s)
- Dawn T. Eriksen
- University of Illinois at Urbana-Champaign; Department of Chemical and Biomolecular Engineering; 600 South Mathews Avenue, Urbana IL 61801 USA
| | - Ran Chao
- University of Illinois at Urbana-Champaign; Department of Chemical and Biomolecular Engineering; 600 South Mathews Avenue, Urbana IL 61801 USA
| | - Huimin Zhao
- University of Illinois at Urbana-Champaign; Department of Chemical and Biomolecular Engineering; 600 South Mathews Avenue, Urbana IL 61801 USA
- University of Illinois at Urbana-Champaign; Departments of Chemistry, Biochemistry, and Bioengineering, 600 South Mathews Avenue; Urbana IL 61801 USA
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20
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Kang Z, Ding W, Jin P, Du G, Chen J. Combinatorial Evolution of DNA with RECODE. Methods Mol Biol 2018; 1772:205-212. [PMID: 29754230 DOI: 10.1007/978-1-4939-7795-6_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
In past decades, DNA engineering protocols have led to the rapid development of synthetic biology. To engineer the natural proteins, many directed evolution methods based on molecular biology have been presented for generating genetic diversity or obtaining specific properties. Here, we provide a simple (PCR operation), efficient (larger amount of products), and powerful (multiple point mutations, deletions, insertions, and combinatorial multipoint mutagenesis) RECODE method, which is capable of reediting the target DNA flexibly to restructure regulatory regions and remodel enzymes by using the combined function of the thermostable DNA polymerase and DNA ligase in one pot. RECODE is expected to be an applicable choice to create diverse mutant libraries for rapid evolution and optimization of enzymes and synthetic pathways.
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Affiliation(s)
- Zhen Kang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China.
- Synergetic Innovation Center of Food Safety and Nutrition, Jiangnan University, Wuxi, Jiangsu, China.
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China.
| | - Wenwen Ding
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Peng Jin
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Guocheng Du
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
- Synergetic Innovation Center of Food Safety and Nutrition, Jiangnan University, Wuxi, Jiangsu, China
| | - Jian Chen
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
- Synergetic Innovation Center of Food Safety and Nutrition, Jiangnan University, Wuxi, Jiangsu, China
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21
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Jin E, Wong L, Jiao Y, Engel J, Holdridge B, Xu P. Rapid evolution of regulatory element libraries for tunable transcriptional and translational control of gene expression. Synth Syst Biotechnol 2017; 2:295-301. [PMID: 29552654 PMCID: PMC5851936 DOI: 10.1016/j.synbio.2017.10.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2017] [Revised: 10/12/2017] [Accepted: 10/12/2017] [Indexed: 12/16/2022] Open
Abstract
Engineering cell factories for producing biofuels and pharmaceuticals has spurred great interests to develop rapid and efficient synthetic biology tools customized for modular pathway engineering. Along the way, combinatorial gene expression control through modification of regulatory element offered tremendous opportunity for fine-tuning gene expression and generating digital-like genetic circuits. In this report, we present an efficient evolutionary approach to build a range of regulatory control elements. The reported method allows for rapid construction of promoter, 5'UTR, terminator and trans-activating RNA libraries. Synthetic overlapping oligos with high portion of degenerate nucleotides flanking the regulatory element could be efficiently assembled to a vector expressing fluorescence reporter. This approach combines high mutation rate of the synthetic DNA with the high assembly efficiency of Gibson Mix. Our constructed library demonstrates broad range of transcriptional or translational gene expression dynamics. Specifically, both the promoter library and 5'UTR library exhibits gene expression dynamics spanning across three order of magnitude. The terminator library and trans-activating RNA library displays relatively narrowed gene expression pattern. The reported study provides a versatile toolbox for rapidly constructing a large family of prokaryotic regulatory elements. These libraries also facilitate the implementation of combinatorial pathway engineering principles and the engineering of more efficient microbial cell factory for various biomanufacturing applications.
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Affiliation(s)
- Erqing Jin
- Department of Chemical, Biochemical and Environmental Engineering, University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, MD 21250, United States.,Department of Food Science and Engineering, Jinan University, 601 West Huangpu Road, Guangzhou 510632, China
| | - Lynn Wong
- Department of Chemical, Biochemical and Environmental Engineering, University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, MD 21250, United States
| | - Yun Jiao
- Department of Chemical, Biochemical and Environmental Engineering, University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, MD 21250, United States
| | - Jake Engel
- Department of Chemical, Biochemical and Environmental Engineering, University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, MD 21250, United States
| | - Benjamin Holdridge
- Department of Chemical, Biochemical and Environmental Engineering, University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, MD 21250, United States
| | - Peng Xu
- Department of Chemical, Biochemical and Environmental Engineering, University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, MD 21250, United States
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22
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Ghodasara A, Voigt CA. Balancing gene expression without library construction via a reusable sRNA pool. Nucleic Acids Res 2017; 45:8116-8127. [PMID: 28609783 PMCID: PMC5737548 DOI: 10.1093/nar/gkx530] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Accepted: 06/07/2017] [Indexed: 01/06/2023] Open
Abstract
Balancing protein expression is critical when optimizing genetic systems. Typically, this requires library construction to vary the genetic parts controlling each gene, which can be expensive and time-consuming. Here, we develop sRNAs corresponding to 15nt ‘target’ sequences that can be inserted upstream of a gene. The targeted gene can be repressed from 1.6- to 87-fold by controlling sRNA expression using promoters of different strength. A pool is built where six sRNAs are placed under the control of 16 promoters that span a ∼103-fold range of strengths, yielding ∼107 combinations. This pool can simultaneously optimize up to six genes in a system. This requires building only a single system-specific construct by placing a target sequence upstream of each gene and transforming it with the pre-built sRNA pool. The resulting library is screened and the top clone is sequenced to determine the promoter controlling each sRNA, from which the fold-repression of the genes can be inferred. The system is then rebuilt by rationally selecting parts that implement the optimal expression of each gene. We demonstrate the versatility of this approach by using the same pool to optimize a metabolic pathway (β-carotene) and genetic circuit (XNOR logic gate).
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Affiliation(s)
- Amar Ghodasara
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Christopher A Voigt
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
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23
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Combinatorial pathway optimization for streamlined metabolic engineering. Curr Opin Biotechnol 2017; 47:142-151. [DOI: 10.1016/j.copbio.2017.06.014] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Accepted: 06/19/2017] [Indexed: 11/20/2022]
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24
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Espah Borujeni A, Cetnar D, Farasat I, Smith A, Lundgren N, Salis HM. Precise quantification of translation inhibition by mRNA structures that overlap with the ribosomal footprint in N-terminal coding sequences. Nucleic Acids Res 2017; 45:5437-5448. [PMID: 28158713 PMCID: PMC5435973 DOI: 10.1093/nar/gkx061] [Citation(s) in RCA: 90] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Accepted: 01/24/2017] [Indexed: 02/06/2023] Open
Abstract
A mRNA's translation rate is controlled by several sequence determinants, including the presence of RNA structures within the N-terminal regions of its coding sequences. However, the physical rules that govern when such mRNA structures will inhibit translation remain unclear. Here, we introduced systematically designed RNA hairpins into the N-terminal coding region of a reporter protein with steadily increasing distances from the start codon, followed by characterization of their mRNA and expression levels in Escherichia coli. We found that the mRNAs' translation rates were repressed, by up to 530-fold, when mRNA structures overlapped with the ribosome's footprint. In contrast, when the mRNA structure was located outside the ribosome's footprint, translation was repressed by <2-fold. By combining our measurements with biophysical modeling, we determined that the ribosomal footprint extends 13 nucleotides into the N-terminal coding region and, when a mRNA structure overlaps or partially overlaps with the ribosomal footprint, the free energy to unfold only the overlapping structure controlled the extent of translation repression. Overall, our results provide precise quantification of the rules governing translation initiation at N-terminal coding regions, improving the predictive design of post-transcriptional regulatory elements that regulate translation rate.
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Affiliation(s)
- Amin Espah Borujeni
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA 16802, USA
| | - Daniel Cetnar
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA 16802, USA
| | - Iman Farasat
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA 16802, USA
| | - Ashlee Smith
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA 16802, USA
| | - Natasha Lundgren
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA 16802, USA
| | - Howard M Salis
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA 16802, USA.,Department of Biological Engineering, The Pennsylvania State University, University Park, PA 16802, USA
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25
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Yang P, Wang J, Pang Q, Zhang F, Wang J, Wang Q, Qi Q. Pathway optimization and key enzyme evolution of N-acetylneuraminate biosynthesis using an in vivo aptazyme-based biosensor. Metab Eng 2017; 43:21-28. [PMID: 28780284 DOI: 10.1016/j.ymben.2017.08.001] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2017] [Revised: 07/18/2017] [Accepted: 08/01/2017] [Indexed: 10/19/2022]
Abstract
N-acetylneuraminate (NeuAc) biosynthesis has drawn much attention owing to its wide applications in many aspects. Previously, we engineered for the first time an artificial NeuAc biosynthetic pathway in Escherichia coli using glucose as sole substrate. However, rigorous requirements for the flux and cofactor balance make subsequent strain improvement rather difficult. In this study, an in vivo NeuAc biosensor was designed and applied for genetic screening the mutant library of NeuAc producer. Its NeuAc responsive manner was demonstrated using sfgfp as a reporter and a Ni2+-based selection system was developed to couple the cell growth with in vivo NeuAc concentration. Employing this selection system, the NeuAc biosynthesis pathway was optimized and the key enzyme NeuAc synthase was evolved, which improved the titer by 34% and 23%, respectively. The final strain produced up to 8.31g/L NeuAc in minimal medium using glucose as sole carbon source. This work demonstrated the effectiveness of NeuAc biosensor in genetic screening and great potential in metabolic engineering of other organisms.
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Affiliation(s)
- Peng Yang
- State Key Laboratory of Microbial Technology, National Glycoengineering Center, Shandong University, Jinan 250100, People's Republic of China
| | - Jing Wang
- State Key Laboratory of Microbial Technology, National Glycoengineering Center, Shandong University, Jinan 250100, People's Republic of China
| | - Qingxiao Pang
- State Key Laboratory of Microbial Technology, National Glycoengineering Center, Shandong University, Jinan 250100, People's Republic of China
| | - Fengyu Zhang
- State Key Laboratory of Microbial Technology, National Glycoengineering Center, Shandong University, Jinan 250100, People's Republic of China
| | - Junshu Wang
- State Key Laboratory of Microbial Technology, National Glycoengineering Center, Shandong University, Jinan 250100, People's Republic of China
| | - Qian Wang
- State Key Laboratory of Microbial Technology, National Glycoengineering Center, Shandong University, Jinan 250100, People's Republic of China.
| | - Qingsheng Qi
- State Key Laboratory of Microbial Technology, National Glycoengineering Center, Shandong University, Jinan 250100, People's Republic of China.
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26
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Van Hove B, Guidi C, De Wannemaeker L, Maertens J, De Mey M. Recursive DNA Assembly Using Protected Oligonucleotide Duplex Assisted Cloning (PODAC). ACS Synth Biol 2017; 6:943-949. [PMID: 28320206 DOI: 10.1021/acssynbio.7b00017] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A problem rarely tackled by current DNA assembly methods is the issue of cloning additional parts into an already assembled construct. Costly PCR workflows are often hindered by repeated sequences, and restriction based strategies impose design constraints for each enzyme used. Here we present Protected Oligonucleotide Duplex Assisted Cloning (PODAC), a novel technique that makes use of an oligonucleotide duplex for iterative Golden Gate cloning using only one restriction enzyme. Methylated bases confer protection from digestion during the assembly reaction and are removed during replication in vivo, unveiling a new cloning site in the process. We used this method to efficiently and accurately assemble a biosynthetic pathway and demonstrated its robustness toward sequence repeats by constructing artificial CRISPR arrays. As PODAC is readily amenable to standardization, it would make a useful addition to the synthetic biology toolkit.
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Affiliation(s)
- Bob Van Hove
- Centre for Synthetic
Biology
(CSB), Department of Biochemical and Microbial Technology, Ghent University, 9000 Ghent, Belgium
| | - Chiara Guidi
- Centre for Synthetic
Biology
(CSB), Department of Biochemical and Microbial Technology, Ghent University, 9000 Ghent, Belgium
| | - Lien De Wannemaeker
- Centre for Synthetic
Biology
(CSB), Department of Biochemical and Microbial Technology, Ghent University, 9000 Ghent, Belgium
| | - Jo Maertens
- Centre for Synthetic
Biology
(CSB), Department of Biochemical and Microbial Technology, Ghent University, 9000 Ghent, Belgium
| | - Marjan De Mey
- Centre for Synthetic
Biology
(CSB), Department of Biochemical and Microbial Technology, Ghent University, 9000 Ghent, Belgium
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27
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Zhou S, Ding R, Chen J, Du G, Li H, Zhou J. Obtaining a Panel of Cascade Promoter-5'-UTR Complexes in Escherichia coli. ACS Synth Biol 2017; 6:1065-1075. [PMID: 28252945 DOI: 10.1021/acssynbio.7b00006] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
A promoter is one of the most important and basic tools used to achieve diverse synthetic biology goals. Escherichia coli is one of the most commonly used model organisms in synthetic biology to produce useful target products and establish complicated regulation networks. During the fine-tuning of metabolic or regulation networks, the limited number of well-characterized inducible promoters has made implementing complicated strategies difficult. In this study, 104 native promoter-5'-UTR complexes (PUTR) from E. coli were screened and characterized based on a series of RNA-seq data. The strength of the 104 PUTRs varied from 0.007% to 4630% of that of the PBAD promoter in the transcriptional level and from 0.1% to 137% in the translational level. To further upregulate gene expression, a series of combinatorial PUTRs and cascade PUTRs were constructed by integrating strong transcriptional promoters with strong translational 5'-UTRs. Finally, two combinatorial PUTRs (PssrA-UTRrpsT and PdnaKJ-UTRrpsT) and two cascade PUTRs (PUTRssrA-PUTRinfC-rplT and PUTRalsRBACE-PUTRinfC-rplT) were identified as having the highest activity, with expression outputs of 170%, 137%, 409%, and 203% of that of the PBAD promoter, respectively. These engineered PUTRs are stable for the expression of different genes, such as the red fluorescence protein gene and the β-galactosidase gene. These results show that the PUTRs characterized and constructed in this study may be useful as a plug-and-play synthetic biology toolbox to achieve complicated metabolic engineering goals in fine-tuning metabolic networks to produce target products.
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Affiliation(s)
- Shenghu Zhou
- Key Laboratory
of Industrial Biotechnology, Ministry of Education,
School of Biotechnology, and ‡National Engineering Laboratory for Cereal Fermentation
Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Renpeng Ding
- Key Laboratory
of Industrial Biotechnology, Ministry of Education,
School of Biotechnology, and ‡National Engineering Laboratory for Cereal Fermentation
Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Jian Chen
- Key Laboratory
of Industrial Biotechnology, Ministry of Education,
School of Biotechnology, and ‡National Engineering Laboratory for Cereal Fermentation
Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Guocheng Du
- Key Laboratory
of Industrial Biotechnology, Ministry of Education,
School of Biotechnology, and ‡National Engineering Laboratory for Cereal Fermentation
Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Huazhong Li
- Key Laboratory
of Industrial Biotechnology, Ministry of Education,
School of Biotechnology, and ‡National Engineering Laboratory for Cereal Fermentation
Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Jingwen Zhou
- Key Laboratory
of Industrial Biotechnology, Ministry of Education,
School of Biotechnology, and ‡National Engineering Laboratory for Cereal Fermentation
Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
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28
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CRISPR EnAbled Trackable genome Engineering for isopropanol production in Escherichia coli. Metab Eng 2017; 41:1-10. [DOI: 10.1016/j.ymben.2017.02.009] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Revised: 01/18/2017] [Accepted: 02/14/2017] [Indexed: 01/08/2023]
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29
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Chen X, Gao C, Guo L, Hu G, Luo Q, Liu J, Nielsen J, Chen J, Liu L. DCEO Biotechnology: Tools To Design, Construct, Evaluate, and Optimize the Metabolic Pathway for Biosynthesis of Chemicals. Chem Rev 2017; 118:4-72. [DOI: 10.1021/acs.chemrev.6b00804] [Citation(s) in RCA: 109] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Xiulai Chen
- State
Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- Key
Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Cong Gao
- State
Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- Key
Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Liang Guo
- State
Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- Key
Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Guipeng Hu
- State
Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- Key
Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Qiuling Luo
- State
Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- Key
Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Jia Liu
- State
Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- Key
Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Jens Nielsen
- Department
of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg SE-412 96, Sweden
- Novo
Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK2800 Lyngby, Denmark
| | - Jian Chen
- State
Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- Key
Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Liming Liu
- State
Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- Department
of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg SE-412 96, Sweden
- Key
Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
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30
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Abstract
Combinatorial engineering approaches are becoming increasingly popular, yet they are hindered by the lack of specialized techniques for both efficient introduction of sequence variability and assembly of numerous DNA parts, required for the construction of lengthy multigene pathways. In this contribution, we introduce a new combinatorial multigene pathway assembly scheme based on Single Strand Assembly (SSA) methods and Golden Gate Assembly, exploiting the strengths of both assembly techniques. With a minimum of intermediary steps and an accompanying set of well-characterized and ready-to-use genetic parts, the developed workflow allows effective introduction of various libraries and efficient assembly of multigene pathways. It was put to the test by optimizing the lycopene pathway as proof-of-principle. The here constructed libraries yield ample variation in lycopene production. In addition, good-performing transformants with a significantly higher lycopene production were obtained as compared to previously published reference strains. The best selected producer yielded 3-fold improvement in lycopene titers up to 448 mg lycopene/g CDW. The proposed workflow in combination with the accompanying sets of ready-to-use expression and carrier plasmids, will allow the combinatorial assembly of increasingly lengthy product pathways with minimal effort.
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Affiliation(s)
- Pieter Coussement
- Department
of Biochemical
and Microbial Technology, Ghent University, Coupure Links 653, 9000 Gent, Belgium
| | - David Bauwens
- Department
of Biochemical
and Microbial Technology, Ghent University, Coupure Links 653, 9000 Gent, Belgium
| | - Jo Maertens
- Department
of Biochemical
and Microbial Technology, Ghent University, Coupure Links 653, 9000 Gent, Belgium
| | - Marjan De Mey
- Department
of Biochemical
and Microbial Technology, Ghent University, Coupure Links 653, 9000 Gent, Belgium
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31
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Development of Synthetic Microbial Platforms to Convert Lignocellulosic Biomass to Biofuels. ADVANCES IN BIOENERGY 2017. [DOI: 10.1016/bs.aibe.2016.12.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
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32
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Liu D, Liu H, Li BZ, Qi H, Jia B, Zhou X, Du HX, Zhang W, Yuan YJ. Multigene Pathway Engineering with Regulatory Linkers (M-PERL). ACS Synth Biol 2016; 5:1535-1545. [PMID: 27389125 DOI: 10.1021/acssynbio.6b00123] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Multigene pathway engineering usually needs amounts of part libraries on transcriptional and translational regulation as well as mutant enzymes to achieve the optimal part combinations of the target pathways. We report a new strategy for multigene pathway engineering with regulatory linkers (M-PERL) focusing on tuning the transcriptional start site (TSS) of yeast promoters. The regulatory linkers are composed of two homologous ends of two adjacent gene parts for assembly and a central regulatory region between them. We investigated the effect of the homologous end's length on multigene assembly, analyzed the influences of truncated, replaced, and elongated TSS and the adjacent region on promoters, and introduced 5 to 40 random bases of N (A/T/C/G) in the central regulatory region of the linkers which effectively varied the promoter's strengths. The distinct libraries of five regulatory linkers were used simultaneously to assemble and tune all five genes in the violacein synthesis pathway. The gene expressions affected the product profiles significantly, and the recombinants for enhanced single component synthesis and varied composition synthesis were obtained. This study offers an efficient tool to assemble and regulate multigene pathways.
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Affiliation(s)
- Duo Liu
- Key
Laboratory of Systems Bioengineering (Ministry of Education), School
of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, P. R. China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin, 300072, P. R. China
| | - Hong Liu
- Key
Laboratory of Systems Bioengineering (Ministry of Education), School
of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, P. R. China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin, 300072, P. R. China
| | - Bing-Zhi Li
- Key
Laboratory of Systems Bioengineering (Ministry of Education), School
of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, P. R. China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin, 300072, P. R. China
| | - Hao Qi
- Key
Laboratory of Systems Bioengineering (Ministry of Education), School
of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, P. R. China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin, 300072, P. R. China
| | - Bin Jia
- Key
Laboratory of Systems Bioengineering (Ministry of Education), School
of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, P. R. China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin, 300072, P. R. China
| | - Xiao Zhou
- Key
Laboratory of Systems Bioengineering (Ministry of Education), School
of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, P. R. China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin, 300072, P. R. China
| | - Hao-Xing Du
- Key
Laboratory of Systems Bioengineering (Ministry of Education), School
of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, P. R. China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin, 300072, P. R. China
| | - Wei Zhang
- Key
Laboratory of Systems Bioengineering (Ministry of Education), School
of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, P. R. China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin, 300072, P. R. China
| | - Ying-Jin Yuan
- Key
Laboratory of Systems Bioengineering (Ministry of Education), School
of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, P. R. China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin, 300072, P. R. China
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Recent progress in therapeutic natural product biosynthesis using Escherichia coli. Curr Opin Biotechnol 2016; 42:7-12. [DOI: 10.1016/j.copbio.2016.02.010] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2016] [Revised: 02/10/2016] [Accepted: 02/12/2016] [Indexed: 01/29/2023]
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Roehner N, Young EM, Voigt CA, Gordon DB, Densmore D. Double Dutch: A Tool for Designing Combinatorial Libraries of Biological Systems. ACS Synth Biol 2016; 5:507-17. [PMID: 27110633 DOI: 10.1021/acssynbio.5b00232] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Recently, semirational approaches that rely on combinatorial assembly of characterized DNA components have been used to engineer biosynthetic pathways. In practice, however, it is not practical to assemble and test millions of pathway variants in order to elucidate how different DNA components affect the behavior of a pathway. To address this challenge, we apply a rigorous mathematical approach known as design of experiments (DOE) that can be used to construct empirical models of system behavior without testing all variants. To support this approach, we have developed a tool named Double Dutch, which uses a formal grammar and heuristic algorithms to automate the process of DOE library design. Compared to designing by hand, Double Dutch enables users to more efficiently and scalably design libraries of pathway variants that can be used in a DOE framework and uniquely provides a means to flexibly balance design considerations of statistical analysis, construction cost, and risk of homologous recombination, thereby demonstrating the utility of automating decision making when faced with complex design trade-offs.
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Affiliation(s)
- Nicholas Roehner
- Department
of Electrical and Computer Engineering, Boston University, Boston, Massachusetts 02215, United States
| | - Eric M. Young
- Department
of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Christopher A. Voigt
- Department
of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - D. Benjamin Gordon
- Department
of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Douglas Densmore
- Department
of Electrical and Computer Engineering, Boston University, Boston, Massachusetts 02215, United States
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Production of specific-molecular-weight hyaluronan by metabolically engineered Bacillus subtilis 168. Metab Eng 2016; 35:21-30. [DOI: 10.1016/j.ymben.2016.01.008] [Citation(s) in RCA: 80] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2015] [Revised: 01/11/2016] [Accepted: 01/27/2016] [Indexed: 12/14/2022]
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Jin P, Kang Z, Zhang J, Zhang L, Du G, Chen J. Combinatorial Evolution of Enzymes and Synthetic Pathways Using One-Step PCR. ACS Synth Biol 2016; 5:259-68. [PMID: 26751617 DOI: 10.1021/acssynbio.5b00240] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
DNA engineering is the fundamental motive driving the rapid development of modern biotechnology. Here, we present a versatile evolution method termed "rapidly efficient combinatorial oligonucleotides for directed evolution" (RECODE) for rapidly introducing multiple combinatorial mutations to the target DNA by combined action of a thermostable high-fidelity DNA polymerase and a thermostable DNA Ligase in one reaction system. By applying this method, we rapidly constructed a variant library of the rpoS promoters (with activity of 8-460%), generated a novel heparinase from the highly specific leech hyaluronidase (with more than 30 mutant residues) and optimized the heme biosynthetic pathway by combinatorial evolution of regulatory elements and pathway enzymes (2500 ± 120 mg L(-1) with 20-fold increase). The simple RECODE method enabled researchers the unparalleled ability to efficiently create diverse mutant libraries for rapid evolution and optimization of enzymes and synthetic pathways.
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Affiliation(s)
- Peng Jin
- The
Key Laboratory of Industrial Biotechnology, Ministry of Education,
School of Biotechnology, Jiangnan University, Wuxi 214122, China
- Synergetic
Innovation Center of Food Safety and Nutrition, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Zhen Kang
- The
Key Laboratory of Industrial Biotechnology, Ministry of Education,
School of Biotechnology, Jiangnan University, Wuxi 214122, China
- Synergetic
Innovation Center of Food Safety and Nutrition, Jiangnan University, Wuxi, Jiangsu 214122, China
- The
Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry
of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Junli Zhang
- The
Key Laboratory of Industrial Biotechnology, Ministry of Education,
School of Biotechnology, Jiangnan University, Wuxi 214122, China
- Synergetic
Innovation Center of Food Safety and Nutrition, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Linpei Zhang
- The
Key Laboratory of Industrial Biotechnology, Ministry of Education,
School of Biotechnology, Jiangnan University, Wuxi 214122, China
- Synergetic
Innovation Center of Food Safety and Nutrition, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Guocheng Du
- The
Key Laboratory of Industrial Biotechnology, Ministry of Education,
School of Biotechnology, Jiangnan University, Wuxi 214122, China
- Synergetic
Innovation Center of Food Safety and Nutrition, Jiangnan University, Wuxi, Jiangsu 214122, China
- The
Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry
of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Jian Chen
- The
Key Laboratory of Industrial Biotechnology, Ministry of Education,
School of Biotechnology, Jiangnan University, Wuxi 214122, China
- Synergetic
Innovation Center of Food Safety and Nutrition, Jiangnan University, Wuxi, Jiangsu 214122, China
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Zhang S, Zhao X, Tao Y, Lou C. A novel approach for metabolic pathway optimization: Oligo-linker mediated assembly (OLMA) method. J Biol Eng 2015; 9:23. [PMID: 26702298 PMCID: PMC4688952 DOI: 10.1186/s13036-015-0021-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Accepted: 11/24/2015] [Indexed: 01/20/2023] Open
Abstract
Background Imbalances in gene expression of a metabolic pathway can result in less-yield of the desired products. Several targets were intensively investigated to balance the gene expression, such as promoter, ribosome binding site (RBS), the order of genes, as well as the species of the enzymes. However, the capability of simultaneous manipulation of multiple targets still needs to be explored. Results We reported a new DNA assembling method to vary all the above types of regulatory targets simultaneously, named oligo-linker mediated assembly (OLMA) method, which can incorporate up to 8 targets in a single assembly step. Two experimental cases were used to demonstrate the capability of the method: (1) assembly of multiple pieces of lacZ expression cassette; (2) optimization of four enzymes in lycopene biosynthetic pathway. Our results indicated that the OLMA method not only exploited larger combinatorial space, but also reduced the inefficient mutants. Conclusions The unique feature of oligo-linker mediated assembly (OLMA) method is inclusion of a set of chemically synthetic double-stranded DNA oligo library, which can be designed as promoters and RBSs, or designed with different overhang to bridge the genes in different orders. The inclusion of the oligos resulted in a PCR-free and zipcode-free DNA assembly reaction for OLMA. Electronic supplementary material The online version of this article (doi:10.1186/s13036-015-0021-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Shasha Zhang
- Chinese Academy of Sciences Key Laboratory of Microbial Physiological, and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101 China.,University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Xuejin Zhao
- Chinese Academy of Sciences Key Laboratory of Microbial Physiological, and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101 China
| | - Yong Tao
- Chinese Academy of Sciences Key Laboratory of Microbial Physiological, and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101 China
| | - Chunbo Lou
- Chinese Academy of Sciences Key Laboratory of Microbial Physiological, and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101 China
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Peters G, Coussement P, Maertens J, Lammertyn J, De Mey M. Putting RNA to work: Translating RNA fundamentals into biotechnological engineering practice. Biotechnol Adv 2015; 33:1829-44. [PMID: 26514597 DOI: 10.1016/j.biotechadv.2015.10.011] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Revised: 10/13/2015] [Accepted: 10/22/2015] [Indexed: 11/19/2022]
Abstract
Synthetic biology, in close concert with systems biology, is revolutionizing the field of metabolic engineering by providing novel tools and technologies to rationally, in a standardized way, reroute metabolism with a view to optimally converting renewable resources into a broad range of bio-products, bio-materials and bio-energy. Increasingly, these novel synthetic biology tools are exploiting the extensive programmable nature of RNA, vis-à-vis DNA- and protein-based devices, to rationally design standardized, composable, and orthogonal parts, which can be scaled and tuned promptly and at will. This review gives an extensive overview of the recently developed parts and tools for i) modulating gene expression ii) building genetic circuits iii) detecting molecules, iv) reporting cellular processes and v) building RNA nanostructures. These parts and tools are becoming necessary armamentarium for contemporary metabolic engineering. Furthermore, the design criteria, technological challenges, and recent metabolic engineering success stories of the use of RNA devices are highlighted. Finally, the future trends in transforming metabolism through RNA engineering are critically evaluated and summarized.
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Affiliation(s)
- Gert Peters
- Centre of Expertise Industrial Biotechnology and Biocatalysis, Ghent University, Coupure Links 653, B-9000 Ghent, Belgium
| | - Pieter Coussement
- Centre of Expertise Industrial Biotechnology and Biocatalysis, Ghent University, Coupure Links 653, B-9000 Ghent, Belgium
| | - Jo Maertens
- Centre of Expertise Industrial Biotechnology and Biocatalysis, Ghent University, Coupure Links 653, B-9000 Ghent, Belgium
| | - Jeroen Lammertyn
- BIOSYST-MeBioS, KU Leuven, Willem de Croylaan 42, 3001 Louvain, Belgium
| | - Marjan De Mey
- Centre of Expertise Industrial Biotechnology and Biocatalysis, Ghent University, Coupure Links 653, B-9000 Ghent, Belgium.
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40
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De Bruyn F, Van Brempt M, Maertens J, Van Bellegem W, Duchi D, De Mey M. Metabolic engineering of Escherichia coli into a versatile glycosylation platform: production of bio-active quercetin glycosides. Microb Cell Fact 2015; 14:138. [PMID: 26377568 PMCID: PMC4573293 DOI: 10.1186/s12934-015-0326-1] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2015] [Accepted: 08/27/2015] [Indexed: 02/01/2023] Open
Abstract
Background Flavonoids are bio-active specialized plant metabolites which mainly occur as different glycosides. Due to the increasing market demand, various biotechnological approaches have been developed which use Escherichia coli as a microbial catalyst for the stereospecific glycosylation of flavonoids. Despite these efforts, most processes still display low production rates and titers, which render them unsuitable for large-scale applications. Results In this contribution, we expanded a previously developed in vivo glucosylation platform in E. coli W, into an efficient system for selective galactosylation and rhamnosylation. The rational of the novel metabolic engineering strategy constitutes of the introduction of an alternative sucrose metabolism in the form of a sucrose phosphorylase, which cleaves sucrose into fructose and glucose 1-phosphate as precursor for UDP-glucose. To preserve these intermediates for glycosylation purposes, metabolization reactions were knocked-out. Due to the pivotal role of UDP-glucose, overexpression of the interconverting enzymes galE and MUM4 ensured the formation of both UDP-galactose and UDP-rhamnose, respectively. By additionally supplying exogenously fed quercetin and overexpressing a flavonol galactosyltransferase (F3GT) or a rhamnosyltransferase (RhaGT), 0.94 g/L hyperoside (quercetin 3-O-galactoside) and 1.12 g/L quercitrin (quercetin 3-O-rhamnoside) could be produced, respectively. In addition, both strains showed activity towards other promising dietary flavonols like kaempferol, fisetin, morin and myricetin. Conclusions Two E. coli W mutants were engineered that could effectively produce the bio-active flavonol glycosides hyperoside and quercitrin starting from the cheap substrates sucrose and quercetin. This novel fermentation-based glycosylation strategy will allow the economically viable production of various glycosides. Electronic supplementary material The online version of this article (doi:10.1186/s12934-015-0326-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Frederik De Bruyn
- Department of Biochemical and Microbial Technology, Centre of Expertise-Industrial Biotechnology and Biocatalysis, Ghent University, Coupure Links 653, 9000, Ghent, Belgium.
| | - Maarten Van Brempt
- Department of Biochemical and Microbial Technology, Centre of Expertise-Industrial Biotechnology and Biocatalysis, Ghent University, Coupure Links 653, 9000, Ghent, Belgium.
| | - Jo Maertens
- Department of Biochemical and Microbial Technology, Centre of Expertise-Industrial Biotechnology and Biocatalysis, Ghent University, Coupure Links 653, 9000, Ghent, Belgium.
| | - Wouter Van Bellegem
- Department of Biochemical and Microbial Technology, Centre of Expertise-Industrial Biotechnology and Biocatalysis, Ghent University, Coupure Links 653, 9000, Ghent, Belgium.
| | - Dries Duchi
- Department of Biochemical and Microbial Technology, Centre of Expertise-Industrial Biotechnology and Biocatalysis, Ghent University, Coupure Links 653, 9000, Ghent, Belgium.
| | - Marjan De Mey
- Department of Biochemical and Microbial Technology, Centre of Expertise-Industrial Biotechnology and Biocatalysis, Ghent University, Coupure Links 653, 9000, Ghent, Belgium.
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41
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Kim SC, Min BE, Hwang HG, Seo SW, Jung GY. Pathway optimization by re-design of untranslated regions for L-tyrosine production in Escherichia coli. Sci Rep 2015; 5:13853. [PMID: 26346938 PMCID: PMC4561953 DOI: 10.1038/srep13853] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Accepted: 08/07/2015] [Indexed: 01/17/2023] Open
Abstract
L-tyrosine is a commercially important compound in the food, pharmaceutical, chemical, and cosmetic industries. Although several attempts have been made to improve L-tyrosine production, translation-level expression control and carbon flux rebalancing around phosphoenolpyruvate (PEP) node still remain to be achieved for optimizing the pathway. Here, we demonstrate pathway optimization by altering gene expression levels for L-tyrosine production in Escherichia coli. To optimize the L-tyrosine biosynthetic pathway, a synthetic constitutive promoter and a synthetic 5′-untranslated region (5′-UTR) were introduced for each gene of interest to allow for control at both transcription and translation levels. Carbon flux rebalancing was achieved by controlling the expression level of PEP synthetase using UTR Designer. The L-tyrosine productivity of the engineered E. coli strain was increased through pathway optimization resulting in 3.0 g/L of L-tyrosine titer, 0.0354 g L-tyrosine/h/g DCW of productivity, and 0.102 g L-tyrosine/g glucose yield. Thus, this work demonstrates that pathway optimization by 5′-UTR redesign is an effective strategy for the development of efficient L-tyrosine-producing bacteria.
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Affiliation(s)
- Seong Cheol Kim
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, 77 Cheongam-ro, Nam-gu, Pohang, Gyeongbuk 790-784, Korea
| | - Byung Eun Min
- Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-ro, Nam-gu, Pohang, Gyeongbuk 790-784, Korea
| | - Hyun Gyu Hwang
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, 77 Cheongam-ro, Nam-gu, Pohang, Gyeongbuk 790-784, Korea
| | - Sang Woo Seo
- Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-ro, Nam-gu, Pohang, Gyeongbuk 790-784, Korea
| | - Gyoo Yeol Jung
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, 77 Cheongam-ro, Nam-gu, Pohang, Gyeongbuk 790-784, Korea.,Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-ro, Nam-gu, Pohang, Gyeongbuk 790-784, Korea
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Metabolic engineering of Escherichia coli using CRISPR–Cas9 meditated genome editing. Metab Eng 2015; 31:13-21. [DOI: 10.1016/j.ymben.2015.06.006] [Citation(s) in RCA: 267] [Impact Index Per Article: 29.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2015] [Revised: 06/19/2015] [Accepted: 06/22/2015] [Indexed: 12/17/2022]
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43
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Takahashi MK, Hayes CA, Chappell J, Sun ZZ, Murray RM, Noireaux V, Lucks JB. Characterizing and prototyping genetic networks with cell-free transcription–translation reactions. Methods 2015; 86:60-72. [DOI: 10.1016/j.ymeth.2015.05.020] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Revised: 05/20/2015] [Accepted: 05/21/2015] [Indexed: 02/07/2023] Open
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Metabolic pathway balancing and its role in the production of biofuels and chemicals. Curr Opin Biotechnol 2015; 33:52-9. [DOI: 10.1016/j.copbio.2014.11.013] [Citation(s) in RCA: 145] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2014] [Revised: 11/10/2014] [Accepted: 11/11/2014] [Indexed: 12/21/2022]
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Wang S, Zhang S, Xiao A, Rasmussen M, Skidmore C, Zhan J. Metabolic engineering of Escherichia coli for the biosynthesis of various phenylpropanoid derivatives. Metab Eng 2015; 29:153-159. [DOI: 10.1016/j.ymben.2015.03.011] [Citation(s) in RCA: 76] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2014] [Revised: 03/05/2015] [Accepted: 03/16/2015] [Indexed: 01/07/2023]
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47
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Liu Y, Shin HD, Li J, Liu L. Toward metabolic engineering in the context of system biology and synthetic biology: advances and prospects. Appl Microbiol Biotechnol 2014; 99:1109-18. [DOI: 10.1007/s00253-014-6298-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2014] [Revised: 12/02/2014] [Accepted: 12/04/2014] [Indexed: 12/22/2022]
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48
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Farasat I, Kushwaha M, Collens J, Easterbrook M, Guido M, Salis HM. Efficient search, mapping, and optimization of multi-protein genetic systems in diverse bacteria. Mol Syst Biol 2014; 10:731. [PMID: 24952589 PMCID: PMC4265053 DOI: 10.15252/msb.20134955] [Citation(s) in RCA: 171] [Impact Index Per Article: 17.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Developing predictive models of multi-protein genetic systems to understand and optimize their behavior remains a combinatorial challenge, particularly when measurement throughput is limited. We developed a computational approach to build predictive models and identify optimal sequences and expression levels, while circumventing combinatorial explosion. Maximally informative genetic system variants were first designed by the RBS Library Calculator, an algorithm to design sequences for efficiently searching a multi-protein expression space across a > 10,000-fold range with tailored search parameters and well-predicted translation rates. We validated the algorithm's predictions by characterizing 646 genetic system variants, encoded in plasmids and genomes, expressed in six gram-positive and gram-negative bacterial hosts. We then combined the search algorithm with system-level kinetic modeling, requiring the construction and characterization of 73 variants to build a sequence-expression-activity map (SEAMAP) for a biosynthesis pathway. Using model predictions, we designed and characterized 47 additional pathway variants to navigate its activity space, find optimal expression regions with desired activity response curves, and relieve rate-limiting steps in metabolism. Creating sequence-expression-activity maps accelerates the optimization of many protein systems and allows previous measurements to quantitatively inform future designs.
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Affiliation(s)
- Iman Farasat
- Department of Chemical Engineering, Pennsylvania State University, University Park, PA, USA
| | - Manish Kushwaha
- Department of Biological Engineering, Pennsylvania State University, University Park, PA, USA
| | - Jason Collens
- Department of Biological Engineering, Pennsylvania State University, University Park, PA, USA
| | - Michael Easterbrook
- Department of Chemical Engineering, Pennsylvania State University, University Park, PA, USA
| | - Matthew Guido
- Department of Chemical Engineering, Pennsylvania State University, University Park, PA, USA
| | - Howard M Salis
- Department of Chemical Engineering, Pennsylvania State University, University Park, PA, USA Department of Biological Engineering, Pennsylvania State University, University Park, PA, USA
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Multivariate modular metabolic engineering for pathway and strain optimization. Curr Opin Biotechnol 2014; 29:156-62. [PMID: 24927371 DOI: 10.1016/j.copbio.2014.05.005] [Citation(s) in RCA: 108] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2014] [Accepted: 05/19/2014] [Indexed: 12/21/2022]
Abstract
Despite the potential in utilizing microbial fermentation for chemical production, the field of industrial biotechnology still lacks a standard, universally applicable principle for strain optimization. A key challenge has been in finding and applying effective ways to address metabolic flux imbalances. Strategies based on rational design require significant a priori knowledge and often fail to take a holistic view of cellular metabolism. Combinatorial approaches enable more global searches but require a high-throughput screen. Here, we present the recent advances and promises of a novel approach to metabolic pathway and strain optimization called multivariate modular metabolic engineering (MMME). In this technique, key enzymes are organized into distinct modules and simultaneously varied based on expression to balance flux through a pathway. Because of its simplicity and broad applicability, MMME has the potential to systematize and revolutionize the field of metabolic engineering and industrial biotechnology.
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